Research
Below is a list of published manuscripts from the MATCH lab and collaborations involving Dr. Marco Marra. Please excuse any errors generated during the automated process.
Highlighted
A longitudinal single-cell atlas of treatment response in pediatric AML.
Sander Lambo, Diane L Trinh, Rhonda E Ries, Dan Jin, Audi Setiadi, ..., Laura M Pardo, Xiaotu Ma, Suzanne M Vercauteren, Soheil Meshinchi, Marco A Marra
Cancer cell
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16 Nov 2023
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pubmed:37977148
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2024
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation.
Vanessa L Porter, Michelle Ng, Kieran O'Neill, Signe MacLennan, Richard D Corbett, ..., Andrew J Mungall, Inanc Birol, Steven J M Jones, Janet S Rader, Marco A Marra
Genome research
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05 Dec 2024
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pubmed:39638560
Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.
Simon Haile, Richard D Corbett, Kieran O'Neill, Jing Xu, Duane E Smailus, ..., Yongjun Zhao, Yussanne Ma, Marco A Marra, Steven J M Jones, Andrew J Mungall
Frontiers in genetics
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02 Dec 2024
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pubmed:39687742
Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities.
Yuka Takemon, Erin D Pleasance, Alessia Gagliardi, Christopher S Hughes, Veronika Csizmok, ..., Howard J Lim, Daniel J Renouf, Steven Jm Jones, Janessa Laskin, Marco A Marra
Genome medicine
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22 Nov 2024
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pubmed:39578878
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes.
Kieran O'Neill, Erin Pleasance, Jeremy Fan, Vahid Akbari, Glenn Chang, ..., Kasmintan A Schrader, Stephen Yip, Marco A Marra, Janessa Laskin, Steven J M Jones
Cell genomics
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10 Oct 2024
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pubmed:39406235
Diagnostic and Therapeutic Implications of a FUS::TFCP2 Fusion and ALK Activation in a Metastatic Rhabdomyosarcoma.
Veronika Csizmok, Cameron J Grisdale, Laura M Williamson, Howard J Lim, Lawrence Lee, Daniel J Renouf, Steven J M Jones, Marco A Marra, Janessa Laskin, Alannah Smrke
Genes, chromosomes & cancer
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01 Sep 2024
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pubmed:39302072
Rapid microdissection of tissue sections via laser ablation.
Robin Jn Coope, Stephen Pleasance, Pawan Pandoh, Colin Schlosser, Richard D Corbett, Marco A Marra
Journal of clinical pathology
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17 May 2024
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pubmed:38429092
Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.
Rebecca J Deyell, Yaoqing Shen, Emma Titmuss, Katherine Dixon, Laura M Williamson, ..., Yongjun Zhao, Steven J M Jones, Janessa Laskin, Marco A Marra, Shahrad R Rassekh
Nature communications
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16 May 2024
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pubmed:38755180
Exploration of Germline Correlates and Risk of Immune-Related Adverse Events in Advanced Cancer Patients Treated with Immune Checkpoint Inhibitors.
Emma Titmuss, Irene S Yu, Erin D Pleasance, Laura M Williamson, Karen Mungall, ..., Richard Moore, Steven J M Jones, Marco A Marra, Janessa J Laskin, Kerry J Savage
Current oncology (Toronto, Ont.)
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30 Mar 2024
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pubmed:38668043
The CMT2D locus: refined genetic position and construction of a bacterial clone-based physical map
[no author info]
Genome Research
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27 Jan 2024
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wosuid:WOS:000081241400005
A public database for gene expression in human cancers
[no author info]
Cancer Research
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27 Jan 2024
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wosuid:WOS:000083500200002
Multisite clinical cross-validation and variant interpretation of a next generation sequencing panel for lymphoid cancer prognostication.
Peter J B Sabatini, Josh Bridgers, Shujun Huang, Gregory Downs, Tong Zhang, ..., Robert Kridel, Marco A Marra, Christian Steidl, David W Scott, Aly Karsan
Journal of clinical pathology
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05 Jan 2024
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pubmed:38182402
2023
A longitudinal single-cell atlas of treatment response in pediatric AML
Sander Lambo, Diane L. Trinh, Rhonda E. Ries, Dan Jin, Audi Setiadi, ..., Laura M. Pardo, Xiaotu Ma, Suzanne M. Vercauteren, Soheil Meshinchi, Marco A. Marra
Cancer Cell
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01 Dec 2023
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doi:10.1016/j.ccell.2023.10.008
Testing.
A longitudinal single-cell atlas of treatment response in pediatric AML.
Sander Lambo, Diane L Trinh, Rhonda E Ries, Dan Jin, Audi Setiadi, ..., Laura M Pardo, Xiaotu Ma, Suzanne M Vercauteren, Soheil Meshinchi, Marco A Marra
Cancer cell
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16 Nov 2023
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pubmed:37977148
Genomic structures and regulation patterns at HPV integration sites in cervical cancer.
Vanessa L Porter, Kieran O'Neill, Signe MacLennan, Richard D Corbett, Michelle Ng, ..., Andrew J Mungall, Inanc Birol, Steven J M Jones, Janet S Rader, Marco A Marra
bioRxiv : the preprint server for biology
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05 Nov 2023
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pubmed:37961641
Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns.
Kostiantyn Dreval, Laura K Hilton, Manuela Cruz, Haya Shaalan, Susana Ben-Neriah, ..., Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott, Ryan D Morin
Blood
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10 Aug 2023
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pubmed:37084389
Chemokine expression predicts T cell-inflammation and improved survival with checkpoint inhibition across solid cancers.
Joan Miguel Romero, Emma Titmuss, Yifan Wang, James Vafiadis, Alain Pacis, ..., Marco A Marra, Julie M Wilson, Steven Gallinger, Janessa Laskin, George Zogopoulos
NPJ precision oncology
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09 Aug 2023
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pubmed:37558751
A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing.
Jing Xu, Pawan K Pandoh, Richard D Corbett, Duane Smailus, Reanne Bowlby, ..., Robin Coope, Richard A Moore, Yongjun Zhao, Steven Jm Jones, Marco A Marra
BioTechniques
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08 Aug 2023
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pubmed:37551834
GRETTA: an R package for mapping in silico genetic interaction and essentiality networks
Yuka Takemon, Marco A Marra
Bioinformatics
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16 Jun 2023
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doi:10.1093/bioinformatics/btad381
Relapse Timing Is Associated With Distinct Evolutionary Dynamics in Diffuse Large B-Cell Lymphoma.
Laura K Hilton, Henry S Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben-Neriah, ..., Marco A Marra, Laurie H Sehn, Christian Steidl, Ryan D Morin, David W Scott
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
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15 Jun 2023
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pubmed:37319384
GRETTA: an R package for mapping in silico genetic interaction and essentiality networks.
Yuka Takemon, Marco A Marra
Bioinformatics (Oxford, England)
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01 Jun 2023
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pubmed:37326978
Oncogenic Viruses and the Epigenome: How Viruses Hijack Epigenetic Mechanisms to Drive Cancer
Signe A. MacLennan, Marco A. Marra
International Journal of Molecular Sciences
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31 May 2023
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doi:10.3390/ijms24119543
Oncogenic Viruses and the Epigenome: How Viruses Hijack Epigenetic Mechanisms to Drive Cancer.
Signe A MacLennan, Marco A Marra
International journal of molecular sciences
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31 May 2023
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pubmed:37298494
Multi-Omic Analysis of CIC’s Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity
Yuka Takemon, Véronique G. LeBlanc, Jungeun Song, Susanna Y. Chan, Stephen Dongsoo Lee, ..., Christopher S. Hughes, Gregg B. Morin, Sharon M. Gorski, Suganthi Chittaranjan, Marco A. Marra
Cancers
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17 May 2023
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doi:10.3390/cancers15102805
Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity.
Yuka Takemon, Véronique G LeBlanc, Jungeun Song, Susanna Y Chan, Stephen Dongsoo Lee, ..., Christopher S Hughes, Gregg B Morin, Sharon M Gorski, Suganthi Chittaranjan, Marco A Marra
Cancers
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17 May 2023
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pubmed:37345142
Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration.
Erica S Tsang, Veronika Csizmok, Laura M Williamson, Erin Pleasance, James T Topham, ..., Janessa Laskin, Marco A Marra, Steven J M Jones, David F Schaeffer, Daniel J Renouf
NPJ precision oncology
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24 Mar 2023
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pubmed:36964191
Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study
E. Titmuss, K. Milne, M. R. Jones, T. Ng, J. T. Topham, ..., B. H. Nelson, S. J. M. Jones, J. Laskin, H. J. Lim, M. A. Marra
International Journal of Molecular Sciences
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20 Mar 2023
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doi:10.3390/ijms24065869
Relapse timing is associated with distinct evolutionary dynamics in DLBCL.
Laura K Hilton, Henry S Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben-Neriah, ..., Marco A Marra, Laurie H Sehn, Christian Steidl, Ryan D Morin, David W Scott
medRxiv : the preprint server for health sciences
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08 Mar 2023
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pubmed:36945587
Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma.
Nicole Thomas, Kostiantyn Dreval, Daniela S Gerhard, Laura K Hilton, Jeremy S Abramson, ..., Jean C ZenKlusen, Marco A Marra, Louis M Staudt, David W Scott, Ryan D Morin
Blood
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23 Feb 2023
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pubmed:36201743
2022
Author Correction: Failure of human rhombic lip differentiation underlies medulloblastoma formation.
Liam D Hendrikse, Parthiv Haldipur, Olivier Saulnier, Jake Millman, Alexandria H Sjoboen, ..., Vijay Ramaswamy, Tamra E Werbowetski-Ogilvie, Hiromichi Suzuki, Kathleen J Millen, Michael D Taylor
Nature
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01 Dec 2022
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pubmed:36446943
Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma
James T. Topham, Erica S. Tsang, Joanna M. Karasinska, Andrew Metcalfe, Hassan Ali, ..., Janessa Laskin, Marco A. Marra, Steven J. M. Jones, David F. Schaeffer, Daniel J. Renouf
Nature Communications
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08 Oct 2022
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doi:10.1038/S41467-022-33718-7
Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma.
James T Topham, Erica S Tsang, Joanna M Karasinska, Andrew Metcalfe, Hassan Ali, ..., Janessa Laskin, Marco A Marra, Steven J M Jones, David F Schaeffer, Daniel J Renouf
Nature communications
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08 Oct 2022
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pubmed:36209277
The Drivers, Mechanisms, and Consequences of Genome Instability in HPV-Driven Cancers
Vanessa L. Porter, Marco A. Marra
Cancers
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23 Sep 2022
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doi:10.3390/cancers14194623
The Drivers, Mechanisms, and Consequences of Genome Instability in HPV-Driven Cancers.
Vanessa L Porter, Marco A Marra
Cancers
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23 Sep 2022
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pubmed:36230545
Failure of human rhombic lip differentiation underlies medulloblastoma formation.
Liam D Hendrikse, Parthiv Haldipur, Olivier Saulnier, Jake Millman, Alexandria H Sjoboen, ..., Vijay Ramaswamy, Tamra E Werbowetski-Ogilvie, Hiromichi Suzuki, Kathleen J Millen, Michael D Taylor
Nature
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21 Sep 2022
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pubmed:36131014
TMBur: a distributable tumor mutation burden approach for whole genome sequencing
Emma Titmuss, Richard D. Corbett, Scott Davidson, Sanna Abbasi, Laura M. Williamson, ..., Adam Shlien, Daniel J. Renouf, Steven J. M. Jones, Janessa Laskin, Marco A. Marra
BMC Medical Genomics
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07 Sep 2022
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doi:10.1186/S12920-022-01348-Z
TMBur: a distributable tumor mutation burden approach for whole genome sequencing.
Emma Titmuss, Richard D Corbett, Scott Davidson, Sanna Abbasi, Laura M Williamson, ..., Adam Shlien, Daniel J Renouf, Steven J M Jones, Janessa Laskin, Marco A Marra
BMC medical genomics
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07 Sep 2022
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pubmed:36071521
Whole-genome and transcriptome analysis enhances precision cancer treatment options
E. Pleasance, A. Bohm, L.M. Williamson, J.M.T. Nelson, Y. Shen, ..., H. Lim, D.J. Renouf, S.J.M. Jones, M.A. Marra, J. Laskin
Annals of Oncology
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01 Sep 2022
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doi:10.1016/J.ANNONC.2022.05.522
Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2.
Robin J N Coope, Nancy Matic, Pawan K Pandoh, Richard D Corbett, Duane E Smailus, ..., Yongjun Zhao, Daniel T Holmes, Marc G Romney, Steven J M Jones, Marco A Marra
The journal of applied laboratory medicine
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01 Sep 2022
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pubmed:35723286
Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A Marra, Martin Hirst, Steven JM Jones
eLife
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05 Jul 2022
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doi:10.7554/eLife.77898
Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing.
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A Marra, Martin Hirst, Steven J M Jones
eLife
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05 Jul 2022
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pubmed:35787786
Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2
Robin J N Coope, Nancy Matic, Pawan K Pandoh, Richard D Corbett, Duane E Smailus, ..., Yongjun Zhao, Daniel T Holmes, Marc G Romney, Steven J M Jones, Marco A Marra
The Journal of Applied Laboratory Medicine
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20 Jun 2022
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doi:10.1093/JALM/JFAC054
Exceptional response to combination ipilimumab and nivolumab in metastatic uveal melanoma: Insights from genomic analysis
Irene S. Yu, Kathleen Wee, Laura Williamson, Emma Titmuss, Jianghong An, ..., Katherine Paton, Brad H. Nelson, Marco Marra, Janessa J. Laskin, Kerry J. Savage
Melanoma Research
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17 Jun 2022
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doi:10.1097/CMR.0000000000000810
The Neoantigen Landscape of the Coding and Noncoding Cancer Genome Space
Tammy T.Y. Lau, Zahra J. Sefid Dashti, Emma Titmuss, Alexandra Pender, James T. Topham, ..., Sophie Sun, Cheryl Ho, Marco A. Marra, Janessa Laskin, Aly Karsan
The Journal of Molecular Diagnostics
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01 Jun 2022
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doi:10.1016/J.JMOLDX.2022.02.004
Whole-genome and transcriptome analysis of advanced adrenocortical cancer highlights multiple alterations affecting epigenome and DNA repair pathways.
Jean-Michel Lavoie, Veronika Csizmok, Laura M Williamson, Luka Culibrk, Gang Wang, Marco A Marra, Janessa Laskin, Steven J M Jones, Daniel J Renouf, Christian K Kollmannsberger
Cold Spring Harbor molecular case studies
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28 Apr 2022
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pubmed:35483882
Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data
Dollina D. Dodani, Matthew H. Nguyen, Ryan D. Morin, Marco A. Marra, Richard D. Corbett
Frontiers in Genetics
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27 Apr 2022
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doi:10.3389/FGENE.2022.834764
Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data.
Dollina D Dodani, Matthew H Nguyen, Ryan D Morin, Marco A Marra, Richard D Corbett
Frontiers in genetics
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27 Apr 2022
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pubmed:35571031
Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity
Véronique G. LeBlanc, Diane L. Trinh, Shaghayegh Aslanpour, Martha Hughes, Dorothea Livingstone, ..., Michael D. Blough, J. Gregory Cairncross, Jennifer A. Chan, John J.P. Kelly, Marco A. Marra
Cancer Cell
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01 Apr 2022
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doi:10.1016/J.CCELL.2022.02.016
The Neoantigen Landscape of the Coding and Noncoding Cancer Genome Space.
Tammy T Y Lau, Zahra J Sefid Dashti, Emma Titmuss, Alexandra Pender, James T Topham, ..., Sophie Sun, Cheryl Ho, Marco A Marra, Janessa Laskin, Aly Karsan
The Journal of molecular diagnostics : JMD
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31 Mar 2022
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pubmed:35367630
Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity.
Véronique G LeBlanc, Diane L Trinh, Shaghayegh Aslanpour, Martha Hughes, Dorothea Livingstone, ..., Michael D Blough, J Gregory Cairncross, Jennifer A Chan, John J P Kelly, Marco A Marra
Cancer cell
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17 Mar 2022
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pubmed:35303420
The impact of whole genome and transcriptome analysis (WGTA ) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies
Basile Tessier‐Cloutier, Jasleen K Grewal, Martin R Jones, Erin Pleasance, Yaoqing Shen, ..., Janessa Laskin, Marco A Marra, C Blake Gilks, Steven JM Jones, Stephen Yip
The Journal of Pathology: Clinical Research
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08 Mar 2022
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doi:10.1002/CJP2.265
The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies.
Basile Tessier-Cloutier, Jasleen K Grewal, Martin R Jones, Erin Pleasance, Yaoqing Shen, ..., Janessa Laskin, Marco A Marra, C Blake Gilks, Steven Jm Jones, Stephen Yip
The journal of pathology. Clinical research
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08 Mar 2022
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pubmed:35257510
Cost-Effectiveness of Molecularly Guided Treatment in Diffuse Large B-Cell Lymphoma (DLBCL) in Patients under 60
Dean A. Regier, Brandon Chan, Sarah Costa, David W. Scott, Christian Steidl, ..., Aly Karsan, Marco A. Marra, Robert Kridel, Ian Cromwell, Samantha Pollard
Cancers
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12 Feb 2022
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doi:10.3390/CANCERS14040908
Cost-Effectiveness of Molecularly Guided Treatment in Diffuse Large B-Cell Lymphoma (DLBCL) in Patients under 60.
Dean A Regier, Brandon Chan, Sarah Costa, David W Scott, Christian Steidl, ..., Aly Karsan, Marco A Marra, Robert Kridel, Ian Cromwell, Samantha Pollard
Cancers
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12 Feb 2022
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pubmed:35205656
A platform for oncogenomic reporting and interpretation
Caralyn Reisle, Laura M. Williamson, Erin Pleasance, Anna Davies, Brayden Pellegrini, ..., Daniel J. Renouf, Stephen Yip, Janessa Laskin, Marco A. Marra, Steven J. M. Jones
Nature Communications
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09 Feb 2022
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doi:10.1038/S41467-022-28348-Y
A platform for oncogenomic reporting and interpretation.
Caralyn Reisle, Laura M Williamson, Erin Pleasance, Anna Davies, Brayden Pellegrini, ..., Daniel J Renouf, Stephen Yip, Janessa Laskin, Marco A Marra, Steven J M Jones
Nature communications
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09 Feb 2022
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pubmed:35140225
Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents
Simon Haile, Aidan M. Nikiforuk, Pawan K. Pandoh, David D.W. Twa, Duane E. Smailus, ..., Robin J. Coope, Natalie Prystajecky, Marco A. Marra, Mel Krajden, Martin Hirst
Journal of Virological Methods
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01 Jan 2022
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doi:10.1016/J.JVIROMET.2021.114339
ICGC-ARGO precision medicine: familial matters in pancreatic cancer
Michele Milella, Claudio Luchini, Rita T Lawlor, Amber L Johns, Raffaella Casolino, ..., Rosalind Eeles, Rebecca Fitzgerald, Carlos Caldas, Jean Abraham, David K Chang
The Lancet Oncology
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01 Jan 2022
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doi:10.1016/S1470-2045(21)00703-8
Retraction Note: Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma.
Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Lianne Q Chau, Meher Beigi Masihi, ..., Oren J Becher, Linda M Bradley, Carl F Ware, Michael D Taylor, Robert J Wechsler-Reya
Nature neuroscience
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01 Jan 2022
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pubmed:34907396
2021
Integrative multi‐omic analysis reveals neurodevelopmental gene dysregulation in CIC ‐knockout and IDH1 ‐mutant cells
Stephen D Lee, Jungeun Song, Veronique G LeBlanc, Marco A Marra
The Journal of Pathology
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22 Dec 2021
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doi:10.1002/path.5835
Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1-mutant cells.
Stephen D Lee, Jungeun Song, Veronique G LeBlanc, Marco A Marra
The Journal of pathology
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22 Dec 2021
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pubmed:34767259
Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury
Laura M. Williamson, Craig M. Rive, Daniela Di Francesco, Emma Titmuss, Hye-Jung E. Chun, ..., Steven J. M. Jones, Janessa Laskin, Shahrad R. Rassekh, Rebecca J. Deyell, Marco A. Marra
npj Precision Oncology
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20 Dec 2021
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doi:10.1038/S41698-021-00238-4
Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury.
Laura M Williamson, Craig M Rive, Daniela Di Francesco, Emma Titmuss, Hye-Jung E Chun, ..., Steven J M Jones, Janessa Laskin, Shahrad R Rassekh, Rebecca J Deyell, Marco A Marra
NPJ precision oncology
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20 Dec 2021
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pubmed:34931022
Early-stage economic analysis of research-based comprehensive genomic sequencing for advanced cancer care
Deirdre Weymann, Janessa Laskin, Steven J. M. Jones, Robyn Roscoe, Howard J. Lim, ..., Kasmintan A. Schrader, Sophie Sun, Stephen Yip, Marco A. Marra, Dean A. Regier
Journal of Community Genetics
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29 Nov 2021
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doi:10.1007/S12687-021-00557-W
Early-stage economic analysis of research-based comprehensive genomic sequencing for advanced cancer care.
Deirdre Weymann, Janessa Laskin, Steven J M Jones, Robyn Roscoe, Howard J Lim, ..., Kasmintan A Schrader, Sophie Sun, Stephen Yip, Marco A Marra, Dean A Regier
Journal of community genetics
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29 Nov 2021
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pubmed:34843087
Rearrangement-mediated cis-regulatory alterations in advanced patient tumors reveal interactions with therapy.
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J Grisdale, ..., Janessa Laskin, Steven J M Jones, Isidro Cortes-Ciriano, Marco A Marra, Chad J Creighton
Cell reports
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16 Nov 2021
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pubmed:34788622
Rearrangement-mediated cis-regulatory alterations in advanced patient tumors reveal interactions with therapy
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J. Grisdale, ..., Janessa Laskin, Steven J.M. Jones, Isidro Cortes-Ciriano, Marco A. Marra, Chad J. Creighton
Cell Reports
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01 Nov 2021
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doi:10.1016/j.celrep.2021.110023
Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents.
Simon Haile, Aidan M Nikiforuk, Pawan K Pandoh, David D W Twa, Duane E Smailus, ..., Robin J Coope, Natalie Prystajecky, Marco A Marra, Mel Krajden, Martin Hirst
Journal of virological methods
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20 Oct 2021
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pubmed:34687784
Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms.
Kevin C Yang, Steve E Kalloger, John J Aird, Michael K C Lee, Christopher Rushton, ..., Marco A Marra, Daniel J Renouf, Gregg B Morin, David F Schaeffer, Sharon M Gorski
Cell reports
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12 Oct 2021
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pubmed:34644566
Robust somatic copy number estimation using coarse-to-fine segmentation
Luka Culibrk, Jasleen K Grewal, Erin D Pleasance, Laura Williamson, Karen Mungall, Janessa Laskin, Marco A Marra, Steven JM Jones
Cold Spring Harbor Laboratory
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08 Aug 2021
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doi:10.1101/2021.08.06.455329
Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, ..., Pu Zheng, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah
Nature
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23 Jun 2021
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doi:10.1038/S41586-021-03648-3
Clonal fitness inferred from time-series modelling of single-cell cancer genomes.
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J Williams, ..., Marco A Marra, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P Shah
Nature
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23 Jun 2021
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pubmed:34163070
Clinical and cost outcomes following genomics‐informed treatment for advanced cancers
Deirdre Weymann, Samantha Pollard, Brandon Chan, Emma Titmuss, Alexandra Bohm, ..., Sophie Sun, Stephen Yip, David F. Schaeffer, Marco A. Marra, Dean A. Regier
Cancer Medicine
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21 Jun 2021
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doi:10.1002/CAM4.4076
Clinical and cost outcomes following genomics-informed treatment for advanced cancers.
Deirdre Weymann, Samantha Pollard, Brandon Chan, Emma Titmuss, Alexandra Bohm, ..., Sophie Sun, Stephen Yip, David F Schaeffer, Marco A Marra, Dean A Regier
Cancer medicine
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21 Jun 2021
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pubmed:34152087
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Simon Haile, Richard D. Corbett, Veronique G. LeBlanc, Lisa Wei, Stephen Pleasance, ..., Martin Hirst, Samuel Aparicio, Inanc Birol, Steven J. M. Jones, Marco A. Marra
Frontiers in Genetics
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03 Jun 2021
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doi:10.3389/FGENE.2021.665888
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells.
Simon Haile, Richard D Corbett, Veronique G LeBlanc, Lisa Wei, Stephen Pleasance, ..., Martin Hirst, Samuel Aparicio, Inanc Birol, Steven J M Jones, Marco A Marra
Frontiers in genetics
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03 Jun 2021
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pubmed:34149808
A Methodology to Evaluate the Effects of Kinematic Measurement Uncertainties on Knee Ligament Properties Estimated From Laxity Measurements.
Michael Skipper Andersen, Christine Mary Dzialo, Marco Antonio Marra, Dennis Pedersen
Journal of biomechanical engineering
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01 Jun 2021
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pubmed:33537754
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease
Bo Zhang, M. Yvonne Kim, GiNell Elliot, Yan Zhou, Guangfeng Zhao, ..., Misha Bilenky, Martin Hirst, Ting Wang, Joseph F. Costello, Susan J. Fisher
Developmental Cell
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01 May 2021
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doi:10.1016/J.DEVCEL.2021.04.001
Molecular attributes underlying central nervous system and systemic relapse in diffuse large B-cell lymphoma.
Keren Isaev, Daisuke Ennishi, Laura Hilton, Brian Skinnider, Karen L Mungall, ..., Randy D Gascoyne, Ryan Morin, Kerry J Savage, David W Scott, Robert Kridel
Haematologica
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01 May 2021
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pubmed:32817292
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia
T. Roderick Docking, Jeremy D. K. Parker, Martin Jädersten, Gerben Duns, Linda Chang, ..., Steven J. M. Jones, İnanç Birol, Marco A. Marra, Donna Hogge, Aly Karsan
Nature Communications
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30 Apr 2021
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doi:10.1038/S41467-021-22625-Y
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia.
T Roderick Docking, Jeremy D K Parker, Martin Jädersten, Gerben Duns, Linda Chang, ..., Steven J M Jones, İnanç Birol, Marco A Marra, Donna Hogge, Aly Karsan
Nature communications
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30 Apr 2021
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Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity
VG LeBlanc, DL Trinh, S Aslanpour, M Hughes, D Livingstone, MD Blough, JG Cairncross, JA Chan, JJ Kelly, MA Marra
Cold Spring Harbor Laboratory
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26 Apr 2021
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doi:10.1101/2021.04.24.441206
The impact of MYC and BCL2 structural variants in tumors of DLBCL morphology and mechanisms of false-negative MYC IHC.
Brett Collinge, Susana Ben-Neriah, Lauren Chong, Merrill Boyle, Aixiang Jiang, ..., Randy D Gascoyne, Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott
Blood
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22 Apr 2021
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pubmed:33120427
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.
Bo Zhang, M Yvonne Kim, GiNell Elliot, Yan Zhou, Guangfeng Zhao, ..., Misha Bilenky, Martin Hirst, Ting Wang, Joseph F Costello, Susan J Fisher
Developmental cell
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22 Apr 2021
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The transcriptional landscape of Shh medulloblastoma
Patryk Skowron, Hamza Farooq, Florence M. G. Cavalli, A. Sorana Morrissy, Michelle Ly, ..., Jiannis Ragoussis, William A. Weiss, Marco A. Marra, Hiromichi Suzuki, Michael D. Taylor
Nature Communications
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19 Mar 2021
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doi:10.1038/S41467-021-21883-0
The transcriptional landscape of Shh medulloblastoma.
Patryk Skowron, Hamza Farooq, Florence M G Cavalli, A Sorana Morrissy, Michelle Ly, ..., Jiannis Ragoussis, William A Weiss, Marco A Marra, Hiromichi Suzuki, Michael D Taylor
Nature communications
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19 Mar 2021
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pubmed:33741928
Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
Vahid Akbari, Jean-Michel Garant, Kieran O’Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Genome Biology
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22 Feb 2021
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doi:10.1186/S13059-021-02283-5
Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase.
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A Marra, Martin Hirst, Steven J M Jones
Genome biology
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22 Feb 2021
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pubmed:33618748
NTRK2 Fusion driven pediatric glioblastoma: Identification of oncogenic Drivers via integrative Genome and transcriptome profiling
Heidi M. Britton, Adrian B. Levine, Yaoqing Shen, Karen Mungall, Jonathan Serrano, ..., Shahrad R. Rassekh, Rebecca Deyell, Stephen Yip, Sylvia Cheng, Chris Dunham
Clinical Case Reports
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10 Feb 2021
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doi:10.1002/CCR3.3804
NTRK2 Fusion driven pediatric glioblastoma: Identification of oncogenic Drivers via integrative Genome and transcriptome profiling.
Heidi M Britton, Adrian B Levine, Yaoqing Shen, Karen Mungall, Jonathan Serrano, ..., Shahrad R Rassekh, Rebecca Deyell, Stephen Yip, Sylvia Cheng, Chris Dunham
Clinical case reports
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10 Feb 2021
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Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
Erica S. Tsang, Cameron J. Grisdale, Erin Pleasance, James T. Topham, Karen Mungall, ..., Stephen Yip, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Jonathan M. Loree
Clinical Cancer Research
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15 Jan 2021
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doi:10.1158/1078-0432.CCR-20-1900
Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity
Laura M. Richards, Owen K. N. Whitley, Graham MacLeod, Florence M. G. Cavalli, Fiona J. Coutinho, ..., Samuel Weiss, Stephane Angers, Peter B. Dirks, Gary D. Bader, Trevor J. Pugh
Nature Cancer
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04 Jan 2021
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doi:10.1038/S43018-020-00154-9
Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity.
Laura M Richards, Owen K N Whitley, Graham MacLeod, Florence M G Cavalli, Fiona J Coutinho, ..., Samuel Weiss, Stephane Angers, Peter B Dirks, Gary D Bader, Trevor J Pugh
Nature cancer
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04 Jan 2021
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Subtype-Discordant Pancreatic Ductal Adenocarcinoma Tumors Show Intermediate Clinical and Molecular Characteristics
James T. Topham, Joanna M. Karasinska, Michael K.C. Lee, Veronika Csizmok, Laura M. Williamson, ..., Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer
Clinical Cancer Research
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01 Jan 2021
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doi:10.1158/1078-0432.CCR-20-2831
Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors
Alexandra Pender, Emma Titmuss, Erin D. Pleasance, Kevin Y. Fan, Hillary Pearson, ..., Sophie Sun, Robert A. Holt, Steven J.M. Jones, Marco A. Marra, Janessa Laskin
Clinical Cancer Research
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01 Jan 2021
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doi:10.1158/1078-0432.CCR-20-1163
Delving into Early-onset Pancreatic Ductal Adenocarcinoma: How Does Age Fit In?
Erica S. Tsang, James T. Topham, Joanna M. Karasinska, Michael K.C. Lee, Laura M. Williamson, ..., Steven J.M. Jones, Marco A. Marra, Steven Gallinger, David F. Schaeffer, Daniel J. Renouf
Clinical Cancer Research
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01 Jan 2021
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doi:10.1158/1078-0432.CCR-20-1042
2020
Tumor infiltrating neutrophils and gland formation predict overall survival and molecular subgroups in pancreatic ductal adenocarcinoma
Julia R. Naso, James T. Topham, Joanna M. Karasinska, Michael K.C. Lee, Steve E. Kalloger, ..., Steven J.M. Jones, Janessa Laskin, Marco A. Marra, Daniel J. Renouf, David F. Schaeffer
Cancer Medicine
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28 Dec 2020
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doi:10.1002/CAM4.3695
Tumor infiltrating neutrophils and gland formation predict overall survival and molecular subgroups in pancreatic ductal adenocarcinoma.
Julia R Naso, James T Topham, Joanna M Karasinska, Michael K C Lee, Steve E Kalloger, ..., Steven J M Jones, Janessa Laskin, Marco A Marra, Daniel J Renouf, David F Schaeffer
Cancer medicine
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28 Dec 2020
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Whole-slide laser microdissection for tumour enrichment.
Robin Jn Coope, Colin Schlosser, Richard D Corbett, Stephen Pleasance, Basile Tessier-Cloutier, ..., Heather Kirk, Simon Haile, Yongjun Zhao, Andrew J Mungall, Marco A Marra
The Journal of pathology
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09 Dec 2020
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pubmed:33135777
Matching methods in precision oncology: An introduction and illustrative example
Deirdre Weymann, Janessa Laskin, Steven J.M. Jones, Howard Lim, Daniel J. Renouf, ..., Kasmintan A. Schrader, Sophie Sun, Stephen Yip, Marco A. Marra, Dean A. Regier
Molecular Genetics & Genomic Medicine
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25 Nov 2020
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doi:10.1002/MGG3.1554
Matching methods in precision oncology: An introduction and illustrative example.
Deirdre Weymann, Janessa Laskin, Steven J M Jones, Howard Lim, Daniel J Renouf, ..., Kasmintan A Schrader, Sophie Sun, Stephen Yip, Marco A Marra, Dean A Regier
Molecular genetics & genomic medicine
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25 Nov 2020
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pubmed:33237632
A three-dimensional finite-element model of gluteus medius muscle incorporating inverse-dynamics-based optimization for simulation of non-uniform muscle contraction.
Junyan Li, Marco A Marra, Nico Verdonschot, Yongtao Lu
Medical engineering & physics
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20 Nov 2020
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pubmed:33461672
Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers.
Erica S Tsang, Cameron J Grisdale, Erin Pleasance, James T Topham, Karen Mungall, ..., Stephen Yip, Janessa Laskin, Marco A Marra, Steven J M Jones, Jonathan M Loree
Clinical cancer research : an official journal of the American Association for Cancer Research
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04 Nov 2020
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pubmed:33148671
Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing
My Linh Thibodeau, Kieran O’Neill, Katherine Dixon, Caralyn Reisle, Karen L. Mungall, ..., Aly Karsan, Janessa Laskin, Marco A. Marra, Kasmintan A. Schrader, Steven J.M. Jones
Genetics in Medicine
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01 Nov 2020
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doi:10.1038/S41436-020-0880-8
Impact of MYC and BCL2 structural variants in tumors of DLBCL morphology and mechanisms of false-negative MYC IHC
Brett J Collinge, Susana Ben-Neriah, Lauren C. Chong, Merrill Boyle, Aixiang Jiang, ..., Randy D. Gascoyne, Marco A. Marra, Joseph M Connors, Christian Steidl, David W. Scott
Blood
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29 Oct 2020
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doi:10.1182/BLOOD.2020007193
TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L
Derek Wong, Lisa Sogerer, Samantha S. Lee, Victor Wong, Amy Lum, Adrian B. Levine, Marco A. Marra, Stephen Yip
BMC Biology
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28 Oct 2020
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doi:10.1186/S12915-020-00895-0
TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L.
Derek Wong, Lisa Sogerer, Samantha S Lee, Victor Wong, Amy Lum, Adrian B Levine, Marco A Marra, Stephen Yip
BMC biology
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28 Oct 2020
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pubmed:33115448
Subtype-Discordant Pancreatic Ductal Adenocarcinoma Tumors Show Intermediate Clinical and Molecular Characteristics.
James T Topham, Joanna M Karasinska, Michael K C Lee, Veronika Csizmok, Laura M Williamson, ..., Janessa Laskin, Marco A Marra, Steven J M Jones, Daniel J Renouf, David F Schaeffer
Clinical cancer research : an official journal of the American Association for Cancer Research
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13 Oct 2020
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pubmed:33051307
Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression
Astrid De Boeck, Bo Young Ahn, Charlotte D’Mello, Xueqing Lun, Shyam V. Menon, ..., Eric C. Holland, Pinaki Bose, Jennifer A. Chan, Stephen M. Robbins, Donna L. Senger
Nature Communications
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05 Oct 2020
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doi:10.1038/S41467-020-18569-4
Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors.
Alexandra Pender, Emma Titmuss, Erin D Pleasance, Kevin Y Fan, Hillary Pearson, ..., Sophie Sun, Robert A Holt, Steven J M Jones, Marco A Marra, Janessa Laskin
Clinical cancer research : an official journal of the American Association for Cancer Research
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05 Oct 2020
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pubmed:33020056
Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression.
Astrid De Boeck, Bo Young Ahn, Charlotte D'Mello, Xueqing Lun, Shyam V Menon, ..., Eric C Holland, Pinaki Bose, Jennifer A Chan, Stephen M Robbins, Donna L Senger
Nature communications
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05 Oct 2020
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, ..., Nicholas van As, Carolien H. M. van Deurzen, Marc J. van de Vijver, L. van’t Veer, Christian von Mering
Nature Communications
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21 Sep 2020
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doi:10.1038/S41467-020-18151-Y
Delving into Early-onset Pancreatic Ductal Adenocarcinoma: How Does Age Fit In?
Erica S Tsang, James T Topham, Joanna M Karasinska, Michael K C Lee, Laura M Williamson, ..., Steven J M Jones, Marco A Marra, Steven Gallinger, David F Schaeffer, Daniel J Renouf
Clinical cancer research : an official journal of the American Association for Cancer Research
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21 Sep 2020
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Sex differences in oncogenic mutational processes
Constance H. Li, Stephenie D. Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, ..., Nicholas van As, Carolien H. M. van Deurzen, Marc J. van de Vijver, L. van’t Veer, Christian von Mering
Nature Communications
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28 Aug 2020
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doi:10.1038/S41467-020-17359-2
Evaluating genomic biomarkers associated with resistance or sensitivity to chemotherapy in patients with advanced breast and colorectal cancer
Jolene Guenter, Shirin Abadi, Howard Lim, Stephen Chia, Ryan Woods, Martin Jones, Nevena Rebic, Daniel J Renouf, Janessa Laskin, Marco Marra
Journal of Oncology Pharmacy Practice
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26 Aug 2020
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doi:10.1177/1078155220951845
Molecular attributes underlying central nervous system and systemic relapse in diffuse large B-cell lymphoma
Keren Isaev, Daisuke Ennishi, Laura Hilton, Brian Skinnider, Karen L. Mungall, ..., Randy D. Gascoyne, Ryan Morin, Kerry J. Savage, David W. Scott, Robert Kridel
Haematologica
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13 Aug 2020
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doi:10.3324/HAEMATOL.2020.255950
Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes.
Alessia Gagliardi, Vanessa L Porter, Zusheng Zong, Reanne Bowlby, Emma Titmuss, ..., Janet S Rader, Akinyemi I Ojesina, Daniela S Gerhard, Andrew J Mungall, Marco A Marra
Nature genetics
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03 Aug 2020
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Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes
Alessia Gagliardi, Vanessa L. Porter, Zusheng Zong, Reanne Bowlby, Emma Titmuss, ..., Janet S. Rader, Akinyemi I. Ojesina, Daniela S. Gerhard, Andrew J. Mungall, Marco A. Marra
Nature Genetics
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01 Aug 2020
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doi:10.1038/S41588-020-0673-7
Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing
Prasath Pararajalingam, Krysta M. Coyle, Sarah E. Arthur, Nicole Thomas, Miguel Alcaide, ..., Timothy E. Audas, Marco A. Marra, Nathalie A. Johnson, David W. Scott, Ryan D. Morin
Blood
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30 Jul 2020
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doi:10.1182/BLOOD.2019002385
Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing.
Prasath Pararajalingam, Krysta M Coyle, Sarah E Arthur, Nicole Thomas, Miguel Alcaide, ..., Timothy E Audas, Marco A Marra, Nathalie A Johnson, David W Scott, Ryan D Morin
Blood
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30 Jul 2020
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Epigenomic programming in early fetal brain development.
Luolan Li, Cecile L Maire, Misha Bilenky, Annaïck Carles, Alireza Heravi-Moussavi, ..., Steven Jm Jones, Marco A Marra, Keith L Ligon, Joseph F Costello, Martin Hirst
Epigenomics
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17 Jul 2020
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pubmed:32677466
Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma.
Christopher K Rushton, Sarah E Arthur, Miguel Alcaide, Matthew Cheung, Aixiang Jiang, ..., Christian Steidl, Mark S Cragg, David W Scott, Nathalie A Johnson, Ryan D Morin
Blood advances
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14 Jul 2020
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Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing.
My Linh Thibodeau, Kieran O'Neill, Katherine Dixon, Caralyn Reisle, Karen L Mungall, ..., Aly Karsan, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
Genetics in medicine : official journal of the American College of Medical Genetics
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06 Jul 2020
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pubmed:32624572
Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma
Christopher K. Rushton, Sarah E. Arthur, Miguel Alcaide, Matthew Cheung, Aixiang Jiang, ..., Christian Steidl, Mark S. Cragg, David W. Scott, Nathalie A. Johnson, Ryan D. Morin
Blood Advances
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26 Jun 2020
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doi:10.1182/BLOODADVANCES.2020001696
Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types.
James T Topham, Emma Titmuss, Erin D Pleasance, Laura M Williamson, Joanna M Karasinska, ..., Janessa Laskin, Marco A Marra, Steven J M Jones, David F Schaeffer, Daniel J Renouf
Molecular cancer therapeutics
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09 Jun 2020
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pubmed:32518206
Validation of the RHL30 digital gene expression assay as a prognostic biomarker for relapsed Hodgkin lymphoma
Lourdes Calvente, Rosemarie Tremblay‐LeMay, Wei Xu, Fong Chun Chan, Michael Hong, ..., Aly Karsan, Christian Steidl, David W. Scott, Peter Sabatini, Robert Kridel
British Journal of Haematology
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08 Jun 2020
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doi:10.1111/BJH.16777
Validation of the RHL30 digital gene expression assay as a prognostic biomarker for relapsed Hodgkin lymphoma.
Lourdes Calvente, Rosemarie Tremblay-LeMay, Wei Xu, Fong Chun Chan, Michael Hong, ..., Aly Karsan, Christian Steidl, David W Scott, Peter Sabatini, Robert Kridel
British journal of haematology
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08 Jun 2020
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pubmed:32510594
Integration of Whole-Genome Sequencing With Circulating Tumor DNA Analysis Captures Clonal Evolution and Tumor Heterogeneity in Non-V600 BRAF Mutant Colorectal Cancer
Shehara Mendis, Miguel Alcaide, James T. Topham, Benny Johnson, Ryan D. Morin, ..., Steven J.M. Jones, Marco A. Marra, David F. Schaeffer, Daniel J. Renouf, Jonathan M. Loree
Clinical Colorectal Cancer
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01 Jun 2020
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doi:10.1016/J.CLCC.2020.02.001
Epigenomic Programming in Early Fetal Brain Development
Luolan Li, Cecile L Maire, Misha Bilenky, Annaïck Carles, Alireza Heravi-Moussavi, ..., Steven JM Jones, Marco A Marra, Keith L Ligon, Joseph F Costello, Martin Hirst
Epigenomics
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01 Jun 2020
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Establishing a Framework for the Clinical Translation of Germline Findings in Precision Oncology
Katherine Dixon, Sean Young, Yaoqing Shen, My Linh Thibodeau, Alexandra Fok, ..., Aly Karsan, Marco Marra, Janessa Laskin, Howard Lim, Kasmintan A Schrader
JNCI Cancer Spectrum
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29 May 2020
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doi:10.1093/JNCICS/PKAA045
Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma.
Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Lianne Q Chau, Meher Beigi Masihi, ..., Oren J Becher, Linda M Bradley, Carl F Ware, Michael D Taylor, Robert J Wechsler-Reya
Nature neuroscience
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18 May 2020
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Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes
Erin Pleasance, Emma Titmuss, Laura Williamson, Harwood Kwan, Luka Culibrk, ..., Howard Lim, Daniel J. Renouf, Janessa Laskin, Steven J. M. Jones, Marco A. Marra
Nature Cancer
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13 Apr 2020
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Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes.
Erin Pleasance, Emma Titmuss, Laura Williamson, Harwood Kwan, Luka Culibrk, ..., Howard Lim, Daniel J Renouf, Janessa Laskin, Steven J M Jones, Marco A Marra
Nature cancer
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13 Apr 2020
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pubmed:35121966
Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.
Michelle Chan-Seng-Yue, Jaeseung C Kim, Gavin W Wilson, Karen Ng, Eugenia Flores Figueroa, ..., David A Tuveson, Jennifer J Knox, Sandra E Fischer, Steven Gallinger, Faiyaz Notta
Nature genetics
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01 Apr 2020
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pubmed:32051610
Single-cell analysis of RORα tracer mouse lung reveals ILC progenitors and effector ILC2 subsets.
Maryam Ghaedi, Zi Yi Shen, Mona Orangi, Itziar Martinez-Gonzalez, Lisa Wei, ..., Arundhoti Das, Alireza Heravi-Moussavi, Marco A Marra, Avinash Bhandoola, Fumio Takei
The Journal of experimental medicine
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02 Mar 2020
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TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma
Daisuke Ennishi, Shannon Healy, Ali Bashashati, Saeed Saberi, Christoffer Hother, ..., Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne, David W. Scott, Christian Steidl
Nature Medicine
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24 Feb 2020
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doi:10.1038/S41591-020-0757-Z
TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma.
Daisuke Ennishi, Shannon Healy, Ali Bashashati, Saeed Saberi, Christoffer Hother, ..., Marco A Marra, Sohrab P Shah, Randy D Gascoyne, David W Scott, Christian Steidl
Nature medicine
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24 Feb 2020
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pubmed:32094924
Integration of Whole-Genome Sequencing With Circulating Tumor DNA Analysis Captures Clonal Evolution and Tumor Heterogeneity in Non-V600 BRAF Mutant Colorectal Cancer.
Shehara Mendis, Miguel Alcaide, James T Topham, Benny Johnson, Ryan D Morin, ..., Steven J M Jones, Marco A Marra, David F Schaeffer, Daniel J Renouf, Jonathan M Loree
Clinical colorectal cancer
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10 Feb 2020
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Pan-cancer analysis of whole genomes
Lauri A. Aaltonen, Federico Abascal, Adam Abeshouse, Hiroyuki Aburatani, David J. Adams, ..., Nicholas van As, Carolien H. M. van Deurzen, Marc J. van de Vijver, L. van’t Veer, Christian von Mering
Nature
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05 Feb 2020
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doi:10.1038/S41586-020-1969-6
Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic
Elisa Majounie, Kathleen Wee, Laura M Williamson, Martin R Jones, Erin Pleasance, ..., Daniel J Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Cold Spring Harbor molecular case studies
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03 Feb 2020
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pubmed:31871216
Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution
Michelle Chan-Seng-Yue, Jaeseung C. Kim, Gavin W. Wilson, Karen Ng, Eugenia Flores Figueroa, ..., David A. Tuveson, Jennifer J. Knox, Sandra E. Fischer, Steven Gallinger, Faiyaz Notta
Nature Genetics
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13 Jan 2020
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Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.
Michelle Chan-Seng-Yue, Jaeseung C Kim, Gavin W Wilson, Karen Ng, Eugenia Flores Figueroa, ..., David A Tuveson, Jennifer J Knox, Sandra E Fischer, Steven Gallinger, Faiyaz Notta
Nature genetics
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13 Jan 2020
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Altered Gene Expression along the Glycolysis–Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer
Joanna M. Karasinska, James T. Topham, Steve E. Kalloger, Gun Ho Jang, Robert E. Denroche, ..., Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer
Clinical Cancer Research
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01 Jan 2020
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Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic DPYD structural variant
Elisa Majounie, Kathleen Wee, Laura M. Williamson, Martin R. Jones, Erin Pleasance, ..., Daniel J. Renouf, Stephen Yip, Steven J.M. Jones, Marco A. Marra, Janessa Laskin
Molecular Case Studies
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23 Dec 2019
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Abstract B56: Endogenous retrovirus transcript levels are associated with immunogenic signatures in multiple metastatic cancer types
James T. Topham, Emma Titmuss, Erin Pleasance, Laura M. Williamson, Joanna M. Karasinska, ..., Dixie L. Mager, Marco A. Marra, Steven J.M. Jones, David F. Schaeffer, Daniel J. Renouf
Cancer Research
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13 Dec 2019
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Single-cell analysis of RORα tracer mouse lung reveals ILC progenitors and effector ILC2 subsets
Maryam Ghaedi, Zi Yi Shen, Mona Orangi, Itziar Martinez-Gonzalez, Lisa Wei, ..., Arundhoti Das, Alireza Heravi-Moussavi, Marco A. Marra, Avinash Bhandoola, Fumio Takei
Journal of Experimental Medicine
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05 Dec 2019
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Therapeutic Implication of Genomic Landscape of Adult Metastatic Sarcoma
Xiaolan Feng, Erin Pleasance, Eric Y. Zhao, Tony Ng, Jasleen K. Grewal, ..., Karen Gelmon, Stephen Yip, Steven J.M. Jones, Marco Marra, Janessa Laskin
JCO Precision Oncology
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01 Dec 2019
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Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, ..., Stephen Chia, Marco A Marra, Carl Hansen, Sohrab P Shah, Samuel Aparicio
Cell
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14 Nov 2019
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Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration.
Hye-Jung E Chun, Pascal D Johann, Katy Milne, Marc Zapatka, Annette Buellesbach, ..., Elizabeth J Perlman, Brad H Nelson, Stefan M Pfister, Marco A Marra, Marcel Kool
Cell reports
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07 Nov 2019
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Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration
Hye-Jung E. Chun, Pascal D. Johann, Katy Milne, Marc Zapatka, Annette Buellesbach, ..., Elizabeth J. Perlman, Brad H. Nelson, Stefan M. Pfister, Marco A. Marra, Marcel Kool
Cell Reports
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01 Nov 2019
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Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, ..., Jean Fan, Hsuan Lee, Leonardo Sepulveda Duran, Chenglong Xia, Pu Zheng
Cell
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01 Nov 2019
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Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA.
Simon Haile, Richard D Corbett, Steve Bilobram, Karen Mungall, Bruno M Grande, ..., Andrew J Mungall, Yongjun Zhao, Ryan D Morin, Steven J Jones, Marco A Marra
PloS one
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31 Oct 2019
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Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer
Olena M. Vaske, Isabel Bjork, Sofie R. Salama, Holly Beale, Avanthi Tayi Shah, ..., Leonard S. Sender, Sabine Mueller, E. Alejandro Sweet-Cordero, Theodore C. Goldstein, David Haussler
JAMA Network Open
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25 Oct 2019
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doi:10.1001/JAMANETWORKOPEN.2019.13968
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma
Hiromichi Suzuki, Sachin A. Kumar, Shimin Shuai, Ander Diaz-Navarro, Ana Gutierrez-Fernandez, ..., Vijay Ramaswamy, Xose S. Puente, John A. Calarco, Lincoln Stein, Michael D. Taylor
Nature
·
09 Oct 2019
·
doi:10.1038/S41586-019-1650-0
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma.
Hiromichi Suzuki, Sachin A Kumar, Shimin Shuai, Ander Diaz-Navarro, Ana Gutierrez-Fernandez, ..., Vijay Ramaswamy, Xose S Puente, John A Calarco, Lincoln Stein, Michael D Taylor
Nature
·
09 Oct 2019
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pubmed:31664194
Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.
Olena M Vaske, Isabel Bjork, Sofie R Salama, Holly Beale, Avanthi Tayi Shah, ..., Leonard S Sender, Sabine Mueller, E Alejandro Sweet-Cordero, Theodore C Goldstein, David Haussler
JAMA network open
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02 Oct 2019
·
pubmed:31651965
Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma
Anja Mottok, Stacy S. Hung, Elizabeth A. Chavez, Bruce Woolcock, Adèle Telenius, ..., Marco A. Marra, Reiner Siebert, David W. Scott, Kerry J. Savage, Christian Steidl
Blood
·
05 Sep 2019
·
doi:10.1182/blood.2019001126
Altered Gene Expression along the Glycolysis-Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer.
Joanna M Karasinska, James T Topham, Steve E Kalloger, Gun Ho Jang, Robert E Denroche, ..., Janessa Laskin, Marco A Marra, Steven J M Jones, Daniel J Renouf, David F Schaeffer
Clinical cancer research : an official journal of the American Association for Cancer Research
·
03 Sep 2019
·
pubmed:31481506
Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments
Yaoqing Shen, Cameron J. Grisdale, Sumaiya A. Islam, Pinaki Bose, Jake Lever, ..., Michael D. Blough, David R. Kaplan, J. Gregory Cairncross, Marco A. Marra, Steven J. M. Jones
Proceedings of the National Academy of Sciences
·
30 Aug 2019
·
doi:10.1073/PNAS.1813495116
Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments.
Yaoqing Shen, Cameron J Grisdale, Sumaiya A Islam, Pinaki Bose, Jake Lever, ..., Michael D Blough, David R Kaplan, J Gregory Cairncross, Marco A Marra, Steven J M Jones
Proceedings of the National Academy of Sciences of the United States of America
·
30 Aug 2019
·
pubmed:31471491
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma
Gian Luca Negri, Bruno M Grande, Alberto Delaidelli, Amal El‐Naggar, Dawn Cochrane, ..., Alexandre Montpetit, Marco A Marra, David Malkin, Ryan D Morin, Poul H Sorensen
The Journal of Pathology
·
28 Aug 2019
·
doi:10.1002/path.5319
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma.
Gian Luca Negri, Bruno M Grande, Alberto Delaidelli, Amal El-Naggar, Dawn Cochrane, ..., Alexandre Montpetit, Marco A Marra, David Malkin, Ryan D Morin, Poul H Sorensen
The Journal of pathology
·
28 Aug 2019
·
pubmed:31236944
NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma
Martin R. Jones, Laura M. Williamson, James T. Topham, Michael K.C. Lee, Angela Goytain, ..., Janessa Laskin, Marco A. Marra, David F. Schaeffer, Steven J.M. Jones, Daniel J. Renouf
Clinical Cancer Research
·
01 Aug 2019
·
doi:10.1158/1078-0432.ccr-19-0191
The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous system
Derek Wong, Yaoqing Shen, Adrian B. Levine, Erin Pleasance, Martin Jones, ..., Brian Toyota, Janessa Laskin, Steven J.M. Jones, Marco A. Marra, Stephen Yip
Molecular Case Studies
·
01 Aug 2019
·
doi:10.1101/mcs.a004143
The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous system.
Derek Wong, Yaoqing Shen, Adrian B Levine, Erin Pleasance, Martin Jones, ..., Brian Toyota, Janessa Laskin, Steven J M Jones, Marco A Marra, Stephen Yip
Cold Spring Harbor molecular case studies
·
01 Aug 2019
·
pubmed:31371350
Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma.
Anja Mottok, Stacy S Hung, Elizabeth A Chavez, Bruce Woolcock, Adèle Telenius, ..., Marco A Marra, Reiner Siebert, David W Scott, Kerry J Savage, Christian Steidl
Blood
·
10 Jul 2019
·
pubmed:31292115
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
Michael J. Johnston, Ana Nikolic, Nicoletta Ninkovic, Paul Guilhamon, Florence M.G. Cavalli, ..., Sorana Morrissy, Bradley St Croix, Douglas J. Mahoney, Mathieu Lupien, Marco Gallo
Genome Research
·
27 Jun 2019
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doi:10.1101/gr.246520.118
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma.
Michael J Johnston, Ana Nikolic, Nicoletta Ninkovic, Paul Guilhamon, Florence M G Cavalli, ..., Sorana Morrissy, Bradley St Croix, Douglas J Mahoney, Mathieu Lupien, Marco Gallo
Genome research
·
27 Jun 2019
·
pubmed:31249064
The Genome of the Steller Sea Lion (Eumetopias jubatus)
Harwood H. Kwan, Luka Culibrk, Gregory A. Taylor, Sreeja Leelakumari, Ryan Tan, ..., Inanc Birol, Marco A. Marra, David A.S. Rosen, Martin Haulena, Steven J. M. Jones
Genes
·
26 Jun 2019
·
doi:10.3390/genes10070486
The Genome of the Steller Sea Lion (
Harwood H Kwan, Luka Culibrk, Gregory A Taylor, Sreeja Leelakumari, Ryan Tan, ..., Inanc Birol, Marco A Marra, David A S Rosen, Martin Haulena, Steven J M Jones
Genes
·
26 Jun 2019
·
pubmed:31248052
Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor.
Laura M Williamson, Michael Steel, Jasleen K Grewal, My Lihn Thibodeau, Eric Y Zhao, ..., Marco A Marra, Janessa Laskin, Daniel J Renouf, David F Schaeffer, Steven J M Jones
Cold Spring Harbor molecular case studies
·
03 Jun 2019
·
pubmed:31160355
Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor
Laura M. Williamson, Michael Steel, Jasleen K. Grewal, My Lihn Thibodeau, Eric Y. Zhao, ..., Marco A. Marra, Janessa Laskin, Daniel J. Renouf, David F. Schaeffer, Steven J.M. Jones
Molecular Case Studies
·
01 Jun 2019
·
doi:10.1101/MCS.A003814
[no title info]
Martin R Jones, Laura M Williamson, James T Topham, Michael K C Lee, Angela Goytain, ..., Janessa Laskin, Marco A Marra, David F Schaeffer, Steven J M Jones, Daniel J Renouf
Clinical cancer research : an official journal of the American Association for Cancer Research
·
08 May 2019
·
pubmed:31068372
Capicua regulates neural stem cell proliferation and lineage specification through control of Ets factors
Shiekh Tanveer Ahmad, Alexandra D. Rogers, Myra J. Chen, Rajiv Dixit, Lata Adnani, ..., Marco A. Marra, Stephen M. Robbins, J. Gregory Cairncross, Carol Schuurmans, Jennifer A. Chan
Nature Communications
·
01 May 2019
·
doi:10.1038/S41467-019-09949-6
Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Mary Hoffman, Aaron H. Gillmor, Daniel J. Kunz, Michael J. Johnston, Ana Nikolic, ..., Donna L. Senger, Benjamin D. Simons, Jennifer A. Chan, A. Sorana Morrissy, Marco Gallo
Cancer Research
·
01 May 2019
·
doi:10.1158/0008-5472.can-18-3441
Childhood cerebellar tumours mirror conserved fetal transcriptional programs
Maria C. Vladoiu, Ibrahim El-Hamamy, Laura K. Donovan, Hamza Farooq, Borja L. Holgado, ..., Claudia L. Kleinman, Alexandra L. Joyner, Nada Jabado, Lincoln Stein, Michael D. Taylor
Nature
·
01 May 2019
·
doi:10.1038/s41586-019-1158-7
Capicua regulates neural stem cell proliferation and lineage specification through control of Ets factors.
Shiekh Tanveer Ahmad, Alexandra D Rogers, Myra J Chen, Rajiv Dixit, Lata Adnani, ..., Marco A Marra, Stephen M Robbins, J Gregory Cairncross, Carol Schuurmans, Jennifer A Chan
Nature communications
·
01 May 2019
·
pubmed:31043608
Childhood cerebellar tumours mirror conserved fetal transcriptional programs.
Maria C Vladoiu, Ibrahim El-Hamamy, Laura K Donovan, Hamza Farooq, Borja L Holgado, ..., Claudia L Kleinman, Alexandra L Joyner, Nada Jabado, Lincoln Stein, Michael D Taylor
Nature
·
01 May 2019
·
pubmed:31043743
Application of a Neural Network Whole Transcriptome–Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers
Jasleen K. Grewal, Basile Tessier-Cloutier, Martin Jones, Sitanshu Gakkhar, Yussanne Ma, ..., Daniel Renouf, Janessa Laskin, Marco Marra, Stephen Yip, Steven J. M. Jones
JAMA Network Open
·
26 Apr 2019
·
doi:10.1001/jamanetworkopen.2019.2597
Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition
Daisuke Ennishi, Katsuyoshi Takata, Wendy Béguelin, Gerben Duns, Anja Mottok, ..., Joseph M. Connors, Randy D. Gascoyne, David W. Scott, Ari M. Melnick, Christian Steidl
Cancer Discovery
·
01 Apr 2019
·
doi:10.1158/2159-8290.cd-18-1090
Base excision repair deficiency signatures implicate germline and somatic
My Linh Thibodeau, Eric Y Zhao, Caralyn Reisle, Carolyn Ch'ng, Hui-Li Wong, ..., Janessa Laskin, Marco A Marra, Daniel J Renouf, Steven J M Jones, Kasmintan A Schrader
Cold Spring Harbor molecular case studies
·
01 Apr 2019
·
pubmed:30833417
Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma
Bruno M. Grande, Daniela S. Gerhard, Aixiang Jiang, Nicholas B. Griner, Jeremy S. Abramson, ..., George W. Wright, Eric Y. Zhao, Marco A. Marra, Ryan D. Morin, Louis M. Staudt
Blood
·
21 Mar 2019
·
doi:10.1182/blood-2018-09-871418
Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma.
Mary Hoffman, Aaron H Gillmor, Daniel J Kunz, Michael J Johnston, Ana Nikolic, ..., Donna L Senger, Benjamin D Simons, Jennifer A Chan, A Sorana Morrissy, Marco Gallo
Cancer research
·
15 Mar 2019
·
pubmed:30877103
Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis
My Linh Thibodeau, Eric Y. Zhao, Caralyn Reisle, Carolyn Ch'ng, Hui-Li Wong, ..., Janessa Laskin, Marco A. Marra, Daniel J. Renouf, Steven J.M. Jones, Kasmintan A. Schrader
Molecular Case Studies
·
04 Mar 2019
·
doi:10.1101/mcs.a003681
Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, ..., E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
Nature medicine
·
01 Mar 2019
·
pubmed:30705421
A High-Throughput Protocol for Isolating Cell-Free Circulating Tumor DNA from Peripheral Blood
Pawan K Pandoh, Richard D Corbett, Helen McDonald, Miguel Alcaide, Heather Kirk, ..., Steven JM Jones, Robert A Holt, Aly Karsan, Ryan D Morin, Marco A Marra
BioTechniques
·
01 Feb 2019
·
doi:10.2144/btn-2018-0148
A high-throughput protocol for isolating cell-free circulating tumor DNA from peripheral blood.
Pawan K Pandoh, Richard D Corbett, Helen McDonald, Miguel Alcaide, Heather Kirk, ..., Steven Jm Jones, Robert A Holt, Aly Karsan, Ryan D Morin, Marco A Marra
BioTechniques
·
01 Feb 2019
·
pubmed:30744412
Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition.
Daisuke Ennishi, Katsuyoshi Takata, Wendy Béguelin, Gerben Duns, Anja Mottok, ..., Joseph M Connors, Randy D Gascoyne, David W Scott, Ari M Melnick, Christian Steidl
Cancer discovery
·
31 Jan 2019
·
pubmed:30705065
Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.
Simon Haile, Richard D Corbett, Steve Bilobram, Morgan H Bye, Heather Kirk, ..., Andrew J Mungall, Yussanne Ma, Rob A Holt, Steven J Jones, Marco A Marra
Nucleic acids research
·
25 Jan 2019
·
pubmed:30418619
A distinct neurodevelopmental syndrome with intellectual disability, autism spectrum disorder, characteristic facies, and macrocephaly is caused by defects in CHD8
Heba Yasin, William T. Gibson, Sylvie Langlois, Robert M. Stowe, Erica S. Tsang, ..., Christine Tyson, Chi Kin Wong, Marco A. Marra, Jan M. Friedman, Farah R. Zahir
Journal of Human Genetics
·
22 Jan 2019
·
doi:10.1038/S10038-019-0561-0
A distinct neurodevelopmental syndrome with intellectual disability, autism spectrum disorder, characteristic facies, and macrocephaly is caused by defects in CHD8.
Heba Yasin, William T Gibson, Sylvie Langlois, Robert M Stowe, Erica S Tsang, ..., Christine Tyson, Chi Kin Wong, Marco A Marra, Jan M Friedman, Farah R Zahir
Journal of human genetics
·
22 Jan 2019
·
pubmed:30670789
Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma
Daisuke Ennishi, Aixiang Jiang, Merrill Boyle, Brett Collinge, Bruno M. Grande, ..., Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, Ryan D. Morin, David W. Scott
Journal of Clinical Oncology
·
20 Jan 2019
·
doi:10.1200/jco.18.01583
Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma.
Bruno M Grande, Daniela S Gerhard, Aixiang Jiang, Nicholas B Griner, Jeremy S Abramson, ..., George W Wright, Eric Y Zhao, Marco A Marra, Ryan D Morin, Louis M Staudt
Blood
·
07 Jan 2019
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pubmed:30617194
2018
Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma.
Jenny J Ko, Jasleen K Grewal, Tony Ng, Jean-Michel Lavoie, My Linh Thibodeau, ..., Kasmintan A Schrader, Steven J M Jones, Christian Kollmannsberger, Janessa Laskin, Marco A Marra
Cold Spring Harbor molecular case studies
·
17 Dec 2018
·
pubmed:30446580
Clinical outcomes after whole-genome sequencing in patients with metastatic non-small-cell lung cancer
Erica S. Tsang, Yaoqing Shen, Negar Chooback, Cheryl Ho, Martin Jones, ..., Andrew Mungall, Richard Moore, Steven J.M. Jones, Marco Marra, Janessa Laskin
Molecular Case Studies
·
04 Dec 2018
·
doi:10.1101/mcs.a002659
Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma.
Daisuke Ennishi, Aixiang Jiang, Merrill Boyle, Brett Collinge, Bruno M Grande, ..., Christian Steidl, Joseph M Connors, Randy D Gascoyne, Ryan D Morin, David W Scott
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
·
03 Dec 2018
·
pubmed:30523716
Integrative Molecular Characterization of Malignant Pleural Mesothelioma
Julija Hmeljak, Francisco Sanchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart, ..., Jean C. Zenklusen, Jiashan Zhang, Hailei Zhang, Hongxin Zhang, Erik Zmuda
Cancer Discovery
·
01 Dec 2018
·
doi:10.1158/2159-8290.cd-18-0804
The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis
Gregory A. Taylor, Heather Kirk, Lauren Coombe, Shaun D. Jackman, Justin Chu, ..., Inanc Birol, Maria Franke, Marco A. Marra, Christopher Dutton, Steven J. M. Jones
Genes
·
30 Nov 2018
·
doi:10.3390/GENES9120598
The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.
Gregory A Taylor, Heather Kirk, Lauren Coombe, Shaun D Jackman, Justin Chu, ..., Inanc Birol, Maria Franke, Marco A Marra, Christopher Dutton, Steven J M Jones
Genes
·
30 Nov 2018
·
pubmed:30513700
Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma
Jenny J. Ko, Jasleen K. Grewal, Tony Ng, Jean-Michel Lavoie, My Linh Thibodeau, ..., Kasmintan A. Schrader, Steven J.M. Jones, Christian Kollmannsberger, Janessa Laskin, Marco A. Marra
Molecular Case Studies
·
16 Nov 2018
·
doi:10.1101/mcs.a003137
Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples
Simon Haile, Richard D Corbett, Steve Bilobram, Morgan H Bye, Heather Kirk, ..., Andrew J Mungall, Yussanne Ma, Rob A Holt, Steven J Jones, Marco A Marra
Nucleic Acids Research
·
12 Nov 2018
·
doi:10.1093/nar/gky1142
Temporal Dynamics of Genomic Alterations in a BRCA1 Germline–Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan
Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, ..., Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, David F. Schaeffer, Daniel J. Renouf
JCO Precision Oncology
·
01 Nov 2018
·
doi:10.1200/PO.18.00057
Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer
Yulia Newton, S. Rod Rassekh, Rebecca J. Deyell, Yaoqing Shen, Martin R. Jones, ..., Colleen Jantzen, Janessa Laskin, Steven J.M. Jones, Marco A. Marra, Olena Morozova
JCO Precision Oncology
·
01 Nov 2018
·
doi:10.1200/PO.17.00198
High-resolution architecture and partner genes of
Lauren C Chong, Susana Ben-Neriah, Graham W Slack, Ciara Freeman, Daisuke Ennishi, ..., Marco A Marra, Joseph M Connors, Andrew J Mungall, Christian Steidl, David W Scott
Blood advances
·
23 Oct 2018
·
pubmed:30348671
High-resolution architecture and partner genes of MYC rearrangements in lymphoma with DLBCL morphology
Lauren C. Chong, Susana Ben-Neriah, Graham W. Slack, Ciara Freeman, Daisuke Ennishi, ..., Marco A. Marra, Joseph M. Connors, Andrew J. Mungall, Christian Steidl, David W. Scott
Blood Advances
·
22 Oct 2018
·
doi:10.1182/bloodadvances.2018023572
Temporal Dynamics of Genomic Alterations in a
Hui-Li Wong, Eric Y Zhao, Martin R Jones, Caralyn R Reisle, Peter Eirew, ..., Marco A Marra, Steven J M Jones, Kasmintan A Schrader, David F Schaeffer, Daniel J Renouf
JCO precision oncology
·
19 Oct 2018
·
pubmed:32913994
A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily
Anil Korkut, Sobia Zaidi, Rupa S. Kanchi, Shuyun Rao, Nancy R. Gough, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Systems
·
01 Oct 2018
·
doi:10.1016/J.CELS.2018.08.010
Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer
Yumeng Wang, Xiaoyan Xu, Dejan Maglic, Michael T. Dill, Kamalika Mojumdar, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Oct 2018
·
doi:10.1016/j.celrep.2018.10.001
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.
Sarah E Arthur, Aixiang Jiang, Bruno M Grande, Miguel Alcaide, Razvan Cojocaru, ..., Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott, Ryan D Morin
Nature communications
·
01 Oct 2018
·
pubmed:30275490
The genetic basis and cell of origin of mixed phenotype acute leukaemia
Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, Kirsten Dickerson, John K. Choi, ..., Jaime M. Guidry Auvil, Daniela S. Gerhard, Stephen P. Hunger, Hiroto Inaba, Charles G. Mullighan
Nature
·
12 Sep 2018
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doi:10.1038/S41586-018-0436-0
The genetic basis and cell of origin of mixed phenotype acute leukaemia.
Thomas B Alexander, Zhaohui Gu, Ilaria Iacobucci, Kirsten Dickerson, John K Choi, ..., Jaime M Guidry Auvil, Daniela S Gerhard, Stephen P Hunger, Hiroto Inaba, Charles G Mullighan
Nature
·
12 Sep 2018
·
pubmed:30209392
ABT-888 restores sensitivity in temozolomide resistant glioma cells and xenografts
Alice L. Yuan, Christian B. Ricks, Alexandra K. Bohm, Xueqing Lun, Lori Maxwell, ..., Donna L. Senger, Daniel P. Cahill, Erik P. Sulman, J. Gregory Cairncross, Michael D. Blough
PLOS ONE
·
28 Aug 2018
·
doi:10.1371/journal.pone.0202860
Transcriptomic analysis of CIC and ATXN1L reveal a functional relationship exploited by cancer
Derek Wong, Kohl Lounsbury, Amy Lum, Jungeun Song, Susanna Chan, Veronique LeBlanc, Suganthi Chittaranjan, Marco Marra, Stephen Yip
Oncogene
·
09 Aug 2018
·
doi:10.1038/s41388-018-0427-5
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
André Kahles, Kjong-Van Lehmann, Nora C. Toussaint, Matthias Hüser, Stefan G. Stark, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cancer Cell
·
01 Aug 2018
·
doi:10.1016/j.ccell.2018.07.001
Corrigendum: Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, ..., Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
Cold Spring Harbor molecular case studies
·
01 Aug 2018
·
pubmed:30068734
Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort
Sebastian M Waszak, Paul A Northcott, Ivo Buchhalter, Giles W Robinson, Christian Sutter, ..., Peter Lichter, David Malkin, Amar Gajjar, Jan O Korbel, Stefan M Pfister
The Lancet Oncology
·
01 Jun 2018
·
doi:10.1016/S1470-2045(18)30242-0
Integrated Molecular Characterization of Testicular Germ Cell Tumors
Hui Shen, Juliann Shih, Daniel P. Hollern, Linghua Wang, Reanne Bowlby, ..., Zhining Wang, Roy Tarnuzzer, Carolyn M. Hutter, Heidi J. Sofia, Tanja M. Davidsen
Cell Reports
·
01 Jun 2018
·
doi:10.1016/j.celrep.2018.05.039
A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases.
Livia Garzia, Noriyuki Kijima, A Sorana Morrissy, Pasqualino De Antonellis, Ana Guerreiro-Stucklin, ..., Marco A Marra, James R Woodgett, Robert J Wechsler-Reya, Daniel W Fults, Michael D Taylor
Cell
·
31 May 2018
·
pubmed:29856958
Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer.
Yulia Newton, S Rod Rassekh, Rebecca J Deyell, Yaoqing Shen, Martin R Jones, ..., Colleen Jantzen, Janessa Laskin, Steven J M Jones, Marco A Marra, Olena Morozova
JCO precision oncology
·
19 Apr 2018
·
pubmed:31372595
Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, ..., E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
Nature medicine
·
10 Apr 2018
·
pubmed:29634680
Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma.
Rebecca Ronsley, S Rod Rassekh, Yaoqing Shen, Anna F Lee, Colleen Jantzen, ..., Helen Nadel, Steven J M Jones, Janessa Laskin, Marco A Marra, Rebecca J Deyell
Cold Spring Harbor molecular case studies
·
02 Apr 2018
·
pubmed:29610391
Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making.
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, ..., Daniel Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Cold Spring Harbor molecular case studies
·
02 Apr 2018
·
pubmed:29610392
lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer
Zehua Wang, Bo Yang, Min Zhang, Weiwei Guo, Zhiyuan Wu, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cancer Cell
·
01 Apr 2018
·
doi:10.1016/j.ccell.2018.03.006
The Immune Landscape of Cancer
Vésteinn Thorsson, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Immunity
·
01 Apr 2018
·
doi:10.1016/j.immuni.2018.03.023
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Christopher J. Ricketts, Aguirre A. De Cubas, Huihui Fan, Christof C. Smith, Martin Lang, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.075
Systematic Analysis of Splice-Site-Creating Mutations in Cancer
Reyka G. Jayasinghe, Song Cao, Qingsong Gao, Michael C. Wendl, Nam Sy Vo, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.052
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Joel Saltz, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.086
Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types
Michael Seiler, Shouyong Peng, Anant A. Agrawal, James Palacino, Teng Teng, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.01.088
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Li Ding, Matthew H. Bailey, Eduard Porta-Pardo, Vesteinn Thorsson, Antonio Colaprico, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.033
Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, ..., Daniel Renouf, Stephen Yip, Steven J.M. Jones, Marco A. Marra, Janessa Laskin
Molecular Case Studies
·
01 Apr 2018
·
doi:10.1101/mcs.a002626
Pathogenic Germline Variants in 10,389 Adult Cancers
Kuan-lin Huang, R. Jay Mashl, Yige Wu, Deborah I. Ritter, Jiayin Wang, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.039
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Hua-Sheng Chiu, Sonal Somvanshi, Ektaben Patel, Ting-Wen Chen, Vivek P. Singh, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.064
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.035
Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers
Xinxin Peng, Zhongyuan Chen, Farshad Farshidfar, Xiaoyan Xu, Philip L. Lorenzi, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.077
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Tathiane M. Malta, Artem Sokolov, Andrew J. Gentles, Tomasz Burzykowski, Laila Poisson, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.034
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.046
Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types
Zhongqi Ge, Jake S. Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.047
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.076
Genomic and Functional Approaches to Understanding Cancer Aneuploidy
Alison M. Taylor, Juliann Shih, Gavin Ha, Galen F. Gao, Xiaoyang Zhang, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cancer Cell
·
01 Apr 2018
·
doi:10.1016/j.ccell.2018.03.007
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Qingsong Gao, Wen-Wei Liang, Steven M. Foltz, Gnanavel Mutharasu, Reyka G. Jayasinghe, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.050
Comprehensive Characterization of Cancer Driver Genes and Mutations
Matthew H. Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.02.060
Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas
Yang Liu, Nilay S. Sethi, Toshinori Hinoue, Barbara G. Schneider, Andrew D. Cherniack, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cancer Cell
·
01 Apr 2018
·
doi:10.1016/j.ccell.2018.03.010
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
Katherine A. Hoadley, Christina Yau, Toshinori Hinoue, Denise M. Wolf, Alexander J. Lazar, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.022
Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma
Rebecca Ronsley, S. Rod Rassekh, Yaoqing Shen, Anna F. Lee, Colleen Jantzen, ..., Helen Nadel, Steven J.M. Jones, Janessa Laskin, Marco A. Marra, Rebecca J. Deyell
Molecular Case Studies
·
01 Apr 2018
·
doi:10.1101/mcs.a002568
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
Jianfang Liu, Tara Lichtenberg, Katherine A. Hoadley, Laila M. Poisson, Alexander J. Lazar, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.02.052
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Han Chen, Chunyan Li, Xinxin Peng, Zhicheng Zhou, John N. Weinstein, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell
·
01 Apr 2018
·
doi:10.1016/j.cell.2018.03.027
A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers
Ashton C. Berger, Anil Korkut, Rupa S. Kanchi, Apurva M. Hegde, Walter Lenoir, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cancer Cell
·
01 Apr 2018
·
doi:10.1016/j.ccell.2018.03.014
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Joshua D. Campbell, Christina Yau, Reanne Bowlby, Yuexin Liu, Kevin Brennan, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports
·
01 Apr 2018
·
doi:10.1016/j.celrep.2018.03.063
Magnetic-resonance-imaging-based three-dimensional muscle reconstruction of hip abductor muscle volume in a person with a transfemoral bone-anchored prosthesis: A feasibility study.
Ruud A Leijendekkers, Marco A Marra, Marieke J M Ploegmakers, Gerben Van Hinte, Jan Paul Frölke, Hendrik Van De Meent, J Bart Staal, Thomas J Hoogeboom, Nico Verdonschot
Physiotherapy theory and practice
·
28 Mar 2018
·
pubmed:29589767
Flexing and downsizing the femoral component is not detrimental to patellofemoral biomechanics in posterior-referencing cruciate-retaining total knee arthroplasty.
Marco A Marra, Marta Strzelczak, Petra J C Heesterbeek, Sebastiaan A W van de Groes, Dennis Janssen, Bart F J M Koopman, Nico Verdonschot, Ate B Wymenga
Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA
·
20 Mar 2018
·
pubmed:29560510
Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma
My Linh Thibodeau, Melika Bonakdar, Eric Zhao, Karen L. Mungall, Caralyn Reisle, ..., Cheryl Ho, Janessa Laskin, Marco A. Marra, Kasmintan A. Schrader, Steven J. M. Jones
npj Precision Oncology
·
19 Mar 2018
·
doi:10.1038/s41698-018-0050-5
Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma.
My Linh Thibodeau, Melika Bonakdar, Eric Zhao, Karen L Mungall, Caralyn Reisle, ..., Cheryl Ho, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
NPJ precision oncology
·
19 Mar 2018
·
pubmed:29872726
Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma.
Daniel J Merk, Jasmin Ohli, Natalie D Merk, Venu Thatikonda, Sorana Morrissy, ..., Stefan M Pfister, Michael D Taylor, Lukas Chavez, Marcel Kool, Ulrich Schüller
Developmental cell
·
15 Mar 2018
·
pubmed:29551561
In situ comparison of A-mode ultrasound tracking system and skin-mounted markers for measuring kinematics of the lower extremity.
Kenan Niu, Thomas Anijs, Victor Sluiter, Jasper Homminga, André Sprengers, Marco A Marra, Nico Verdonschot
Journal of biomechanics
·
10 Mar 2018
·
pubmed:29573792
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Kyle Ellrott, Matthew H. Bailey, Gordon Saksena, Kyle R. Covington, Cyriac Kandoth, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Systems
·
01 Mar 2018
·
doi:10.1016/j.cels.2018.03.002
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Franz X. Schaub, Varsha Dhankani, Ashton C. Berger, Mihir Trivedi, Anne B. Richardson, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Systems
·
01 Mar 2018
·
doi:10.1016/j.cels.2018.03.003
Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma
Daniel J. Merk, Jasmin Ohli, Natalie D. Merk, Venu Thatikonda, Sorana Morrissy, ..., Stefan M. Pfister, Michael D. Taylor, Lukas Chavez, Marcel Kool, Ulrich Schüller
Developmental Cell
·
01 Mar 2018
·
doi:10.1016/j.devcel.2018.02.012
Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management
Stacy S. Hung, Barbara Meissner, Elizabeth A. Chavez, Susana Ben-Neriah, Daisuke Ennishi, ..., Andrew J. Mungall, Marco A. Marra, David W. Scott, Joseph M. Connors, Christian Steidl
The Journal of Molecular Diagnostics
·
01 Mar 2018
·
doi:10.1016/j.jmoldx.2017.11.010
Gait symmetry and hip strength in women with developmental dysplasia following hip arthroplasty compared to healthy subjects: A cross-sectional study.
Ruud A Leijendekkers, Marco A Marra, Sjoerd Kolk, Geert van Bon, B Wim Schreurs, Vivian Weerdesteyn, Nico Verdonschot
PloS one
·
23 Feb 2018
·
pubmed:29474431
A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases.
Livia Garzia, Noriyuki Kijima, A Sorana Morrissy, Pasqualino De Antonellis, Ana Guerreiro-Stucklin, ..., Marco A Marra, James R Woodgett, Robert J Wechsler-Reya, Daniel W Fults, Michael D Taylor
Cell
·
22 Feb 2018
·
pubmed:29474906
Molecular characterization of ERBB2-amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: a report of two instructive cases
Daniel R. Owen, Hui-li Wong, Melika Bonakdar, Martin Jones, Christopher S. Hughes, ..., Howard Lim, Janessa Laskin, Marco Marra, Stephen Yip, David F. Schaeffer
Molecular Case Studies
·
08 Feb 2018
·
doi:10.1101/mcs.a002535
Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management.
Stacy S Hung, Barbara Meissner, Elizabeth A Chavez, Susana Ben-Neriah, Daisuke Ennishi, ..., Andrew J Mungall, Marco A Marra, David W Scott, Joseph M Connors, Christian Steidl
The Journal of molecular diagnostics : JMD
·
08 Feb 2018
·
pubmed:29429887
The Integrated Genomic Landscape of Thymic Epithelial Tumors
Milan Radovich, Curtis R. Pickering, Ina Felau, Gavin Ha, Hailei Zhang, ..., Hsin-Ta Wu, Ye Wu, Liming Yang, Jiashan Zhang, Erik Zmuda
Cancer Cell
·
01 Feb 2018
·
doi:10.1016/j.ccell.2018.01.003
A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases
Livia Garzia, Noriyuki Kijima, A. Sorana Morrissy, Pasqualino De Antonellis, Ana Guerreiro-Stucklin, ..., Marco A. Marra, James R. Woodgett, Robert J. Wechsler-Reya, Daniel W. Fults, Michael D. Taylor
Cell
·
01 Feb 2018
·
doi:10.1016/j.cell.2018.01.038
Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole-genome and transcriptome sequencing.
Hui-Li Wong, Kevin C Yang, Yaoqing Shen, Eric Y Zhao, Jonathan M Loree, ..., Janessa Laskin, Marco A Marra, David F Schaeffer, Sharon M Gorski, Daniel J Renouf
Cold Spring Harbor molecular case studies
·
01 Feb 2018
·
pubmed:29092957
2017
Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer.
Eric Y Zhao, Yaoqing Shen, Erin Pleasance, Katayoon Kasaian, Sreeja Leelakumari, ..., Ian Bosdet, Aly Karsan, Janessa Laskin, Marco A Marra, Steven J M Jones
Clinical cancer research : an official journal of the American Association for Cancer Research
·
15 Dec 2017
·
pubmed:29246904
Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer
Eric Y. Zhao, Yaoqing Shen, Erin Pleasance, Katayoon Kasaian, Sreeja Leelakumari, ..., Ian Bosdet, Aly Karsan, Janessa Laskin, Marco A. Marra, Steven J.M. Jones
Clinical Cancer Research
·
14 Dec 2017
·
doi:10.1158/1078-0432.ccr-17-1941
Specific muscle strength is reduced in facioscapulohumeral dystrophy: An MRI based musculoskeletal analysis.
Marco A Marra, Linda Heskamp, Karlien Mul, Saskia Lassche, Baziel G M van Engelen, Arend Heerschap, Nico Verdonschot
Neuromuscular disorders : NMD
·
12 Dec 2017
·
pubmed:29395674
The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)
Samantha Jones, Martin Haulena, Gregory Taylor, Simon Chan, Steven Bilobram, ..., Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra, Steven Jones
Genes
·
11 Dec 2017
·
doi:10.3390/genes8120379
The Genome of the Beluga Whale (Delphinapterus leucas)
Steven Jones, Gregory Taylor, Simon Chan, René Warren, S. Hammond, ..., Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra, Martin Haulena
Genes
·
11 Dec 2017
·
doi:10.3390/genes8120378
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, ..., E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
Nature Medicine
·
11 Dec 2017
·
doi:10.1038/nm.4439
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, ..., E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
Nature medicine
·
11 Dec 2017
·
pubmed:29227476
MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia
Emilia L. Lim, Diane L. Trinh, Rhonda E. Ries, Jim Wang, Robert B. Gerbing, ..., Malcolm Smith, Daniela S. Gerhard, Todd A. Alonzo, Soheil Meshinchi, Marco A. Marra
Journal of Clinical Oncology
·
10 Dec 2017
·
doi:10.1200/JCO.2017.74.7451
Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer
M.R. Jones, H. Lim, Y. Shen, E. Pleasance, C. Ch'ng, ..., D.J. Renouf, K. Gelmon, S.J.M. Jones, M.A. Marra, J. Laskin
Annals of Oncology
·
01 Dec 2017
·
doi:10.1093/annonc/mdx523
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
Adam Abeshouse, Clement Adebamowo, Sally N. Adebamowo, Rehan Akbani, Teniola Akeredolu, ..., Jean C. Zenklusen, Jiashan (Julia) Zhang, Hailei Zhang, Hongxin Zhang, Erik Zmuda
Cell
·
01 Nov 2017
·
doi:10.1016/j.cell.2017.10.014
Characterization of the human thyroid epigenome
Celia Siu, Sam Wiseman, Sitanshu Gakkhar, Alireza Heravi-Moussavi, Misha Bilenky, ..., Blair Walker, Thomas Thomson, Marco A Marra, Martin Hirst, Steven J M Jones
Journal of Endocrinology
·
01 Nov 2017
·
doi:10.1530/JOE-17-0145
Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole-genome and transcriptome sequencing
Hui-li Wong, Kevin C. Yang, Yaoqing Shen, Eric Y. Zhao, Jonathan M. Loree, ..., Janessa Laskin, Marco A. Marra, David F. Schaeffer, Sharon M. Gorski, Daniel J. Renouf
Molecular Case Studies
·
01 Nov 2017
·
doi:10.1101/mcs.a002329
MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia.
Emilia L Lim, Diane L Trinh, Rhonda E Ries, Jim Wang, Robert B Gerbing, ..., Malcolm Smith, Daniela S Gerhard, Todd A Alonzo, Soheil Meshinchi, Marco A Marra
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
·
25 Oct 2017
·
pubmed:29068783
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
A. Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, ..., Erik Zmuda, Ellen C. Zwarthoff, John N. Weinstein, David J. Kwiatkowski, Seth P. Lerner
Cell
·
01 Oct 2017
·
doi:10.1016/j.cell.2017.09.007
Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant
IDH1
Tali Mazor, Charles Chesnelong, Aleksandr Pankov, Llewellyn E. Jalbert, Chibo Hong, ..., Adam B. Olshen, Samuel Weiss, Joanna J. Phillips, H. Artee Luchman, Joseph F. Costello
Proceedings of the National Academy of Sciences
·
15 Sep 2017
·
doi:10.1073/pnas.1708914114
Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant
Tali Mazor, Charles Chesnelong, Aleksandr Pankov, Llewellyn E Jalbert, Chibo Hong, ..., Adam B Olshen, Samuel Weiss, Joanna J Phillips, H Artee Luchman, Joseph F Costello
Proceedings of the National Academy of Sciences of the United States of America
·
15 Sep 2017
·
pubmed:28916733
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.
Kristopher R Bosse, Pichai Raman, Zhongyu Zhu, Maria Lane, Daniel Martinez, ..., Marco A Marra, Michael D Taylor, Dimiter S Dimitrov, Crystal L Mackall, John M Maris
Cancer cell
·
11 Sep 2017
·
pubmed:28898695
Detection and genomic characterization of a mammary-like adenocarcinoma
Jasleen K. Grewal, Peter Eirew, Martin Jones, Kenrry Chiu, Basile Tessier-Cloutier, ..., Stephen Yip, Anna V. Tinker, Janessa Laskin, Marco Marra, Steven J.M. Jones
Molecular Case Studies
·
06 Sep 2017
·
doi:10.1101/mcs.a002170
Whole-genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia
Ivan Sloma, Maria Teresa Mitjavila-Garcia, Olivier Feraud, Frank Griscelli, Noufissa Oudrhiri, ..., Martin Hirst, Marco A. Marra, Connie J. Eaves, Annelise Bennaceur-Griscelli, Ali G. Turhan
Experimental Hematology
·
01 Sep 2017
·
doi:10.1016/j.exphem.2017.05.007
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma
Kristopher R. Bosse, Pichai Raman, Zhongyu Zhu, Maria Lane, Daniel Martinez, ..., Marco A. Marra, Michael D. Taylor, Dimiter S. Dimitrov, Crystal L. Mackall, John M. Maris
Cancer Cell
·
01 Sep 2017
·
doi:10.1016/j.ccell.2017.08.003
Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, ..., Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
Cold Spring Harbor molecular case studies
·
01 Sep 2017
·
pubmed:28514723
A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor
Samantha Gadd, Vicki Huff, Amy L Walz, Ariadne H A G Ooms, Amy E Armstrong, ..., Oliver A Hampton, Nicole Ross, Julie M Gastier-Foster, Stefan T Arold, Elizabeth J Perlman
Nature Genetics
·
21 Aug 2017
·
doi:10.1038/ng.3940
A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor.
Samantha Gadd, Vicki Huff, Amy L Walz, Ariadne H A G Ooms, Amy E Armstrong, ..., Oliver A Hampton, Nicole Ross, Julie M Gastier-Foster, Stefan T Arold, Elizabeth J Perlman
Nature genetics
·
21 Aug 2017
·
pubmed:28825729
Characterization of the human thyroid epigenome.
Celia Siu, Sam Wiseman, Sitanshu Gakkhar, Alireza Heravi-Moussavi, Misha Bilenky, ..., Blair Walker, Thomas Thomson, Marco A Marra, Martin Hirst, Steven J M Jones
The Journal of endocrinology
·
14 Aug 2017
·
pubmed:28808080
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma
A. Gordon Robertson, Juliann Shih, Christina Yau, Ewan A. Gibb, Junna Oba, ..., Christina Yau, Jean C. Zenklusen, Jiashan Zhang, Hailei Zhang, Erik Zmuda
Cancer Cell
·
01 Aug 2017
·
doi:10.1016/j.ccell.2017.07.003
Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
Benjamin J. Raphael, Ralph H. Hruban, Andrew J. Aguirre, Richard A. Moffitt, Jen Jen Yeh, ..., Zhining Wang, Liming Yang, Jiashan (Julia) Zhang, Ina Felau, Jean C. Zenklusen
Cancer Cell
·
01 Aug 2017
·
doi:10.1016/j.ccell.2017.07.007
Evaluation of a Surrogate Contact Model in Force-Dependent Kinematic Simulations of Total Knee Replacement.
Marco A Marra, Michael S Andersen, Michael Damsgaard, Bart F J M Koopman, Dennis Janssen, Nico Verdonschot
Journal of biomechanical engineering
·
01 Aug 2017
·
pubmed:28462424
The whole-genome landscape of medulloblastoma subtypes.
Paul A Northcott, Ivo Buchhalter, A Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, ..., Roland Eils, Marco A Marra, Stefan M Pfister, Michael D Taylor, Peter Lichter
Nature
·
19 Jul 2017
·
pubmed:28726821
Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing
Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, ..., Yussanne Ma, Yongjun Zhao, Rob A. Holt, Steven J. Jones, Marco A. Marra
BMC Genomics
·
05 Jul 2017
·
doi:10.1186/s12864-017-3900-6
Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing.
Simon Haile, Richard D Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, ..., Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra
BMC genomics
·
05 Jul 2017
·
pubmed:28679365
The whole-genome landscape of medulloblastoma subtypes
Paul A. Northcott, Ivo Buchhalter, A. Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, ..., Roland Eils, Marco A. Marra, Stefan M. Pfister, Michael D. Taylor, Peter Lichter
Nature
·
01 Jul 2017
·
doi:10.1038/nature22973
Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
Katherine Tech, Andrey P. Tikunov, Hamza Farooq, A. Sorana Morrissy, Jessica Meidinger, ..., Marco A. Marra, Matthew G. Vander Heiden, Michael D. Taylor, Jeffrey M. Macdonald, Timothy R. Gershon
Cancer Research
·
14 Jun 2017
·
doi:10.1158/0008-5472.CAN-16-3304
Whole-genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia.
Ivan Sloma, Maria Teresa Mitjavila-Garcia, Olivier Feraud, Frank Griscelli, Noufissa Oudrhiri, ..., Martin Hirst, Marco A Marra, Connie J Eaves, Annelise Bennaceur-Griscelli, Ali G Turhan
Experimental hematology
·
08 Jun 2017
·
pubmed:28602946
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Eric Chuah, Amanda Clarke, ..., Daniel J. Weisenberger, Phillip H. Lai, Andrea Holbrook, Mario Berrios, Peter W. Laird
Cell
·
01 Jun 2017
·
doi:10.1016/j.cell.2017.05.046
Carcinoma Ex Pleomorphic Adenoma: Case Report and Options for Systemic Therapy
N. Chooback, Y. Shen, M. Jones, K. Kasaian, M. Martin, T. Ng, T. Thomson, M. Marra, J. Laskin, Cheryl Ho
Current Oncology
·
01 Jun 2017
·
doi:10.3747/co.24.3588
Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis
Simon Haile, Pawan Pandoh, Helen McDonald, Richard D. Corbett, Philip Tsao, ..., Yussanne Ma, Yongjun Zhao, Rob A. Holt, Steven J. Jones, Marco A. Marra
PLOS ONE
·
01 Jun 2017
·
doi:10.1371/journal.pone.0178706
Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles
Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, ..., Jean C. Zenklusen, Hailei Zhang, Jiashan (Julia) Zhang, Siyuan Zheng, Erik Zmuda
Cell Reports
·
01 Jun 2017
·
doi:10.1016/j.celrep.2017.06.008
Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis.
Simon Haile, Pawan Pandoh, Helen McDonald, Richard D Corbett, Philip Tsao, ..., Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra
PloS one
·
01 Jun 2017
·
pubmed:28570594
Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability
Farah R. Zahir, Jill C. Mwenifumbo, Hye-Jung E. Chun, Emilia L. Lim, Clara D. M. Van Karnebeek, ..., Sylvie L. Langlois, Barbara M. McGillivray, Steven J. M. Jones, Jan M. Friedman, Marco A. Marra
BMC Genomics
·
24 May 2017
·
doi:10.1186/s12864-017-3671-0
Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability.
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, ..., Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BMC genomics
·
24 May 2017
·
pubmed:28539120
Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin–specific clinical impact
Daisuke Ennishi, Anja Mottok, Susana Ben-Neriah, Hennady P. Shulha, Pedro Farinha, ..., Laurie H. Sehn, Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, David W. Scott
Blood
·
18 May 2017
·
doi:10.1182/blood-2016-11-747022
Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation.
Katherine Tech, Andrey P Tikunov, Hamza Farooq, A Sorana Morrissy, Jessica Meidinger, ..., Marco A Marra, Matthew G Vander Heiden, Michael D Taylor, Jeffrey M Macdonald, Timothy R Gershon
Cancer research
·
17 May 2017
·
pubmed:28515149
Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germlineCHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, ..., Malcolm Hayes, Janessa Laskin, Marco A. Marra, Kasmintan A. Schrader, Steven J. M. Jones
Molecular Case Studies
·
16 May 2017
·
doi:10.1101/mcs.a001628
Anterior referencing of tibial slope in total knee arthroplasty considerably influences knee kinematics: a musculoskeletal simulation study.
Marco A Marra, Marta Strzelczak, Petra J C Heesterbeek, Sebastiaan A W van de Groes, Dennis W Janssen, Bart F J M Koopman, Ate B Wymenga, Nico J J Verdonschot
Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA
·
12 May 2017
·
pubmed:28500391
Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC ) loss to activation of the MAPK signalling cascade
Veronique G LeBlanc, Marlo Firme, Jungeun Song, Susanna Y Chan, Min Hye Lee, Stephen Yip, Suganthi Chittaranjan, Marco A Marra
The Journal of Pathology
·
26 Apr 2017
·
doi:10.1002/path.4894
Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade.
Veronique G LeBlanc, Marlo Firme, Jungeun Song, Susanna Y Chan, Min Hye Lee, Stephen Yip, Suganthi Chittaranjan, Marco A Marra
The Journal of pathology
·
26 Apr 2017
·
pubmed:28295365
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes
Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, ..., Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
Nature Genetics
·
24 Apr 2017
·
doi:10.1038/ng.3849
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.
Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, ..., Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
Nature genetics
·
24 Apr 2017
·
pubmed:28436987
Spatial heterogeneity in medulloblastoma
A Sorana Morrissy, Florence M G Cavalli, Marc Remke, Vijay Ramaswamy, David J H Shih, ..., Sunit Das, David Malkin, Nada Jabado, Marco A Marra, Michael D Taylor
Nature Genetics
·
10 Apr 2017
·
doi:10.1038/ng.3838
Spatial heterogeneity in medulloblastoma.
A Sorana Morrissy, Florence M G Cavalli, Marc Remke, Vijay Ramaswamy, David J H Shih, ..., Sunit Das, David Malkin, Nada Jabado, Marco A Marra, Michael D Taylor
Nature genetics
·
10 Apr 2017
·
pubmed:28394352
Genetic profiling of
Daisuke Ennishi, Anja Mottok, Susana Ben-Neriah, Hennady P Shulha, Pedro Farinha, ..., Laurie H Sehn, Christian Steidl, Joseph M Connors, Randy D Gascoyne, David W Scott
Blood
·
28 Mar 2017
·
pubmed:28351934
The cost and cost trajectory of whole‐genome analysis guiding treatment of patients with advanced cancers
Deirdre Weymann, Janessa Laskin, Robyn Roscoe, Kasmintan A. Schrader, Stephen Chia, ..., Karen A. Gelmon, Aly Karsan, Daniel J. Renouf, Marco Marra, Dean A. Regier
Molecular Genetics & Genomic Medicine
·
12 Mar 2017
·
doi:10.1002/mgg3.281
Correction: miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer.
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, ..., Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
Oncotarget
·
07 Mar 2017
·
pubmed:28403581
Integrated Molecular Characterization of Uterine Carcinosarcoma
Andrew D. Cherniack, Hui Shen, Vonn Walter, Chip Stewart, Bradley A. Murray, ..., Hailei Zhang, Wei Zhang, Jing-chun Zhu, Erik Zmuda, Rosemary E. Zuna
Cancer Cell
·
01 Mar 2017
·
doi:10.1016/j.ccell.2017.02.010
Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma
Lauren Fishbein, Ignaty Leshchiner, Vonn Walter, Ludmila Danilova, A. Gordon Robertson, ..., Jiashan (Julia) Zhang, Wei Zhang, Jingchun Zhu, Franck Zinzindohoué, Erik Zmuda
Cancer Cell
·
01 Feb 2017
·
doi:10.1016/j.ccell.2017.01.001
Integrated genomic and molecular characterization of cervical cancer
[no author info]
Nature
·
23 Jan 2017
·
doi:10.1038/nature21386
Integrated genomic characterization of oesophageal carcinoma
[no author info]
Nature
·
01 Jan 2017
·
doi:10.1038/nature20805
2016
Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study
Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, ..., David W. Scott, Christian Steidl, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah
PLOS Medicine
·
13 Dec 2016
·
doi:10.1371/journal.pmed.1002197
Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.
Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, ..., David W Scott, Christian Steidl, Marco A Marra, Randy D Gascoyne, Sohrab P Shah
PLoS medicine
·
13 Dec 2016
·
pubmed:27959929
Sequencing Strategies to Guide Decision Making in Cancer Treatment
James T. Topham, Marco A. Marra
PLOS Medicine
·
06 Dec 2016
·
doi:10.1371/journal.pmed.1002189
Sequencing Strategies to Guide Decision Making in Cancer Treatment.
James T Topham, Marco A Marra
PLoS medicine
·
06 Dec 2016
·
pubmed:27923042
Personalized Oncogenomics in the Management of Gastrointestinal Carcinomas—Early Experiences from a Pilot Study
B.S. Sheffield, B. Tessier-Cloutier, H. Li-Chang, Y. Shen, E. Pleasance, ..., D.G. Huntsman, S. Yip, J. Laskin, M. Marra, D.F. Schaeffer
Current Oncology
·
01 Dec 2016
·
doi:10.3747/co.23.3165
A novel diffusion-tensor MRI approach for skeletal muscle fascicle length measurements.
Jos Oudeman, Valentina Mazzoli, Marco A Marra, Klaas Nicolay, Mario Maas, Nico Verdonschot, Andre M Sprengers, Aart J Nederveen, Gustav J Strijkers, Martijn Froeling
Physiological reports
·
01 Dec 2016
·
pubmed:28003562
Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.
Davide Pellacani, Misha Bilenky, Nagarajan Kannan, Alireza Heravi-Moussavi, David J H F Knapp, ..., Marco A Marra, Steven J M Jones, Samuel Aparicio, Martin Hirst, Connie J Eaves
Cell reports
·
15 Nov 2016
·
pubmed:27851968
Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
Ariadne H.A.G. Ooms, Samantha Gadd, Daniela S. Gerhard, Malcolm A. Smith, Jaime M. Guidry Auvil, ..., Marry M. van den Heuvel-Eibrink, Ronald R. de Krijger, Nicole Ross, Julie M. Gastier-Foster, Elizabeth J. Perlman
Clinical Cancer Research
·
14 Nov 2016
·
doi:10.1158/1078-0432.CCR-16-0985
Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia
Zhaohui Gu, Michelle Churchman, Kathryn Roberts, Yongjin Li, Yu Liu, ..., Elisabeth Paietta, Cheryl L. Willman, Mignon L. Loh, Stephen P. Hunger, Charles G. Mullighan
Nature Communications
·
08 Nov 2016
·
doi:10.1038/ncomms13331
Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour
Clara K. Chan, Yinghong Pan, Kendra Nyberg, Marco A. Marra, Emilia L. Lim, ..., Dianna Maar, Ewan A. Gibb, Preethi H. Gunaratne, A. Gordon Robertson, Amy C. Rowat
Open Biology
·
01 Nov 2016
·
doi:10.1098/rsob.160275
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
Hendrik G. Stunnenberg, Martin Hirst, Sergio Abrignani, David Adams, Melanie de Almeida, ..., Kevin Y. Yip, Stephen Yip, Jae-Il Yoo, Daniel Zerbino, Gideon Zipprich
Cell
·
01 Nov 2016
·
doi:10.1016/j.cell.2016.11.007
Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks
Davide Pellacani, Misha Bilenky, Nagarajan Kannan, Alireza Heravi-Moussavi, David J.H.F. Knapp, ..., Marco A. Marra, Steven J.M. Jones, Samuel Aparicio, Martin Hirst, Connie J. Eaves
Cell Reports
·
01 Nov 2016
·
doi:10.1016/j.celrep.2016.10.058
Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes.
Farah R Zahir, Tracy Tucker, Sonia Mayo, Carolyn J Brown, Emilia L Lim, Jonathan Taylor, Marco A Marra, Fadi F Hamdan, Jacques L Michaud, Jan M Friedman
American journal of medical genetics. Part A
·
01 Nov 2016
·
pubmed:27748065
Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour.
Clara K Chan, Yinghong Pan, Kendra Nyberg, Marco A Marra, Emilia L Lim, ..., Dianna Maar, Ewan A Gibb, Preethi H Gunaratne, A Gordon Robertson, Amy C Rowat
Open biology
·
01 Nov 2016
·
pubmed:27906134
Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes
Farah R. Zahir, Tracy Tucker, Sonia Mayo, Carolyn J. Brown, Emilia L. Lim, Jonathan Taylor, Marco A. Marra, Fadi F. Hamdan, Jacques L. Michaud, Jan M. Friedman
American Journal of Medical Genetics Part A
·
17 Oct 2016
·
doi:10.1002/ajmg.a.37669
Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group.
Ariadne H A G Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, ..., Marry M van den Heuvel-Eibrink, Ronald R de Krijger, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
Clinical cancer research : an official journal of the American Association for Cancer Research
·
04 Oct 2016
·
pubmed:27702824
A Time-and-Motion Approach to Micro-Costing of High-Throughput Genomic Assays
S. Costa, D.A. Regier, B. Meissner, I. Cromwell, S. Ben-Neriah, ..., C. Steidl, D.W. Scott, M.A. Marra, S.J. Peacock, J.M. Connors
Current Oncology
·
01 Oct 2016
·
doi:10.3747/co.23.2987
Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells.
Natalie Grinshtein, Constanza C Rioseco, Richard Marcellus, David Uehling, Ahmed Aman, ..., Steven J Jones, Marco A Marra, Rima Al-Awar, Donna L Senger, David R Kaplan
Oncotarget
·
13 Sep 2016
·
pubmed:27449082
Investigation of PD-L1 Biomarker Testing Methods for PD-1 Axis Inhibition in Non-squamous Non–small Cell Lung Cancer
Brandon S. Sheffield, Regan Fulton, Steve E. Kalloger, Katy Milne, Georgia Geller, ..., Stephen Yip, Brad H. Nelson, Allen M. Gown, Cheryl Ho, Diana N. Ionescu
Journal of Histochemistry & Cytochemistry
·
02 Sep 2016
·
doi:10.1369/0022155416665338
Investigation of PD-L1 Biomarker Testing Methods for PD-1 Axis Inhibition in Non-squamous Non-small Cell Lung Cancer.
Brandon S Sheffield, Regan Fulton, Steve E Kalloger, Katy Milne, Georgia Geller, ..., Stephen Yip, Brad H Nelson, Allen M Gown, Cheryl Ho, Diana N Ionescu
The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society
·
02 Sep 2016
·
pubmed:27591097
Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas
Lauren C. Chong, David D. W. Twa, Anja Mottok, Susana Ben-Neriah, Bruce W. Woolcock, ..., David W. Scott, Randy D. Gascoyne, Ryan D. Morin, Andrew J. Mungall, Christian Steidl
Blood
·
01 Sep 2016
·
doi:10.1182/blood-2015-11-683003
ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis
Maria Anna Zipeto, Angela C. Court, Anil Sadarangani, Nathaniel P. Delos Santos, Larisa Balaian, ..., Kelly A. Frazer, Marco A. Marra, Leslie A. Crews, Qingfei Jiang, Catriona H.M. Jamieson
Cell Stem Cell
·
01 Aug 2016
·
doi:10.1016/j.stem.2016.05.004
ETV6-NTRK3 Is Expressed in a Subset of ALK-Negative Inflammatory Myofibroblastic Tumors
Ali H. Alassiri, Rola H. Ali, Yaoqing Shen, Amy Lum, Caron Strahlendorf, ..., Janessa Laskin, Marco Marra, Stephen Yip, Cheng-Han Lee, Tony L. Ng
American Journal of Surgical Pathology
·
01 Aug 2016
·
doi:10.1097/pas.0000000000000677
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
Siyuan Zheng, Andrew D. Cherniack, Ninad Dewal, Richard A. Moffitt, Ludmila Danilova, ..., Sam Meier, Timothy Defreitas, Gary D. Hammer, Thomas J. Giordano, Roel G.W. Verhaak
Cancer Cell
·
01 Aug 2016
·
doi:10.1016/j.ccell.2016.07.013
Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells
Natalie Grinshtein, Constanza C. Rioseco, Richard Marcellus, David Uehling, Ahmed Aman, ..., Steven J. Jones, Marco A. Marra, Rima Al-Awar, Donna L. Senger, David R. Kaplan
Oncotarget
·
18 Jul 2016
·
doi:10.18632/oncotarget.10661
CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AML
Julia E. Maxson, Rhonda E. Ries, Yi-Cheng Wang, Robert B. Gerbing, E. Anders Kolb, ..., Malcolm A. Smith, Daniela S. Gerhard, Alan S. Gamis, Todd A. Alonzo, Soheil Meshinchi
Blood
·
16 Jun 2016
·
doi:10.1182/blood-2016-04-709899
DNA methylation in adult diffuse gliomas
Veronique G. LeBlanc, Marco A. Marra
Briefings in Functional Genomics
·
10 Jun 2016
·
doi:10.1093/bfgp/elw019
DNA methylation in adult diffuse gliomas.
Veronique G LeBlanc, Marco A Marra
Briefings in functional genomics
·
10 Jun 2016
·
pubmed:27288434
ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis.
Maria Anna Zipeto, Angela C Court, Anil Sadarangani, Nathaniel P Delos Santos, Larisa Balaian, ..., Kelly A Frazer, Marco A Marra, Leslie A Crews, Qingfei Jiang, Catriona H M Jamieson
Cell stem cell
·
09 Jun 2016
·
pubmed:27292188
Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas.
Lauren C Chong, David D W Twa, Anja Mottok, Susana Ben-Neriah, Bruce W Woolcock, ..., David W Scott, Randy D Gascoyne, Ryan D Morin, Andrew J Mungall, Christian Steidl
Blood
·
07 Jun 2016
·
pubmed:27268263
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, ..., C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
Nature Genetics
·
16 May 2016
·
doi:10.1038/ng.3573
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, ..., C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
Nature genetics
·
16 May 2016
·
pubmed:27182968
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
Sekyung Oh, Ryan A Flynn, Stephen N Floor, James Purzner, Lance Martin, ..., Jennifer A Doudna, Stefan M Pfister, Michael D Taylor, Howard Y Chang, Yoon-Jae Cho
Oncotarget
·
10 May 2016
·
pubmed:27058758
miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer.
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, ..., Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
Oncotarget
·
03 May 2016
·
pubmed:27036018
CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AML.
Julia E Maxson, Rhonda E Ries, Yi-Cheng Wang, Robert B Gerbing, E Anders Kolb, ..., Malcolm A Smith, Daniela S Gerhard, Alan S Gamis, Todd A Alonzo, Soheil Meshinchi
Blood
·
03 May 2016
·
pubmed:27143256
Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells
Julie S. Nielsen, Colin G. Sedgwick, Aniqa Shahid, Zusheng Zong, Zabrina L. Brumme, ..., Brian R. Berry, Marco A. Marra, Ryan D. Morin, Nicol Macpherson, Brad H. Nelson
Clinical Cancer Research
·
01 May 2016
·
doi:10.1158/1078-0432.ccr-15-2023
Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer
M.R. Jones, K.A. Schrader, Y. Shen, E. Pleasance, C. Ch'ng, ..., T. Ng, S.J.M. Jones, M.A. Marra, J. Laskin, H.J. Lim
Annals of Oncology
·
01 May 2016
·
doi:10.1093/annonc/mdw060
Immunohistochemistry for NF2, LATS1/2, and YAP/TAZ Fails to Separate Benign From Malignant Mesothelial Proliferations.
Brandon S Sheffield, Julie Lorette, Yaoqing Shen, Marco A Marra, Andrew Churg
Archives of pathology & laboratory medicine
·
01 May 2016
·
pubmed:27128293
A somatic reference standard for cancer genome sequencing
David W. Craig, Sara Nasser, Richard Corbett, Simon K. Chan, Lisa Murray, ..., Yussanne Ma, Steven J. M. Jones, Marco A. Marra, John D. Carpten, Winnie S. Liang
Scientific Reports
·
20 Apr 2016
·
doi:10.1038/srep24607
A somatic reference standard for cancer genome sequencing.
David W Craig, Sara Nasser, Richard Corbett, Simon K Chan, Lisa Murray, ..., Yussanne Ma, Steven J M Jones, Marco A Marra, John D Carpten, Winnie S Liang
Scientific reports
·
20 Apr 2016
·
pubmed:27094764
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress
Sekyung Oh, Ryan A. Flynn, Stephen N. Floor, James Purzner, Lance Martin, ..., Jennifer A. Doudna, Stefan M. Pfister, Michael D. Taylor, Howard Y. Chang, Yoon-Jae Cho
Oncotarget
·
05 Apr 2016
·
doi:10.18632/oncotarget.8612
Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche
Gabriel Pineda, Kathleen M. Lennon, Nathaniel P. Delos Santos, Florence Lambert-Fliszar, Gennarina L. Riso, ..., Marco A. Marra, Sheldon Morris, Asako Sakaue-Sawano, Atsushi Miyawaki, Catriona H. M. Jamieson
Scientific Reports
·
04 Apr 2016
·
doi:10.1038/srep23885
Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche.
Gabriel Pineda, Kathleen M Lennon, Nathaniel P Delos Santos, Florence Lambert-Fliszar, Gennarina L Riso, ..., Marco A Marra, Sheldon Morris, Asako Sakaue-Sawano, Atsushi Miyawaki, Catriona H M Jamieson
Scientific reports
·
04 Apr 2016
·
pubmed:27041210
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.
Hye-Jung E Chun, Emilia L Lim, Alireza Heravi-Moussavi, Saeed Saberi, Karen L Mungall, ..., Yussanne Ma, Steven J M Jones, Elizabeth J Perlman, Martin Hirst, Marco A Marra
Cancer cell
·
14 Mar 2016
·
pubmed:26977886
Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing
Jeremy D.K. Parker, Yaoqing Shen, Erin Pleasance, Yvonne Li, Jacqueline E. Schein, ..., Randy D. Gascoyne, Steven Jones, Marco Marra, Janessa Laskin, Aly Karsan
Molecular Case Studies
·
01 Mar 2016
·
doi:10.1101/mcs.a000679
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways
Hye-Jung E. Chun, Emilia L. Lim, Alireza Heravi-Moussavi, Saeed Saberi, Karen L. Mungall, ..., Yussanne Ma, Steven J.M. Jones, Elizabeth J. Perlman, Martin Hirst, Marco A. Marra
Cancer Cell
·
01 Mar 2016
·
doi:10.1016/j.ccell.2016.02.009
Putative BRAF activating fusion in a medullary thyroid cancer.
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
Cold Spring Harbor molecular case studies
·
01 Mar 2016
·
pubmed:27148585
MEF2 transcription factors: developmental regulators and emerging cancer genes.
Julia R Pon, Marco A Marra
Oncotarget
·
19 Jan 2016
·
pubmed:26506234
Clinical impact of molecular features in diffuse large B-cell lymphoma and follicular lymphoma
Julia R. Pon, Marco A. Marra
Blood
·
14 Jan 2016
·
doi:10.1182/blood-2015-07-658401
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma
[no author info]
New England Journal of Medicine
·
14 Jan 2016
·
doi:10.1056/NEJMoa1505917
Divergent clonal selection dominates medulloblastoma at recurrence.
A Sorana Morrissy, Livia Garzia, David J H Shih, Scott Zuyderduyn, Xi Huang, ..., Gary D Bader, Steven J M Jones, David Malkin, Marco A Marra, Michael D Taylor
Nature
·
13 Jan 2016
·
pubmed:26760213
Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma
Michele Ceccarelli, Floris P. Barthel, Tathiane M. Malta, Thais S. Sabedot, Sofie R. Salama, ..., Jean C. Zenklusen, Jianhua Zhang, Wei Zhang, Jiashan Zhang, Erik Zmuda
Cell
·
01 Jan 2016
·
doi:10.1016/j.cell.2015.12.028
Divergent clonal selection dominates medulloblastoma at recurrence
A. Sorana Morrissy, Livia Garzia, David J. H. Shih, Scott Zuyderduyn, Xi Huang, ..., Gary D. Bader, Steven J. M. Jones, David Malkin, Marco A. Marra, Michael D. Taylor
Nature
·
01 Jan 2016
·
doi:10.1038/nature16478
2015
Putative BRAF activating fusion in a medullary thyroid cancer
Katayoon Kasaian, Sam M. Wiseman, Blair A. Walker, Jacqueline E. Schein, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Molecular Case Studies
·
23 Dec 2015
·
doi:10.1101/mcs.a000729
The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy.
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Yongjun Zhao, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
BMC cancer
·
18 Dec 2015
·
pubmed:26680454
MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours
Elizabeth J. Perlman, Samantha Gadd, Stefan T. Arold, Anand Radhakrishnan, Daniela S. Gerhard, ..., David A. Wheeler, Oliver A. Hampton, Julie M. Gastier-Foster, Nicole Ross, Malcolm A. Smith
Nature Communications
·
04 Dec 2015
·
doi:10.1038/ncomms10013
MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours.
Elizabeth J Perlman, Samantha Gadd, Stefan T Arold, Anand Radhakrishnan, Daniela S Gerhard, ..., David A Wheeler, Oliver A Hampton, Julie M Gastier-Foster, Nicole Ross, Malcolm A Smith
Nature communications
·
04 Dec 2015
·
pubmed:26635203
Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells.
Julie S Nielsen, Colin G Sedgwick, Aniqa Shahid, Zusheng Zong, Zabrina L Brumme, ..., Brian R Berry, Marco A Marra, Ryan D Morin, Nicol Macpherson, Brad H Nelson
Clinical cancer research : an official journal of the American Association for Cancer Research
·
02 Dec 2015
·
pubmed:26631611
The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Katayoon Kasaian, Sam M. Wiseman, Blair A. Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven JM Jones
BMC Cancer
·
01 Dec 2015
·
doi:10.1186/s12885-015-1955-9
Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal
Frida Holm, Eva Hellqvist, Cayla N. Mason, Shawn A. Ali, Nathaniel Delos-Santos, ..., Marco A. Marra, Valeria Runza, Kelly A. Frazer, Anil Sadarangani, Catriona H. M. Jamieson
Proceedings of the National Academy of Sciences
·
30 Nov 2015
·
doi:10.1073/pnas.1506943112
Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal.
Frida Holm, Eva Hellqvist, Cayla N Mason, Shawn A Ali, Nathaniel Delos-Santos, ..., Marco A Marra, Valeria Runza, Kelly A Frazer, Anil Sadarangani, Catriona H M Jamieson
Proceedings of the National Academy of Sciences of the United States of America
·
30 Nov 2015
·
pubmed:26621726
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
W Marston Linehan, Paul T Spellman, Christopher J Ricketts, Chad J Creighton, Suzanne S Fei, ..., Kelinda Tucker, Paul M Weinberger, Cynthia Winemiller, Leigh Anne Zach, Rosemary Zuna
The New England journal of medicine
·
04 Nov 2015
·
pubmed:26536169
SOX9 modulates the expression of key transcription factors required for heart valve development.
Victoria C Garside, Rebecca Cullum, Olivia Alder, Daphne Y Lu, Ryan Vander Werff, ..., Yongjun Zhao, Steven J M Jones, Marco A Marra, T Michael Underhill, Pamela A Hoodless
Development (Cambridge, England)
·
02 Nov 2015
·
pubmed:26525672
The Molecular Taxonomy of Primary Prostate Cancer
Adam Abeshouse, Jaeil Ahn, Rehan Akbani, Adrian Ally, Samirkumar Amin, ..., Jiashan Zhang, Wei Zhang, Yi Zhong, Kelsey Zhu, Erik Zmuda
Cell
·
01 Nov 2015
·
doi:10.1016/j.cell.2015.10.025
Cell of origin of transformed follicular lymphoma
Robert Kridel, Anja Mottok, Pedro Farinha, Susana Ben-Neriah, Daisuke Ennishi, ..., Sohrab P. Shah, Christian Steidl, Joseph M. Connors, David W. Scott, Randy D. Gascoyne
Blood
·
29 Oct 2015
·
doi:10.1182/BLOOD-2015-06-649905
MEF2 transcription factors: developmental regulators and emerging cancer genes
Julia R. Pon, Marco A. Marra
Oncotarget
·
25 Oct 2015
·
doi:10.18632/oncotarget.6223
Clinical impact of molecular features in diffuse large B-cell lymphoma and follicular lymphoma.
Julia R Pon, Marco A Marra
Blood
·
07 Oct 2015
·
pubmed:26447189
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer
Giovanni Ciriello, Michael L. Gatza, Andrew H. Beck, Matthew D. Wilkerson, Suhn K. Rhie, ..., Travis I. Zack, Jean C. Zenklusen, Hailei Zhang, Jiashan Zhang, Erik Zmuda
Cell
·
01 Oct 2015
·
doi:10.1016/j.cell.2015.09.033
Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers.
Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch'ng, ..., Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, Marco A Marra
Cold Spring Harbor molecular case studies
·
01 Oct 2015
·
pubmed:27148575
Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers
Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch'ng, ..., Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, Marco A. Marra
Molecular Case Studies
·
24 Sep 2015
·
doi:10.1101/mcs.a000570
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?
Veronique G. LeBlanc, Marco A. Marra
Cancers
·
23 Sep 2015
·
doi:10.3390/cancers7030869
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?
Veronique G LeBlanc, Marco A Marra
Cancers
·
23 Sep 2015
·
pubmed:26404381
Integrative genomic analysis of ghost cell odontogenic carcinoma
Pinaki Bose, Erin D. Pleasance, Martin Jones, Yaoqing Shen, Carolyn Ch’ng, ..., Christopher W. Lee, Cheryl Ho, Janessa Laskin, Marco A. Marra, Steven J. Jones
Oral Oncology
·
01 Sep 2015
·
doi:10.1016/j.oraloncology.2015.06.013
Cell of origin of transformed follicular lymphoma.
Robert Kridel, Anja Mottok, Pedro Farinha, Susana Ben-Neriah, Daisuke Ennishi, ..., Sohrab P Shah, Christian Steidl, Joseph M Connors, David W Scott, Randy D Gascoyne
Blood
·
25 Aug 2015
·
pubmed:26307535
Large-scale profiling of microRNAs for The Cancer Genome Atlas
Andy Chu, Gordon Robertson, Denise Brooks, Andrew J. Mungall, Inanc Birol, Robin Coope, Yussanne Ma, Steven Jones, Marco A. Marra
Nucleic Acids Research
·
13 Aug 2015
·
doi:10.1093/nar/gkv808
Large-scale profiling of microRNAs for The Cancer Genome Atlas.
Andy Chu, Gordon Robertson, Denise Brooks, Andrew J Mungall, Inanc Birol, Robin Coope, Yussanne Ma, Steven Jones, Marco A Marra
Nucleic acids research
·
13 Aug 2015
·
pubmed:26271990
MEF2B mutations in non-Hodgkin lymphoma dysregulate cell migration by decreasing MEF2B target gene activation
Julia R. Pon, Jackson Wong, Saeed Saberi, Olivia Alder, Michelle Moksa, S. -W. Grace Cheng, Gregg B. Morin, Pamela A. Hoodless, Martin Hirst, Marco A. Marra
Nature Communications
·
06 Aug 2015
·
doi:10.1038/ncomms8953
MEF2B mutations in non-Hodgkin lymphoma dysregulate cell migration by decreasing MEF2B target gene activation.
Julia R Pon, Jackson Wong, Saeed Saberi, Olivia Alder, Michelle Moksa, S-W Grace Cheng, Gregg B Morin, Pamela A Hoodless, Martin Hirst, Marco A Marra
Nature communications
·
06 Aug 2015
·
pubmed:26245647
Comparative genomic and genetic analysis of glioblastoma-derived brain tumor-initiating cells and their parent tumors
Brad Davis, Yaoqing Shen, Candice C. Poon, H. Artee Luchman, Owen D. Stechishin, Carly S. Pontifex, Wei Wu, John J. Kelly, Michael D. Blough
Neuro-Oncology
·
05 Aug 2015
·
doi:10.1093/neuonc/nov143
Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development
Jean-François Schmouth, David Arenillas, Ximena Corso-Díaz, Yuan-Yun Xie, Slavita Bohacec, ..., Siaw H. Wong, Steven J. M. Jones, Marco A. Marra, Elizabeth M. Simpson, Wyeth W. Wasserman
BMC Genomics
·
24 Jul 2015
·
doi:10.1186/s12864-015-1770-3
Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.
Jean-François Schmouth, David Arenillas, Ximena Corso-Díaz, Yuan-Yun Xie, Slavita Bohacec, ..., Siaw H Wong, Steven J M Jones, Marco A Marra, Elizabeth M Simpson, Wyeth W Wasserman
BMC genomics
·
24 Jul 2015
·
pubmed:26204903
Integrative genomic analysis of ghost cell odontogenic carcinoma.
Pinaki Bose, Erin D Pleasance, Martin Jones, Yaoqing Shen, Carolyn Ch'ng, ..., Christopher W Lee, Cheryl Ho, Janessa Laskin, Marco A Marra, Steven J Jones
Oral oncology
·
11 Jul 2015
·
pubmed:26173781
Precursor States of Brain Tumor Initiating Cell Lines Are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes
Carlo Cusulin, Charles Chesnelong, Pinaki Bose, Misha Bilenky, Karen Kopciuk, ..., J. Gregory Cairncross, Steven J. Jones, Marco A. Marra, H. Artee Luchman, Samuel Weiss
Stem Cell Reports
·
01 Jul 2015
·
doi:10.1016/j.stemcr.2015.05.010
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas
[no author info]
New England Journal of Medicine
·
25 Jun 2015
·
doi:10.1056/NEJMoa1402121
Precursor States of Brain Tumor Initiating Cell Lines Are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes.
Carlo Cusulin, Charles Chesnelong, Pinaki Bose, Misha Bilenky, Karen Kopciuk, ..., J Gregory Cairncross, Steven J Jones, Marco A Marra, H Artee Luchman, Samuel Weiss
Stem cell reports
·
18 Jun 2015
·
pubmed:26095605
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
Daniel J Brat, Roel G W Verhaak, Kenneth D Aldape, W K Alfred Yung, Sofie R Salama, ..., Chip Stewart, Franklin Huang, Jonna L Grimsby, Amie J Radenbaugh, Jianan Zhang
The New England journal of medicine
·
10 Jun 2015
·
pubmed:26061751
Genomic Classification of Cutaneous Melanoma
Rehan Akbani, Kadir C. Akdemir, B. Arman Aksoy, Monique Albert, Adrian Ally, ..., Jingchun Zhu, Kelsey Zhu, Lisa Zimmer, Erik Zmuda, Lihua Zou
Cell
·
01 Jun 2015
·
doi:10.1016/j.cell.2015.05.044
The Drosophila TIPE family member Sigmar interacts with the Ste20-like kinase Misshapen and modulates JNK signaling, cytoskeletal remodeling and autophagy
Suganthi Chittaranjan, Jing Xu, Michael Kuzyk, Harpreet K. Dullat, James Wilton, Lindsay DeVorkin, Chandra Lebovitz, Gregg B. Morin, Marco A. Marra, Sharon M. Gorski
Biology Open
·
15 May 2015
·
doi:10.1242/bio.20148417
The Drosophila TIPE family member Sigmar interacts with the Ste20-like kinase Misshapen and modulates JNK signaling, cytoskeletal remodeling and autophagy.
Suganthi Chittaranjan, Jing Xu, Michael Kuzyk, Harpreet K Dullat, James Wilton, Lindsay DeVorkin, Chandra Lebovitz, Gregg B Morin, Marco A Marra, Sharon M Gorski
Biology open
·
02 Apr 2015
·
pubmed:25836674
MEN1 Mutations in Hürthle Cell (Oncocytic) Thyroid Carcinoma
Katayoon Kasaian, Ana-Maria Chindris, Sam M. Wiseman, Karen L. Mungall, Thomas Zeng, ..., Marco A. Marra, John A. Copland, E. Aubrey Thompson, Robert C. Smallridge, Steven J. M. Jones
The Journal of Clinical Endocrinology & Metabolism
·
01 Apr 2015
·
doi:10.1210/jc.2014-3622
Use of Affymetrix Arrays in the Diagnosis of Gene Copy-Number Variation.
Farah R Zahir, Marco A Marra
Current protocols in human genetics
·
01 Apr 2015
·
pubmed:25827348
Recurrent genomic rearrangements in primary testicular lymphoma
David DW Twa, Anja Mottok, Fong Chun Chan, Susana Ben‐Neriah, Bruce W Woolcock, ..., Ryan D Morin, Marco A Marra, David W Scott, Randy D Gascoyne, Christian Steidl
The Journal of Pathology
·
26 Mar 2015
·
doi:10.1002/path.4522
Recurrent genomic rearrangements in primary testicular lymphoma.
David D W Twa, Anja Mottok, Fong Chun Chan, Susana Ben-Neriah, Bruce W Woolcock, ..., Ryan D Morin, Marco A Marra, David W Scott, Randy D Gascoyne, Christian Steidl
The Journal of pathology
·
26 Mar 2015
·
pubmed:25712539
Personalized Oncogenomics: Clinical Experience with Malignant Peritoneal Mesothelioma Using Whole Genome Sequencing
Brandon S. Sheffield, Anna V. Tinker, Yaoqing Shen, Harry Hwang, Hector H. Li-Chang, ..., David F. Schaeffer, Andrew Churg, Stephen Yip, Janessa Laskin, Marco A. Marra
PLOS ONE
·
23 Mar 2015
·
doi:10.1371/journal.pone.0119689
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden
Michael S Anglesio, Ali Bashashati, Yi Kan Wang, Janine Senz, Gavin Ha, ..., Paul J Yong, Martin Hirst, Blake Gilks, Sohrab P Shah, David G Huntsman
The Journal of Pathology
·
23 Mar 2015
·
doi:10.1002/path.4516
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.
Michael S Anglesio, Ali Bashashati, Yi Kan Wang, Janine Senz, Gavin Ha, ..., Paul J Yong, Martin Hirst, Blake Gilks, Sohrab P Shah, David G Huntsman
The Journal of pathology
·
23 Mar 2015
·
pubmed:25692284
Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing.
Brandon S Sheffield, Anna V Tinker, Yaoqing Shen, Harry Hwang, Hector H Li-Chang, ..., David F Schaeffer, Andrew Churg, Stephen Yip, Janessa Laskin, Marco A Marra
PloS one
·
23 Mar 2015
·
pubmed:25798586
GLI2 inhibition abrogates human leukemia stem cell dormancy
Anil Sadarangani, Gabriel Pineda, Kathleen M Lennon, Hye-Jung Chun, Alice Shih, ..., Karen Messer, Hanna KA Mikkola, Marco A Marra, Thomas J Hudson, Catriona HM Jamieson
Journal of Translational Medicine
·
21 Mar 2015
·
doi:10.1186/s12967-015-0453-9
GLI2 inhibition abrogates human leukemia stem cell dormancy.
Anil Sadarangani, Gabriel Pineda, Kathleen M Lennon, Hye-Jung Chun, Alice Shih, ..., Karen Messer, Hanna K A Mikkola, Marco A Marra, Thomas J Hudson, Catriona H M Jamieson
Journal of translational medicine
·
21 Mar 2015
·
pubmed:25889765
Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, ..., Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis
Nature
·
19 Feb 2015
·
pubmed:25693563
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, ..., Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
Nature
·
18 Feb 2015
·
doi:10.1038/nature14248
Intermediate DNA methylation is a conserved signature of genome regulation
GiNell Elliott, Chibo Hong, Xiaoyun Xing, Xin Zhou, Daofeng Li, ..., Aleksandar Milosavljevic, Martin Hirst, Gary D. Stormo, Ting Wang, Joseph F. Costello
Nature Communications
·
18 Feb 2015
·
doi:10.1038/ncomms7363
Epigenetic and transcriptional determinants of the human breast
Philippe Gascard, Misha Bilenky, Mahvash Sigaroudinia, Jianxin Zhao, Luolan Li, ..., Steven J.M. Jones, Marco A. Marra, Thea D. Tlsty, Joseph F. Costello, Martin Hirst
Nature Communications
·
18 Feb 2015
·
doi:10.1038/ncomms7351
Epigenetic and transcriptional determinants of the human breast.
Philippe Gascard, Misha Bilenky, Mahvash Sigaroudinia, Jianxin Zhao, Luolan Li, ..., Steven J M Jones, Marco A Marra, Thea D Tlsty, Joseph F Costello, Martin Hirst
Nature communications
·
18 Feb 2015
·
pubmed:25690954
Intermediate DNA methylation is a conserved signature of genome regulation.
GiNell Elliott, Chibo Hong, Xiaoyun Xing, Xin Zhou, Daofeng Li, ..., Aleksandar Milosavljevic, Martin Hirst, Gary D Stormo, Ting Wang, Joseph F Costello
Nature communications
·
18 Feb 2015
·
pubmed:25691127
Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors.
Amy L Walz, Ariadne Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, ..., Oliver A Hampton, Nadereh Jafari, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
Cancer cell
·
09 Feb 2015
·
pubmed:25670082
An RCOR1 loss–associated gene expression signature identifies a prognostically significant DLBCL subgroup
Fong Chun Chan, Adele Telenius, Shannon Healy, Susana Ben-Neriah, Anja Mottok, ..., Joseph M. Connors, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah, Christian Steidl
Blood
·
05 Feb 2015
·
doi:10.1182/BLOOD-2013-06-507152
Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors
Amy L. Walz, Ariadne Ooms, Samantha Gadd, Daniela S. Gerhard, Malcolm A. Smith, ..., Oliver A. Hampton, Nadereh Jafari, Nicole Ross, Julie M. Gastier-Foster, Elizabeth J. Perlman
Cancer Cell
·
01 Feb 2015
·
doi:10.1016/J.CCELL.2015.01.003
Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.
Emilia L Lim, Diane L Trinh, David W Scott, Andy Chu, Martin Krzywinski, ..., Christian Steidl, Joseph M Connors, Ryan D Morin, Randy D Gascoyne, Marco A Marra
Genome biology
·
29 Jan 2015
·
pubmed:25723320
Comprehensive genomic characterization of head and neck squamous cell carcinomas
[no author info]
Nature
·
28 Jan 2015
·
doi:10.1038/NATURE14129
MEN1 mutations in Hürthle cell (oncocytic) thyroid carcinoma.
Katayoon Kasaian, Ana-Maria Chindris, Sam M Wiseman, Karen L Mungall, Thomas Zeng, ..., Marco A Marra, John A Copland, E Aubrey Thompson, Robert C Smallridge, Steven J M Jones
The Journal of clinical endocrinology and metabolism
·
27 Jan 2015
·
pubmed:25625803
A subject-specific musculoskeletal modeling framework to predict in vivo mechanics of total knee arthroplasty.
Marco A Marra, Valentine Vanheule, René Fluit, Bart H F J M Koopman, John Rasmussen, Nico Verdonschot, Michael S Andersen
Journal of biomechanical engineering
·
26 Jan 2015
·
pubmed:25429519
The Release 6 reference sequence of the Drosophila melanogaster genome
Roger A. Hoskins, Joseph W. Carlson, Kenneth H. Wan, Soo Park, Ivonne Mendez, ..., Alfredo Villasante, Igor F. Zhimulev, Gerald M. Rubin, Gary H. Karpen, Susan E. Celniker
Genome Research
·
14 Jan 2015
·
doi:10.1101/gr.185579.114
SOX9 modulates the expression of key transcription factors required for heart valve development
Victoria C. Garside, Rebecca Cullum, Olivia Alder, Daphne Y. Lu, Ryan Vander Werff, ..., Yongjun Zhao, Steven J. M. Jones, Marco A. Marra, T. Michael Underhill, Pamela A. Hoodless
Development
·
01 Jan 2015
·
doi:10.1242/dev.125252
Cross-cancer profiling of molecular alterations within the human autophagy interaction network.
Chandra B Lebovitz, A Gordon Robertson, Rodrigo Goya, Steven J Jones, Ryan D Morin, Marco A Marra, Sharon M Gorski
Autophagy
·
01 Jan 2015
·
pubmed:26208877
2014
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, ..., Carl Hansen, Marco A. Marra, Carlos Caldas, Sohrab P. Shah, Samuel Aparicio
Nature
·
26 Nov 2014
·
doi:10.1038/nature13952
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.
Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, ..., Carl Hansen, Marco A Marra, Carlos Caldas, Sohrab P Shah, Samuel Aparicio
Nature
·
26 Nov 2014
·
pubmed:25470049
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types
Rebecca F. Lowdon, Bo Zhang, Misha Bilenky, Thea Mauro, Daofeng Li, ..., Marco A. Marra, Martin Hirst, Joseph F. Costello, Ting Wang, Jeffrey B. Cheng
Nature Communications
·
25 Nov 2014
·
doi:10.1038/NCOMMS6442
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
Rebecca F Lowdon, Bo Zhang, Misha Bilenky, Thea Mauro, Daofeng Li, ..., Marco A Marra, Martin Hirst, Joseph F Costello, Ting Wang, Jeffrey B Cheng
Nature communications
·
25 Nov 2014
·
pubmed:25421844
An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.
Fong Chun Chan, Adele Telenius, Shannon Healy, Susana Ben-Neriah, Anja Mottok, ..., Joseph M Connors, Marco A Marra, Randy D Gascoyne, Sohrab P Shah, Christian Steidl
Blood
·
13 Nov 2014
·
pubmed:25395426
Driver and passenger mutations in cancer.
Julia R Pon, Marco A Marra
Annual review of pathology
·
17 Oct 2014
·
pubmed:25340638
Characterization of HPV and host genome interactions in primary head and neck cancers
Michael Parfenov, Chandra Sekhar Pedamallu, Nils Gehlenborg, Samuel S. Freeman, Ludmila Danilova, ..., Raja Seethala, Brandee T. Brown, Yan Guo, Michelle Pham, Wendell G. Yarbrough
Proceedings of the National Academy of Sciences
·
13 Oct 2014
·
doi:10.1073/PNAS.1416074111
Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation.
Olivia Alder, Rebecca Cullum, Sam Lee, Arohumam C Kan, Wei Wei, ..., Qian Chen, Duojia Pan, Steven J M Jones, Marco A Marra, Pamela A Hoodless
Cell reports
·
25 Sep 2014
·
pubmed:25263553
Mutations in CIC and IDH1 cooperatively regulate 2-hydroxyglutarate levels and cell clonogenicity.
Suganthi Chittaranjan, Susanna Chan, Cindy Yang, Kevin C Yang, Vincent Chen, ..., J Gregory Cairncross, Sharon M Gorski, Gregg B Morin, Stephen Yip, Marco A Marra
Oncotarget
·
15 Sep 2014
·
pubmed:25277207
The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
Caleb F. Davis, Christopher J. Ricketts, Min Wang, Lixing Yang, Andrew D. Cherniack, ..., Jean Claude Zenklusen, Carolyn M. Hutter, Mark S. Guyer, Bradley A. Ozenberger, Heidi J. Sofia
Cancer Cell
·
01 Sep 2014
·
doi:10.1016/J.CCR.2014.07.014
The molecular landscape of pediatric brain tumors in the next-generation sequencing era.
Marlo R Firme, Marco A Marra
Current neurology and neuroscience reports
·
01 Sep 2014
·
pubmed:25037717
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, ..., C. Blake Gilks, David G. Huntsman, Jessica N. McAlpine, Samuel Aparicio, Sohrab P. Shah
Genome Research
·
24 Jul 2014
·
doi:10.1101/GR.180281.114
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, ..., C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
Genome research
·
24 Jul 2014
·
pubmed:25060187
The Molecular Landscape of Pediatric Brain Tumors in the Next-Generation Sequencing Era
Marlo R. Firme, Marco A. Marra
Current Neurology and Neuroscience Reports
·
20 Jul 2014
·
doi:10.1007/S11910-014-0474-4
Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
Robert J. Vanner, Marc Remke, Marco Gallo, Hayden J. Selvadurai, Fiona Coutinho, ..., Gary Bader, Konrad Hochedlinger, Andrey Korshunov, Michael D. Taylor, Peter B. Dirks
Cancer Cell
·
01 Jul 2014
·
doi:10.1016/J.CCR.2014.05.005
A transgenic mouse model demonstrating the oncogenic role of mutations in the polycomb-group gene EZH2 in lymphomagenesis
Tobias Berg, Silvia Thoene, Damian Yap, Tracee Wee, Nathalie Schoeler, ..., Marco A. Marra, Gregg B. Morin, Randy D. Gascoyne, Samuel A. Aparicio, R. Keith Humphries
Blood
·
19 Jun 2014
·
doi:10.1182/BLOOD-2012-12-473439
Quiescent sox2(+) cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma.
Robert J Vanner, Marc Remke, Marco Gallo, Hayden J Selvadurai, Fiona Coutinho, ..., Gary Bader, Konrad Hochedlinger, Andrey Korshunov, Michael D Taylor, Peter B Dirks
Cancer cell
·
19 Jun 2014
·
pubmed:24954133
Diagnostic value of next-generation sequencing in an unusual sphenoid tumor.
Farzad Jamshidi, Erin Pleasance, Yvonne Li, Yaoqing Shen, Katayoon Kasaian, ..., Steven J M Jones, Marco A Marra, Torsten O Nielsen, Janessa Laskin, Stephen Yip
The oncologist
·
07 May 2014
·
pubmed:24807916
A transgenic mouse model demonstrating the oncogenic role of mutations in the polycomb-group gene EZH2 in lymphomagenesis.
Tobias Berg, Silvia Thoene, Damian Yap, Tracee Wee, Nathalie Schoeler, ..., Marco A Marra, Gregg B Morin, Randy D Gascoyne, Samuel A Aparicio, R Keith Humphries
Blood
·
06 May 2014
·
pubmed:24802772
Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, ..., Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
PLoS Genetics
·
17 Apr 2014
·
doi:10.1371/JOURNAL.PGEN.1004261
A Notch‐dependent transcriptional hierarchy promotes mesenchymal transdifferentiation in the cardiac cushion
Alex C.Y. Chang, Victoria C. Garside, Michele Fournier, Justin Smrz, Pavle Vrljicak, ..., Angela Tam, Steven J. M. Jones, Marco A. Marra, Pamela A. Hoodless, Aly Karsan
Developmental Dynamics
·
17 Apr 2014
·
doi:10.1002/DVDY.24127
A Notch-dependent transcriptional hierarchy promotes mesenchymal transdifferentiation in the cardiac cushion.
Alex C Y Chang, Victoria C Garside, Michele Fournier, Justin Smrz, Pavle Vrljicak, ..., Angela Tam, Steven J M Jones, Marco A Marra, Pamela A Hoodless, Aly Karsan
Developmental dynamics : an official publication of the American Association of Anatomists
·
17 Apr 2014
·
pubmed:24633789
Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4
Pilar Ramos, Anthony N Karnezis, David W Craig, Aleksandar Sekulic, Megan L Russell, ..., Stephen P Anthony, Richard B S Roden, Heather E Cunliffe, David G Huntsman, Jeffrey M Trent
Nature Genetics
·
23 Mar 2014
·
doi:10.1038/NG.2928
Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.
Pilar Ramos, Anthony N Karnezis, David W Craig, Aleksandar Sekulic, Megan L Russell, ..., Stephen P Anthony, Richard B S Roden, Heather E Cunliffe, David G Huntsman, Jeffrey M Trent
Nature genetics
·
23 Mar 2014
·
pubmed:24658001
The expression level of small non‐coding
RNA
s derived from the first exon of protein‐coding genes is predictive of cancer status
Athanasios Zovoilis, Andrew J Mungall, Richard Moore, Richard Varhol, Andy Chu, Tina Wong, Marco Marra, Steven JM Jones
EMBO reports
·
17 Feb 2014
·
doi:10.1002/EMBR.201337950
Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma
Jay Gunawardana, Fong Chun Chan, Adèle Telenius, Bruce Woolcock, Robert Kridel, ..., Kerry J Savage, Joseph M Connors, Sohrab P Shah, Randy D Gascoyne, Christian Steidl
Nature Genetics
·
16 Feb 2014
·
doi:10.1038/NG.2900
Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.
Jay Gunawardana, Fong Chun Chan, Adèle Telenius, Bruce Woolcock, Robert Kridel, ..., Kerry J Savage, Joseph M Connors, Sohrab P Shah, Randy D Gascoyne, Christian Steidl
Nature genetics
·
16 Feb 2014
·
pubmed:24531327
2013
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
Brett E Johnson, Tali Mazor, Chibo Hong, Michael Barnes, Koki Aihara, ..., Akitake Mukasa, Mitchel S Berger, Susan M Chang, Barry S Taylor, Joseph F Costello
Science (New York, N.Y.)
·
12 Dec 2013
·
pubmed:24336570
Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes
Tracy Tucker, Farah R Zahir, Malachi Griffith, Allen Delaney, David Chai, ..., Patrice Eydoux, Sylvie Langlois, Fadi F Hamdan, Jacques L Michaud, Jan M Friedman
European Journal of Human Genetics
·
20 Nov 2013
·
doi:10.1038/EJHG.2013.248
A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1 and BRCA2 Mutations
Ian E. Bosdet, T. Roderick Docking, Yaron S. Butterfield, Andrew J. Mungall, Thomas Zeng, ..., Richard A. Moore, Steven J. Jones, Marco A. Marra, Rob Holt, Aly Karsan
The Journal of Molecular Diagnostics
·
01 Nov 2013
·
doi:10.1016/J.JMOLDX.2013.07.004
Genomic testing to determine drug response: measuring preferences of the public and patients using Discrete Choice Experiment (DCE).
Mehdi Najafzadeh, Karissa M Johnston, Stuart J Peacock, Joseph M Connors, Marco A Marra, Larry D Lynd, Carlo A Marra
BMC health services research
·
31 Oct 2013
·
pubmed:24176050
A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.
Ian E Bosdet, T Roderick Docking, Yaron S Butterfield, Andrew J Mungall, Thomas Zeng, ..., Richard A Moore, Steven J Jones, Marco A Marra, Rob Holt, Aly Karsan
The Journal of molecular diagnostics : JMD
·
04 Oct 2013
·
pubmed:24094589
The Somatic Genomic Landscape of Glioblastoma
Cameron W. Brennan, Roel G.W. Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, ..., Narra S. Devi, Zhaobin Zhang, Darell Bigner, Eric Lipp, Roger McLendon
Cell
·
01 Oct 2013
·
doi:10.1016/J.CELL.2013.09.034
A Phosphoproteomics Approach to Identify Candidate Kinase Inhibitor Pathway Targets in Lymphoma-Like Primary Cell Lines
Miliana Vojvodic, Loen Hansford, Olena Morozova, Kim Blakely, Paul Taylor, ..., Jason Moffat, Marco Marra, Kristen Smith, Michael Moran, David Kaplan
Current Drug Discovery Technologies
·
01 Oct 2013
·
doi:10.2174/15701638113109990001
The Cancer Genome Atlas Pan-Cancer analysis project
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart
Nature Genetics
·
26 Sep 2013
·
doi:10.1038/NG.2764
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
Ali Bashashati, Gavin Ha, Alicia Tone, Jiarui Ding, Leah M Prentice, ..., Blake Gilks, Stephen Yip, David G Huntsman, Jessica N McAlpine, Sohrab P Shah
The Journal of pathology
·
01 Sep 2013
·
pubmed:23780408
Complete genomic landscape of a recurring sporadic parathyroid carcinoma.
Katayoon Kasaian, Sam M Wiseman, Nina Thiessen, Karen L Mungall, Richard D Corbett, ..., Yongjun Zhao, Martin Hirst, Marco A Marra, Blair A Walker, Steven J M Jones
The Journal of pathology
·
01 Jul 2013
·
pubmed:23616356
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.
Bo Zhang, Yan Zhou, Nan Lin, Rebecca F Lowdon, Chibo Hong, ..., Martin Hirst, Marco A Marra, Baoxue Zhang, Joseph F Costello, Ting Wang
Genome research
·
26 Jun 2013
·
pubmed:23804400
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
Michael Stevens, Jeffrey B Cheng, Daofeng Li, Mingchao Xie, Chibo Hong, ..., Keith L Ligon, Martin Hirst, Marco A Marra, Joseph F Costello, Ting Wang
Genome research
·
26 Jun 2013
·
pubmed:23804401
Complete genomic landscape of a recurring sporadic parathyroid carcinoma
Katayoon Kasaian, Sam M Wiseman, Nina Thiessen, Karen L Mungall, Richard D Corbett, ..., Yongjun Zhao, Martin Hirst, Marco A Marra, Blair A Walker, Steven JM Jones
The Journal of Pathology
·
07 Jun 2013
·
doi:10.1002/PATH.4203
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.
Mingchao Xie, Chibo Hong, Bo Zhang, Rebecca F Lowdon, Xiaoyun Xing, ..., Richard Moore, Martin Hirst, Marco A Marra, Joseph F Costello, Ting Wang
Nature genetics
·
26 May 2013
·
pubmed:23708189
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.
Ryan D Morin, Karen Mungall, Erin Pleasance, Andrew J Mungall, Rodrigo Goya, ..., Inanc Birol, Richard Moore, Joseph M Connors, Randy D Gascoyne, Marco A Marra
Blood
·
22 May 2013
·
pubmed:23699601
Analysis of FOXO1 mutations in diffuse large B-cell lymphoma
Diane L. Trinh, David W. Scott, Ryan D. Morin, Maria Mendez-Lago, Jianghong An, ..., Jacqueline Schein, Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra
Blood
·
02 May 2013
·
doi:10.1182/BLOOD-2013-01-479865
Cancer genome-sequencing study design.
Jill C Mwenifumbo, Marco A Marra
Nature reviews. Genetics
·
01 May 2013
·
pubmed:23594910
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
Timothy J Ley, Christopher Miller, Li Ding, Benjamin J Raphael, Andrew J Mungall, ..., Margi Sheth, Heidi J Sofia, Liming Yang, James R Downing, Greg Eley
The New England journal of medicine
·
01 May 2013
·
pubmed:23634996
Genome-wide microRNA and messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling.
Wei Wei, Juan Hou, Olivia Alder, Xin Ye, Sam Lee, ..., Darryl A Knight, Decheng Yang, Steven J M Jones, Marco A Marra, Pamela A Hoodless
Hepatology (Baltimore, Md.)
·
26 Apr 2013
·
pubmed:23315977
The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma
Barbara Meissner, Robert Kridel, Raymond S. Lim, Sanja Rogic, Kane Tse, ..., Andy J. Mungall, Marco A. Marra, Joseph M. Connors, Christian Steidl, Randy D. Gascoyne
Blood
·
18 Apr 2013
·
doi:10.1182/BLOOD-2013-01-478834
Cancer genome-sequencing study design
Jill C. Mwenifumbo, Marco A. Marra
Nature Reviews Genetics
·
18 Apr 2013
·
doi:10.1038/NRG3445
Analysis of FOXO1 mutations in diffuse large B-cell lymphoma.
Diane L Trinh, David W Scott, Ryan D Morin, Maria Mendez-Lago, Jianghong An, ..., Jacqueline Schein, Christian Steidl, Joseph M Connors, Randy D Gascoyne, Marco A Marra
Blood
·
04 Mar 2013
·
pubmed:23460611
A Pan-BCL2 Inhibitor Renders Bone-Marrow-Resident Human Leukemia Stem Cells Sensitive to Tyrosine Kinase Inhibition
Daniel J. Goff, Angela Court Recart, Anil Sadarangani, Hye-Jung Chun, Christian L. Barrett, ..., Marco Marra, Kelly A. Frazer, Maurizio Pellecchia, John C. Reed, Catriona H.M. Jamieson
Cell Stem Cell
·
01 Mar 2013
·
doi:10.1016/J.STEM.2012.12.011
A Cancer Stem Cell Model for Studying Brain Metastases From Primary Lung Cancer
Sara M. Nolte, Chitra Venugopal, Nicole McFarlane, Olena Morozova, Robin M. Hallett, ..., John P. Provias, Forough Farrokhyar, John A. Hassell, Marco Marra, Sheila K. Singh
JNCI: Journal of the National Cancer Institute
·
15 Feb 2013
·
doi:10.1093/JNCI/DJT022
The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma.
Barbara Meissner, Robert Kridel, Raymond S Lim, Sanja Rogic, Kane Tse, ..., Andy J Mungall, Marco A Marra, Joseph M Connors, Christian Steidl, Randy D Gascoyne
Blood
·
13 Feb 2013
·
pubmed:23407552
The genetic landscape of high-risk neuroblastoma
Trevor J Pugh, Olena Morozova, Edward F Attiyeh, Shahab Asgharzadeh, Jun S Wei, ..., Robert C Seeger, Javed Khan, Marco A Marra, Matthew Meyerson, John M Maris
Nature Genetics
·
20 Jan 2013
·
doi:10.1038/NG.2529
The genetic landscape of high-risk neuroblastoma.
Trevor J Pugh, Olena Morozova, Edward F Attiyeh, Shahab Asgharzadeh, Jun S Wei, ..., Robert C Seeger, Javed Khan, Marco A Marra, Matthew Meyerson, John M Maris
Nature genetics
·
20 Jan 2013
·
pubmed:23334666
Cell culture andDrosophilamodel systems define three classes of anaplastic lymphoma kinase mutations in neuroblastoma
Damini Chand, Yasuo Yamazaki, Kristina Ruuth, Christina Schönherr, Tommy Martinsson, ..., Miki Ohira, Akira Nakagawara, Per-Erik Sandström, Ruth H. Palmer, Bengt Hallberg
Disease Models & Mechanisms
·
01 Jan 2013
·
doi:10.1242/DMM.010348
2012
ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia
Qingfei Jiang, Leslie A. Crews, Christian L. Barrett, Hye-Jung Chun, Angela C. Court, ..., Sheldon R. Morris, Lawrence S. B. Goldstein, Marco A. Marra, Kelly A. Frazer, Catriona H. M. Jamieson
Proceedings of the National Academy of Sciences
·
28 Dec 2012
·
doi:10.1073/PNAS.1213021110
ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia.
Qingfei Jiang, Leslie A Crews, Christian L Barrett, Hye-Jung Chun, Angela C Court, ..., Sheldon R Morris, Lawrence S B Goldstein, Marco A Marra, Kelly A Frazer, Catriona H M Jamieson
Proceedings of the National Academy of Sciences of the United States of America
·
28 Dec 2012
·
pubmed:23275297
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma
Adrian M. Dubuc, Marc Remke, Andrey Korshunov, Paul A. Northcott, Shing H. Zhan, ..., Steven J. M. Jones, Charles G. Eberhart, Marco A. Marra, Stefan M. Pfister, Michael D. Taylor
Acta Neuropathologica
·
25 Nov 2012
·
doi:10.1007/S00401-012-1070-9
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma.
Adrian M Dubuc, Marc Remke, Andrey Korshunov, Paul A Northcott, Shing H Zhan, ..., Steven J M Jones, Charles G Eberhart, Marco A Marra, Stefan M Pfister, Michael D Taylor
Acta neuropathologica
·
25 Nov 2012
·
pubmed:23184418
Recurrent targets of aberrant somatic hypermutation in lymphoma
Alireza Hadj Khodabakhshi, Ryan D. Morin, Anthony P. Fejes, Andrew J. Mungall, Karen L. Mungall, ..., Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Inanc Birol, Steven J. M. Jones
Oncotarget
·
12 Nov 2012
·
doi:10.18632/ONCOTARGET.653
Recurrent targets of aberrant somatic hypermutation in lymphoma.
Alireza Hadj Khodabakhshi, Ryan D Morin, Anthony P Fejes, Andrew J Mungall, Karen L Mungall, ..., Joseph M Connors, Randy D Gascoyne, Marco A Marra, Inanc Birol, Steven J M Jones
Oncotarget
·
01 Nov 2012
·
pubmed:23131835
Cell culture and Drosophila model systems define three classes of anaplastic lymphoma kinase mutations in neuroblastoma.
Damini Chand, Yasuo Yamazaki, Kristina Ruuth, Christina Schönherr, Tommy Martinsson, ..., Miki Ohira, Akira Nakagawara, Per-Erik Sandström, Ruth H Palmer, Bengt Hallberg
Disease models & mechanisms
·
25 Oct 2012
·
pubmed:23104988
Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II.
S-W Grace Cheng, Michael A Kuzyk, Annie Moradian, Taka-Aki Ichu, Vicky C-D Chang, Jerry F Tien, Sarah E Vollett, Malachi Griffith, Marco A Marra, Gregg B Morin
Molecular and cellular biology
·
17 Sep 2012
·
pubmed:22988298
Comprehensive genomic characterization of squamous cell lung cancers
[no author info]
Nature
·
09 Sep 2012
·
doi:10.1038/NATURE11404
Poly‐gene fusion transcripts and chromothripsis in prostate cancer
Chunxiao Wu, Alexander W. Wyatt, Andrew McPherson, Dong Lin, Brian J. McConeghy, ..., Martin E. Gleave, Stanislav V. Volik, Yuzhuo Wang, S. Cenk Sahinalp, Colin C. Collins
Genes, Chromosomes and Cancer
·
25 Aug 2012
·
doi:10.1002/GCC.21999
Poly-gene fusion transcripts and chromothripsis in prostate cancer.
Chunxiao Wu, Alexander W Wyatt, Andrew McPherson, Dong Lin, Brian J McConeghy, ..., Martin E Gleave, Stanislav V Volik, Yuzhuo Wang, S Cenk Sahinalp, Colin C Collins
Genes, chromosomes & cancer
·
25 Aug 2012
·
pubmed:22927308
Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.
Anamaria Crisan, Rodrigo Goya, Gavin Ha, Jiarui Ding, Leah M Prentice, ..., Marco A Marra, David G Huntsman, Martin Hirst, Sam Aparicio, Sohrab Shah
PloS one
·
16 Aug 2012
·
pubmed:22916110
Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.
Kathryn G Roberts, Ryan D Morin, Jinghui Zhang, Martin Hirst, Yongjun Zhao, ..., Cheryl L Willman, Mignon Loh, Stephen P Hunger, Marco A Marra, Charles G Mullighan
Cancer cell
·
14 Aug 2012
·
pubmed:22897847
Subgroup-specific structural variation across 1,000 medulloblastoma genomes.
Paul A Northcott, David J H Shih, John Peacock, Livia Garzia, A Sorana Morrissy, ..., Steven J M Jones, Jan O Korbel, Stefan M Pfister, Marco A Marra, Michael D Taylor
Nature
·
02 Aug 2012
·
pubmed:22832581
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
Paul A. Northcott, David J. H. Shih, John Peacock, Livia Garzia, A. Sorana Morrissy, ..., Steven J. M. Jones, Jan O. Korbel, Stefan M. Pfister, Marco A. Marra, Michael D. Taylor
Nature
·
25 Jul 2012
·
doi:10.1038/NATURE11327
Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse.
Pavle Vrljicak, Rebecca Cullum, Eric Xu, Alex C Y Chang, Elizabeth D Wederell, Mikhail Bilenky, Steven J M Jones, Marco A Marra, Aly Karsan, Pamela A Hoodless
PloS one
·
16 Jul 2012
·
pubmed:22815831
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.
Anna V Lapuk, Chunxiao Wu, Alexander W Wyatt, Andrew McPherson, Brian J McConeghy, ..., Himisha Beltran, S Cenk Sahinalp, Martin E Gleave, Stanislav V Volik, Colin C Collins
The Journal of pathology
·
01 Jul 2012
·
pubmed:22553170
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.
Gavin Ha, Andrew Roth, Daniel Lai, Ali Bashashati, Jiarui Ding, ..., Martin Hirst, Carlos Caldas, Marco A Marra, Samuel Aparicio, Sohrab P Shah
Genome research
·
25 May 2012
·
pubmed:22637570
TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma
David W. Scott, Karen L. Mungall, Susana Ben-Neriah, Sanja Rogic, Ryan D. Morin, ..., Joseph M. Connors, Marco A. Marra, Andrew J. Mungall, Christian Steidl, Randy D. Gascoyne
Blood
·
24 May 2012
·
doi:10.1182/BLOOD-2012-02-414441
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Ken Chen, John W. Wallis, Cyriac Kandoth, Joelle M. Kalicki−Veizer, Karen L. Mungall, ..., Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, John N. Weinstein, Li Ding
Bioinformatics
·
04 May 2012
·
doi:10.1093/BIOINFORMATICS/BTS272
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
Ken Chen, John W Wallis, Cyriac Kandoth, Joelle M Kalicki-Veizer, Karen L Mungall, ..., Timothy J Ley, Elaine R Mardis, Richard K Wilson, John N Weinstein, Li Ding
Bioinformatics (Oxford, England)
·
04 May 2012
·
pubmed:22563071
Barriers to integrating personalized medicine into clinical practice: a best–worst scaling choice experiment
Mehdi Najafzadeh, Larry D. Lynd, Jennifer C. Davis, Stirling Bryan, Aslam Anis, Marco Marra, Carlo A. Marra
Genetics in Medicine
·
01 May 2012
·
doi:10.1038/GIM.2011.26
TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma.
David W Scott, Karen L Mungall, Susana Ben-Neriah, Sanja Rogic, Ryan D Morin, ..., Joseph M Connors, Marco A Marra, Andrew J Mungall, Christian Steidl, Randy D Gascoyne
Blood
·
11 Apr 2012
·
pubmed:22496164
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Sohrab P. Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, ..., David Huntsman, Martin Hirst, Carlos Caldas, Marco A. Marra, Samuel Aparicio
Nature
·
04 Apr 2012
·
doi:10.1038/NATURE10933
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
Sohrab P Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, ..., David Huntsman, Martin Hirst, Carlos Caldas, Marco A Marra, Samuel Aparicio
Nature
·
04 Apr 2012
·
pubmed:22495314
Allelic Ratios and the Mutational Landscape Reveal Biologically Significant Heterozygous SNVs
Jeffrey S-C Chu, Robert C Johnsen, Shu Yi Chua, Domena Tu, Mark Dennison, Marco Marra, Steven J M Jones, David L Baillie, Ann M Rose
Genetics
·
01 Apr 2012
·
doi:10.1534/GENETICS.111.137208
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.
Chunxiao Wu, Alexander W Wyatt, Anna V Lapuk, Andrew McPherson, Brian J McConeghy, ..., Arul M Chinnaiyan, S Cenk Sahinalp, Martin E Gleave, Stanislav V Volik, Colin C Collins
The Journal of pathology
·
21 Mar 2012
·
pubmed:22294438
Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression
Alireza Baradaran-Heravi, Kyoung Sang Cho, Bas Tolhuis, Mrinmoy Sanyal, Olena Morozova, ..., Marco A. Marra, Maarten van Lohuizen, David B. Lewis, Chad Shaw, Cornelius F. Boerkoel
Human Molecular Genetics
·
28 Feb 2012
·
doi:10.1093/HMG/DDS083
Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression.
Alireza Baradaran-Heravi, Kyoung Sang Cho, Bas Tolhuis, Mrinmoy Sanyal, Olena Morozova, ..., Marco A Marra, Maarten van Lohuizen, David B Lewis, Chad Shaw, Cornelius F Boerkoel
Human molecular genetics
·
28 Feb 2012
·
pubmed:22378147
Subgroup-specific alternative splicing in medulloblastoma
Adrian M. Dubuc, A. Sorana Morrissy, Nanne K. Kloosterhof, Paul A. Northcott, Emily P. Y. Yu, ..., William A. Weiss, Stephen W. Scherer, James T. Rutka, Pim J. French, Michael D. Taylor
Acta Neuropathologica
·
23 Feb 2012
·
doi:10.1007/S00401-012-0959-7
Subgroup-specific alternative splicing in medulloblastoma.
Adrian M Dubuc, A Sorana Morrissy, Nanne K Kloosterhof, Paul A Northcott, Emily Py Yu, ..., William A Weiss, Stephen W Scherer, James T Rutka, Pim J French, Michael D Taylor
Acta neuropathologica
·
23 Feb 2012
·
pubmed:22358458
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Andrew Roth, Jiarui Ding, Ryan Morin, Anamaria Crisan, Gavin Ha, ..., Gulisa Turashvili, Arusha Oloumi, Marco A Marra, Samuel Aparicio, Sohrab P Shah
Bioinformatics (Oxford, England)
·
27 Jan 2012
·
pubmed:22285562
Recurrent SomaticDICER1Mutations in Nonepithelial Ovarian Cancers
Alireza Heravi-Moussavi, Michael S. Anglesio, S.-W. Grace Cheng, Janine Senz, Winnie Yang, ..., Blake Gilks, Sohrab P. Shah, William D. Foulkes, Gregg B. Morin, David G. Huntsman
New England Journal of Medicine
·
19 Jan 2012
·
doi:10.1056/NEJMOA1102903
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma
Cheng-Han Lee, Wen-Bin Ou, Adrian Mariño-Enriquez, Meijun Zhu, Mark Mayeda, ..., David G. Huntsman, Paola Dal Cin, Maria Debiec-Rychter, Marisa R. Nucci, Jonathan A. Fletcher
Proceedings of the National Academy of Sciences
·
05 Jan 2012
·
doi:10.1073/PNAS.1115528109
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma.
Cheng-Han Lee, Wen-Bin Ou, Adrian Mariño-Enriquez, Meijun Zhu, Mark Mayeda, ..., David G Huntsman, Paola Dal Cin, Maria Debiec-Rychter, Marisa R Nucci, Jonathan A Fletcher
Proceedings of the National Academy of Sciences of the United States of America
·
05 Jan 2012
·
pubmed:22223660
2011
Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma.
Robert Kridel, Barbara Meissner, Sanja Rogic, Merrill Boyle, Adele Telenius, ..., Joseph M Connors, Marco A Marra, Andrew P Weng, Christian Steidl, Randy D Gascoyne
Blood
·
30 Dec 2011
·
pubmed:22210878
BCL2 mutations in diffuse large B-cell lymphoma
J M Schuetz, N A Johnson, R D Morin, D W Scott, K Tan, ..., G W Slack, M A Marra, J M Connors, A R Brooks-Wilson, R D Gascoyne
Leukemia
·
22 Dec 2011
·
doi:10.1038/LEU.2011.378
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.
Alireza Heravi-Moussavi, Michael S Anglesio, S-W Grace Cheng, Janine Senz, Winnie Yang, ..., Blake Gilks, Sohrab P Shah, William D Foulkes, Gregg B Morin, David G Huntsman
The New England journal of medicine
·
21 Dec 2011
·
pubmed:22187960
Mutations in EZH2 cause Weaver syndrome.
William T Gibson, Rebecca L Hood, Shing Hei Zhan, Dennis E Bulman, Anthony P Fejes, ..., Marco A Marra, David Chitayat, Kym M Boycott, David D Weaver, Steven J M Jones
American journal of human genetics
·
15 Dec 2011
·
pubmed:22177091
Hive plots--rational approach to visualizing networks.
Martin Krzywinski, Inanc Birol, Steven J M Jones, Marco A Marra
Briefings in bioinformatics
·
09 Dec 2011
·
pubmed:22155641
Next-generation sequencing of prostate tumors provides independent evidence of xenotropic murine leukemia virus-related gammaretrovirus contamination.
Fan Mo, Alexander W Wyatt, Chunxiao Wu, Anna V Lapuk, Marco A Marra, Martin E Gleave, Stanislav V Volik, Colin C Collins
Journal of clinical microbiology
·
07 Dec 2011
·
pubmed:22162557
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, ..., Martin Hirst, Marco A Marra, Anne Condon, Samuel Aparicio, Sohrab P Shah
Bioinformatics (Oxford, England)
·
13 Nov 2011
·
pubmed:22084253
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.
Stephen Yip, Yaron S Butterfield, Olena Morozova, Suganthi Chittaranjan, Michael D Blough, ..., Steven J M Jones, Gregg B Morin, Jennifer A Chan, J Gregory Cairncross, Marco A Marra
The Journal of pathology
·
10 Nov 2011
·
pubmed:22072542
Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples
Paul A. Northcott, David J. H. Shih, Marc Remke, Yoon-Jae Cho, Marcel Kool, ..., David Malkin, James T. Rutka, Andrey Korshunov, Stefan Pfister, Michael D. Taylor
Acta Neuropathologica
·
06 Nov 2011
·
doi:10.1007/S00401-011-0899-7
Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells
Florian Kuchenbauer, Sarah M. Mah, Michael Heuser, Andrew McPherson, Jens Rüschmann, ..., Marco A. Marra, Fernando D. Camargo, Lars Palmqvist, Christian Buske, R. Keith Humphries
Blood
·
22 Sep 2011
·
doi:10.1182/BLOOD-2010-10-312454
Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
Kasmintan A Schrader, Alireza Heravi-Moussavi, Paula J Waters, Janine Senz, James Whelan, ..., Martin Hirst, Sohrab P Shah, Marco A Marra, Jane Green, David G Huntsman
The Journal of pathology
·
01 Sep 2011
·
pubmed:21792934
Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance
Michael D. O’Connor, Elizabeth Wederell, Gordon Robertson, Allen Delaney, Olena Morozova, ..., Thomas Zeng, Martin Hirst, Marco A. Marra, Samuel A.J.R. Aparicio, Connie J. Eaves
Experimental Hematology
·
01 Aug 2011
·
doi:10.1016/J.EXPHEM.2011.05.008
High-throughput microfluidic single-cell RT-qPCR.
Adam K White, Michael VanInsberghe, Oleh I Petriv, Mani Hamidi, Darek Sikorski, Marco A Marra, James Piret, Samuel Aparicio, Carl L Hansen
Proceedings of the National Academy of Sciences of the United States of America
·
01 Aug 2011
·
pubmed:21808033
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.
Ryan D Morin, Maria Mendez-Lago, Andrew J Mungall, Rodrigo Goya, Karen L Mungall, ..., Steven J M Jones, Joseph M Connors, Martin Hirst, Randy D Gascoyne, Marco A Marra
Nature
·
27 Jul 2011
·
pubmed:21796119
Cell of Origin in AML: Susceptibility to MN1-Induced Transformation Is Regulated by the MEIS1/AbdB-like HOX Protein Complex
Michael Heuser, Haiyang Yun, Tobias Berg, Eric Yung, Bob Argiropoulos, ..., Connie Eaves, Michael L. Cleary, Marco Marra, Arnold Ganser, R. Keith Humphries
Cancer Cell
·
01 Jul 2011
·
doi:10.1016/J.CCR.2011.06.020
Extensive relationship between antisense transcription and alternative splicing in the human genome.
A Sorana Morrissy, Malachi Griffith, Marco A Marra
Genome research
·
30 Jun 2011
·
pubmed:21719572
Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells.
Florian Kuchenbauer, Sarah M Mah, Michael Heuser, Andrew McPherson, Jens Rüschmann, ..., Marco A Marra, Fernando D Camargo, Lars Palmqvist, Christian Buske, R Keith Humphries
Blood
·
31 May 2011
·
pubmed:21628414
Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance.
Michael D O'Connor, Elizabeth Wederell, Gordon Robertson, Allen Delaney, Olena Morozova, ..., Thomas Zeng, Martin Hirst, Marco A Marra, Samuel A J R Aparicio, Connie J Eaves
Experimental hematology
·
27 May 2011
·
pubmed:21689726
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, ..., Martin Hirst, Torsten O Nielsen, S Cenk Sahinalp, David Huntsman, Sohrab P Shah
PLoS computational biology
·
19 May 2011
·
pubmed:21625565
Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation
Tracy Tucker, Alexandre Montpetit, David Chai, Susanna Chan, Sébastien Chénier, ..., Hong Qian, Guy A Rouleau, David Vincent, Jacques L Michaud, Jan M Friedman
BMC Medical Genomics
·
25 Mar 2011
·
doi:10.1186/1755-8794-4-25
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.
Christian Steidl, Sohrab P Shah, Bruce W Woolcock, Lixin Rui, Masahiro Kawahara, ..., Douglas E Horsman, Louis M Staudt, Ulrich Steidl, Marco A Marra, Randy D Gascoyne
Nature
·
02 Mar 2011
·
pubmed:21368758
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation
Damian B. Yap, Justin Chu, Tobias Berg, Matthieu Schapira, S.-W. Grace Cheng, ..., Randy D. Gascoyne, R. Keith Humphries, Cheryl H. Arrowsmith, Gregg B. Morin, Samuel A. J. R. Aparicio
Blood
·
24 Feb 2011
·
doi:10.1182/BLOOD-2010-11-321208
Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes
Kimberly R. Blahnik, Lei Dou, Lorigail Echipare, Sushma Iyengar, Henriette O'Geen, ..., Marco A. Marra, Martin Hirst, Joseph F. Costello, Ian Korf, Peggy J. Farnham
PLoS ONE
·
15 Feb 2011
·
doi:10.1371/JOURNAL.PONE.0017121
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.
Kimberly R Blahnik, Lei Dou, Lorigail Echipare, Sushma Iyengar, Henriette O'Geen, ..., Marco A Marra, Martin Hirst, Joseph F Costello, Ian Korf, Peggy J Farnham
PloS one
·
15 Feb 2011
·
pubmed:21347206
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen.
Scott DiGuistini, Ye Wang, Nancy Y Liao, Greg Taylor, Philippe Tanguay, ..., Richard C Hamelin, Martin Hirst, Steven J M Jones, Jörg Bohlmann, Colette Breuil
Proceedings of the National Academy of Sciences of the United States of America
·
24 Jan 2011
·
pubmed:21262841
2010
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation.
Damian B Yap, Justin Chu, Tobias Berg, Matthieu Schapira, S-W Grace Cheng, ..., Randy D Gascoyne, R Keith Humphries, Cheryl H Arrowsmith, Gregg B Morin, Samuel A J R Aparicio
Blood
·
29 Dec 2010
·
pubmed:21190999
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.
Eugene Berezikov, Nicolas Robine, Anastasia Samsonova, Jakub O Westholm, Ammar Naqvi, ..., Gregory J Hannon, Marco A Marra, Zhiping Weng, Norbert Perrimon, Eric C Lai
Genome research
·
22 Dec 2010
·
pubmed:21177969
Hypomorphic temperature-sensitive alleles of NSDHL cause CK syndrome.
Keith W McLarren, Tesa M Severson, Christèle du Souich, David W Stockton, Lisa E Kratz, ..., Steven J M Jones, Robert D Steiner, F Lucy Raymond, Marco A Marra, Cornelius F Boerkoel
American journal of human genetics
·
10 Dec 2010
·
pubmed:21129721
BCL6 repression of EP300 in human diffuse large B cell lymphoma cells provides a basis for rational combinatorial therapy
Leandro C. Cerchietti, Katerina Hatzi, Eloisi Caldas-Lopes, Shao Ning Yang, Maria E. Figueroa, ..., Kapil Bhalla, Randy D. Gascoyne, Marco Marra, Gabriela Chiosis, Ari Melnick
Journal of Clinical Investigation
·
01 Dec 2010
·
doi:10.1172/JCI42869
Next generation sequencing based approaches to epigenomics.
Martin Hirst, Marco A Marra
Briefings in functional genomics
·
01 Dec 2010
·
pubmed:21266347
Acquired TNFRSF14 Mutations in Follicular Lymphoma Are Associated with Worse Prognosis
K-John J. Cheung, Nathalie A. Johnson, Joslynn G. Affleck, Tesa Severson, Christian Steidl, ..., Joseph M. Connors, Carolyn Brown, Marco A. Marra, Randy D. Gascoyne, Douglas E. Horsman
Cancer Research
·
14 Nov 2010
·
doi:10.1158/0008-5472.CAN-10-2460
Convergent genesis of an adult neural crest-like dermal stem cell from distinct developmental origins.
Hiroyuki Jinno, Olena Morozova, Karen L Jones, Jeffrey A Biernaskie, Maryline Paris, ..., Michael A Rudnicki, Yang Chai, Fabio Rossi, Marco A Marra, Freda D Miller
Stem cells (Dayton, Ohio)
·
01 Nov 2010
·
pubmed:20848654
ARID1AMutations in Endometriosis-Associated Ovarian Carcinomas
Kimberly C. Wiegand, Sohrab P. Shah, Osama M. Al-Agha, Yongjun Zhao, Kane Tse, ..., David D. Bowtell, Martin Hirst, Blake Gilks, Marco A. Marra, David G. Huntsman
New England Journal of Medicine
·
14 Oct 2010
·
doi:10.1056/NEJMOA1008433
De novo assembly and analysis of RNA-seq data
Gordon Robertson, Jacqueline Schein, Readman Chiu, Richard Corbett, Matthew Field, ..., Martin Hirst, Marco A Marra, Steven J M Jones, Pamela A Hoodless, Inanc Birol
Nature Methods
·
10 Oct 2010
·
doi:10.1038/NMETH.1517
De novo assembly and analysis of RNA-seq data.
Gordon Robertson, Jacqueline Schein, Readman Chiu, Richard Corbett, Matthew Field, ..., Martin Hirst, Marco A Marra, Steven J M Jones, Pamela A Hoodless, Inanc Birol
Nature methods
·
10 Oct 2010
·
pubmed:20935650
The NIH Roadmap Epigenomics Mapping Consortium
Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, ..., Peggy J Farnham, Martin Hirst, Eric S Lander, Tarjei S Mikkelsen, James A Thomson
Nature Biotechnology
·
01 Oct 2010
·
doi:10.1038/NBT1010-1045
ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner
Martin J. Law, Karen M. Lower, Hsiao P.J. Voon, Jim R. Hughes, David Garrick, ..., Jiannis Ragoussis, Daniela Rhodes, Ian Dunham, Douglas R. Higgs, Richard J. Gibbons
Cell
·
01 Oct 2010
·
doi:10.1016/J.CELL.2010.09.023
The NIH Roadmap Epigenomics Mapping Consortium.
Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, ..., Peggy J Farnham, Martin Hirst, Eric S Lander, Tarjei S Mikkelsen, James A Thomson
Nature biotechnology
·
01 Oct 2010
·
pubmed:20944595
Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis.
K-John J Cheung, Nathalie A Johnson, Joslynn G Affleck, Tesa Severson, Christian Steidl, ..., Joseph M Connors, Carolyn Brown, Marco A Marra, Randy D Gascoyne, Douglas E Horsman
Cancer research
·
30 Sep 2010
·
pubmed:20884631
LNCaP Atlas: gene expression associated with in vivo progression to castration-recurrent prostate cancer.
Tammy L Romanuik, Gang Wang, Olena Morozova, Allen Delaney, Marco A Marra, Marianne D Sadar
BMC medical genomics
·
24 Sep 2010
·
pubmed:20868494
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
R Alan Harris, Ting Wang, Cristian Coarfa, Raman P Nagarajan, Chibo Hong, ..., Alexander Meissner, Marco A Marra, Martin Hirst, Aleksandar Milosavljevic, Joseph F Costello
Nature Biotechnology
·
19 Sep 2010
·
doi:10.1038/NBT.1682
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
R Alan Harris, Ting Wang, Cristian Coarfa, Raman P Nagarajan, Chibo Hong, ..., Alexander Meissner, Marco A Marra, Martin Hirst, Aleksandar Milosavljevic, Joseph F Costello
Nature biotechnology
·
19 Sep 2010
·
pubmed:20852635
System-Level Analysis of Neuroblastoma Tumor–Initiating Cells Implicates AURKB as a Novel Drug Target for Neuroblastoma
Olena Morozova, Milijana Vojvodic, Natalie Grinshtein, Loen M. Hansford, Kim M. Blakely, ..., Jason Moffat, Thomas Kislinger, Michael F. Moran, David R. Kaplan, Marco A. Marra
Clinical Cancer Research
·
14 Sep 2010
·
doi:10.1158/1078-0432.CCR-10-0627
Alternative expression analysis by RNA sequencing
Malachi Griffith, Obi L Griffith, Jill Mwenifumbo, Rodrigo Goya, A Sorana Morrissy, ..., Martin Hirst, Gregg B Morin, Steven J M Jones, Isabella T Tai, Marco A Marra
Nature Methods
·
12 Sep 2010
·
doi:10.1038/NMETH.1503
Alternative expression analysis by RNA sequencing.
Malachi Griffith, Obi L Griffith, Jill Mwenifumbo, Rodrigo Goya, A Sorana Morrissy, ..., Martin Hirst, Gregg B Morin, Steven J M Jones, Isabella T Tai, Marco A Marra
Nature methods
·
12 Sep 2010
·
pubmed:20835245
ARID1A mutations in endometriosis-associated ovarian carcinomas.
Kimberly C Wiegand, Sohrab P Shah, Osama M Al-Agha, Yongjun Zhao, Kane Tse, ..., David D Bowtell, Martin Hirst, Blake Gilks, Marco A Marra, David G Huntsman
The New England journal of medicine
·
08 Sep 2010
·
pubmed:20942669
Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens.
Kristen M Smith, Alessandro Datti, Mayumi Fujitani, Natalie Grinshtein, Libo Zhang, ..., Jason Moffat, Marco A Marra, Sylvain Baruchel, Jeffrey L Wrana, David R Kaplan
EMBO molecular medicine
·
01 Sep 2010
·
pubmed:20721990
Selective targeting of neuroblastoma tumour‐initiating cells by compounds identified in stem cell‐based small molecule screens
Kristen M. Smith, Alessandro Datti, Mayumi Fujitani, Natalie Grinshtein, Libo Zhang, ..., Jason Moffat, Marco A. Marra, Sylvain Baruchel, Jeffrey L. Wrana, David R. Kaplan
EMBO Molecular Medicine
·
18 Aug 2010
·
doi:10.1002/EMMM.201000093
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.
Steven Jm Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, ..., David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra
Genome biology
·
09 Aug 2010
·
pubmed:20696054
High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes.
K-John J Cheung, Allen Delaney, Susana Ben-Neriah, Jacquie Schein, Tang Lee, ..., Merrill Boyle, Joseph M Connors, Randy D Gascoyne, Marco A Marra, Douglas E Horsman
Genes, chromosomes & cancer
·
01 Aug 2010
·
pubmed:20544841
System-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma.
Olena Morozova, Milijana Vojvodic, Natalie Grinshtein, Loen M Hansford, Kim M Blakely, ..., Jason Moffat, Thomas Kislinger, Michael F Moran, David R Kaplan, Marco A Marra
Clinical cancer research : an official journal of the American Association for Cancer Research
·
22 Jul 2010
·
pubmed:20651058
Conserved role of intragenic DNA methylation in regulating alternative promoters.
Alika K Maunakea, Raman P Nagarajan, Mikhail Bilenky, Tracy J Ballinger, Cletus D'Souza, ..., David Haussler, Marco A Marra, Martin Hirst, Ting Wang, Joseph F Costello
Nature
·
08 Jul 2010
·
pubmed:20613842
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.
Brad G Hoffman, Gordon Robertson, Bogard Zavaglia, Mike Beach, Rebecca Cullum, ..., C Bruce Verchere, Cheryl D Helgason, Marco A Marra, Steven J M Jones, Pamela A Hoodless
Genome research
·
15 Jun 2010
·
pubmed:20551221
Whole-genome profiling of mutagenesis in Caenorhabditis elegans.
Stephane Flibotte, Mark L Edgley, Iasha Chaudhry, Jon Taylor, Sarah E Neil, ..., Yaron Butterfield, Steven J Jones, Marco A Marra, Robert J Barstead, Donald G Moerman
Genetics
·
03 May 2010
·
pubmed:20439774
MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing.
Hyo Won Ahn, Ryan D Morin, Han Zhao, Ronald A Harris, Cristian Coarfa, Zi-Jiang Chen, Aleksandar Milosavljevic, Marco A Marra, Aleksandar Rajkovic
Molecular human reproduction
·
09 Mar 2010
·
pubmed:20215419
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors
Rodrigo Goya, Mark G.F. Sun, Ryan D. Morin, Gillian Leung, Gavin Ha, ..., Martin Hirst, David Huntsman, Kevin P. Murphy, Sam Aparicio, Sohrab P. Shah
Bioinformatics
·
03 Feb 2010
·
doi:10.1093/BIOINFORMATICS/BTQ040
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Rodrigo Goya, Mark G F Sun, Ryan D Morin, Gillian Leung, Gavin Ha, ..., Martin Hirst, David Huntsman, Kevin P Murphy, Sam Aparicio, Sohrab P Shah
Bioinformatics (Oxford, England)
·
03 Feb 2010
·
pubmed:20130035
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
Ryan D Morin, Nathalie A Johnson, Tesa M Severson, Andrew J Mungall, Jianghong An, ..., Steven Jones, Samuel Aparicio, Martin Hirst, Randy D Gascoyne, Marco A Marra
Nature Genetics
·
17 Jan 2010
·
doi:10.1038/NG.518
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.
Ryan D Morin, Nathalie A Johnson, Tesa M Severson, Andrew J Mungall, Jianghong An, ..., Steven Jones, Samuel Aparicio, Martin Hirst, Randy D Gascoyne, Marco A Marra
Nature genetics
·
17 Jan 2010
·
pubmed:20081860
2009
SKPs Derive from Hair Follicle Precursors and Exhibit Properties of Adult Dermal Stem Cells
Jeffrey Biernaskie, Maryline Paris, Olena Morozova, B. Matthew Fagan, Marco Marra, Larysa Pevny, Freda D. Miller
Cell Stem Cell
·
01 Dec 2009
·
doi:10.1016/J.STEM.2009.10.019
A first look at entire human methylomes
Joseph F Costello, Martin Krzywinski, Marco A Marra
Nature Biotechnology
·
01 Dec 2009
·
doi:10.1038/NBT1209-1130
Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal.
Pavle Vrljicak, Alex C Y Chang, Olena Morozova, Elizabeth D Wederell, Kyle Niessen, Marco A Marra, Aly Karsan, Pamela A Hoodless
Physiological genomics
·
01 Dec 2009
·
pubmed:19952280
A first look at entire human methylomes.
Joseph F Costello, Martin Krzywinski, Marco A Marra
Nature biotechnology
·
01 Dec 2009
·
pubmed:20010593
Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization.
Jm Friedman, Shelin Adam, Laura Arbour, Linlea Armstrong, Agnes Baross, ..., Margot I Van Allen, Siu-Li Yong, Farah R Zahir, Patrice Eydoux, Marco A Marra
BMC genomics
·
16 Nov 2009
·
pubmed:19917086
A characteristic syndrome associated with microduplication of 8q12, inclusive of CHD7
Anna M. Lehman, Jan M. Friedman, David Chai, Farah R. Zahir, Marco A. Marra, Larraine Prisman, Erica Tsang, Patrice Eydoux, Linlea Armstrong
European Journal of Medical Genetics
·
01 Nov 2009
·
doi:10.1016/J.EJMG.2009.09.006
Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries.
Tammy L Romanuik, Gang Wang, Robert A Holt, Steven J M Jones, Marco A Marra, Marianne D Sadar
BMC genomics
·
15 Oct 2009
·
pubmed:19832994
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
Sohrab P Shah, Ryan D Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, ..., Carlos Caldas, David Huntsman, Martin Hirst, Marco A Marra, Samuel Aparicio
Nature
·
08 Oct 2009
·
pubmed:19812674
The completion of the Mammalian Gene Collection (MGC)
Gary Temple, Daniela S. Gerhard, Rebekah Rasooly, Elise A. Feingold, Peter J. Good, ..., James Hartley, Vanessa E. Wall, Ralph F. Hopkins, Osamu Ohara, Stefan Wiemann
Genome Research
·
18 Sep 2009
·
doi:10.1101/GR.095976.109
The completion of the Mammalian Gene Collection (MGC).
Gary Temple, Daniela S Gerhard, Rebekah Rasooly, Elise A Feingold, Peter J Good, ..., James Hartley, Vanessa E Wall, Ralph F Hopkins, Osamu Ohara, Stefan Wiemann
Genome research
·
18 Sep 2009
·
pubmed:19767417
A characteristic syndrome associated with microduplication of 8q12, inclusive of CHD7.
Anna M Lehman, Jan M Friedman, David Chai, Farah R Zahir, Marco A Marra, Larraine Prisman, Erica Tsang, Patrice Eydoux, Linlea Armstrong
European journal of medical genetics
·
17 Sep 2009
·
pubmed:19772954
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, ..., Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones
Genome Biology
·
11 Sep 2009
·
doi:10.1186/GB-2009-10-9-R94
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.
Scott Diguistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, ..., Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven Jm Jones
Genome biology
·
11 Sep 2009
·
pubmed:19747388
Applications of New Sequencing Technologies for Transcriptome Analysis
Olena Morozova, Martin Hirst, Marco A. Marra
Annual Review of Genomics and Human Genetics
·
01 Sep 2009
·
doi:10.1146/ANNUREV-GENOM-082908-145957
Genetic variation in healthy oldest-old.
Julius Halaschek-Wiener, Mahsa Amirabbasi-Beik, Nasim Monfared, Markus Pieczyk, Christian Sailer, ..., Marco A Marra, Kenneth M Madden, Nhu D Le, Joseph M Connors, Angela R Brooks-Wilson
PloS one
·
14 Aug 2009
·
pubmed:19680556
Sequence Variant Discovery in DNA Repair Genes from Radiosensitive and Radiotolerant Prostate Brachytherapy Patients
Trevor J. Pugh, Mira Keyes, Lorena Barclay, Allen Delaney, Martin Krzywinski, ..., Michael McKenzie, W. Jim Morris, Peggy L. Olive, Marco A. Marra, Richard A. Moore
Clinical Cancer Research
·
29 Jul 2009
·
doi:10.1158/1078-0432.CCR-08-3357
Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients.
Trevor J Pugh, Mira Keyes, Lorena Barclay, Allen Delaney, Martin Krzywinski, ..., Michael McKenzie, W Jim Morris, Peggy L Olive, Marco A Marra, Richard A Moore
Clinical cancer research : an official journal of the American Association for Cancer Research
·
28 Jul 2009
·
pubmed:19638463
An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans
Barbara Meissner, Adam Warner, Kim Wong, Nicholas Dube, Adam Lorch, ..., David L. Baillie, Robert A. Holt, Steven J. M. Jones, Marco A. Marra, Donald G. Moerman
PLoS Genetics
·
26 Jun 2009
·
doi:10.1371/JOURNAL.PGEN.1000537
An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.
Barbara Meissner, Adam Warner, Kim Wong, Nicholas Dube, Adam Lorch, ..., David L Baillie, Robert A Holt, Steven J M Jones, Marco A Marra, Donald G Moerman
PLoS genetics
·
26 Jun 2009
·
pubmed:19557190
Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential
David G. Kent, Michael R. Copley, Claudia Benz, Stefan Wöhrer, Brad J. Dykstra, ..., Maura Gasparetto, Allen Delaney, Clayton Smith, Marco Marra, Connie J. Eaves
Blood
·
18 Jun 2009
·
doi:10.1182/BLOOD-2008-12-192054
Circos: An information aesthetic for comparative genomics
Martin Krzywinski, Jacqueline Schein, İnanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, Marco A. Marra
Genome Research
·
18 Jun 2009
·
doi:10.1101/GR.092759.109
Next-generation tag sequencing for cancer gene expression profiling.
A Sorana Morrissy, Ryan D Morin, Allen Delaney, Thomas Zeng, Helen McDonald, Steven Jones, Yongjun Zhao, Martin Hirst, Marco A Marra
Genome research
·
18 Jun 2009
·
pubmed:19541910
Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra
Genome research
·
18 Jun 2009
·
pubmed:19541911
De novo transcriptome assembly with ABySS
Inanç Birol, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, ..., Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones
Bioinformatics
·
15 Jun 2009
·
doi:10.1093/BIOINFORMATICS/BTP367
De novo transcriptome assembly with ABySS.
Inanç Birol, Shaun D Jackman, Cydney B Nielsen, Jenny Q Qian, Richard Varhol, ..., Doug E Horsman, Joseph M Connors, Randy D Gascoyne, Marco A Marra, Steven J M Jones
Bioinformatics (Oxford, England)
·
15 Jun 2009
·
pubmed:19528083
A novel de novo 1.1 Mb duplication of 17q21.33 associated with cognitive impairment and other anomalies.
Farah R Zahir, Sylvie Langlois, Kim Gall, Patrice Eydoux, Marco A Marra, Jan M Friedman
American journal of medical genetics. Part A
·
01 Jun 2009
·
pubmed:19449402
A novel de novo 1.1 Mb duplication of 17q21.33 associated with cognitive impairment and other anomalies
Farah R. Zahir, Sylvie Langlois, Kim Gall, Patrice Eydoux, Marco A. Marra, Jan M. Friedman
American Journal of Medical Genetics Part A
·
15 May 2009
·
doi:10.1002/AJMG.A.32827
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE.
Xin Wang, Yongjun Zhao, Kim Wong, Peter Ehlers, Yuji Kohara, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman, Dave Hansen
BMC genomics
·
09 May 2009
·
pubmed:19426519
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
Christine G. Elsik, Ross L. Tellam, Kim C. Worley, Richard A. Gibbs, Donna M. Muzny, ..., Stephen N. White, Laurens G. Wilming, Kris R. Wunderlich, Jianqi Yang, Feng-Qi Zhao
Science
·
24 Apr 2009
·
doi:10.1126/SCIENCE.1169588
The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Christine G Elsik, Ross L Tellam, Kim C Worley, Richard A Gibbs, Donna M Muzny, ..., Stephen N White, Laurens G Wilming, Kris R Wunderlich, Jianqi Yang, Feng-Qi Zhao
Science (New York, N.Y.)
·
24 Apr 2009
·
pubmed:19390049
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.
Ladeana W Hillier, Valerie Reinke, Philip Green, Martin Hirst, Marco A Marra, Robert H Waterston
Genome research
·
30 Jan 2009
·
pubmed:19181841
Applications of new sequencing technologies for transcriptome analysis.
Olena Morozova, Martin Hirst, Marco A Marra
Annual review of genomics and human genetics
·
01 Jan 2009
·
pubmed:19715439
2008
ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult.
James D McGhee, Tetsunari Fukushige, Michael W Krause, Stephanie E Minnema, Barbara Goszczynski, ..., Peter Ruzanov, Adam Warner, Richard Zapf, Donald G Moerman, John M Kalb
Developmental biology
·
09 Dec 2008
·
pubmed:19111532
Applications of next-generation sequencing technologies in functional genomics
Olena Morozova, Marco A. Marra
Genomics
·
01 Nov 2008
·
doi:10.1016/J.YGENO.2008.07.001
A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)
Steven G Ralph, Hye Jung E Chun, Natalia Kolosova, Dawn Cooper, Claire Oddy, ..., Steven JM Jones, Marco A Marra, Carl J Douglas, Kermit Ritland, Jörg Bohlmann
BMC Genomics
·
14 Oct 2008
·
doi:10.1186/1471-2164-9-484
A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis).
Steven G Ralph, Hye Jung E Chun, Natalia Kolosova, Dawn Cooper, Claire Oddy, ..., Steven J M Jones, Marco A Marra, Carl J Douglas, Kermit Ritland, Jörg Bohlmann
BMC genomics
·
14 Oct 2008
·
pubmed:18854048
In-depth characterization of the microRNA transcriptome in a leukemia progression model.
Florian Kuchenbauer, Ryan D Morin, Bob Argiropoulos, Oleh I Petriv, Malachi Griffith, ..., Thomas Zeng, Martin Hirst, Carl L Hansen, Marco A Marra, R Keith Humphries
Genome research
·
10 Oct 2008
·
pubmed:18849523
Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation.
Allen D Delaney, Hong Qian, Jan M Friedman, Marco A Marra
Current protocols in human genetics
·
01 Oct 2008
·
pubmed:18972373
Epigenetics and human disease.
Martin Hirst, Marco A Marra
The international journal of biochemistry & cell biology
·
24 Sep 2008
·
pubmed:18852064
A Seriation Approach for Visualization-Driven Discovery of Co-Expression Patterns in Serial Analysis of Gene Expression (SAGE) Data
Olena Morozova, Vyacheslav Morozov, Brad G. Hoffman, Cheryl D. Helgason, Marco A. Marra
PLoS ONE
·
12 Sep 2008
·
doi:10.1371/JOURNAL.PONE.0003205
A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data.
Olena Morozova, Vyacheslav Morozov, Brad G Hoffman, Cheryl D Helgason, Marco A Marra
PloS one
·
12 Sep 2008
·
pubmed:18787709
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.
A Gordon Robertson, Mikhail Bilenky, Angela Tam, Yongjun Zhao, Thomas Zeng, ..., Michael Snyder, Pamela A Hoodless, Martin Hirst, Marco A Marra, Steven J M Jones
Genome research
·
11 Sep 2008
·
pubmed:18787082
Applications of next-generation sequencing technologies in functional genomics.
Olena Morozova, Marco A Marra
Genomics
·
24 Aug 2008
·
pubmed:18703132
Identification of a set of genes showing regionally enriched expression in the mouse brain.
Cletus A D'Souza, Vikramjit Chopra, Richard Varhol, Yuan-Yun Xie, Slavita Bohacec, ..., Daniel Goldowitz, Marco A Marra, Robert A Holt, Elizabeth M Simpson, Steven J M Jones
BMC neuroscience
·
14 Jul 2008
·
pubmed:18625066
Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags
Heesun Shin, Martin Hirst, Matthew N Bainbridge, Vincent Magrini, Elaine Mardis, Donald G Moerman, Marco A Marra, David L Baillie, Steven JM Jones
BMC Biology
·
08 Jul 2008
·
doi:10.1186/1741-7007-6-30
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.
Heesun Shin, Martin Hirst, Matthew N Bainbridge, Vincent Magrini, Elaine Mardis, Donald G Moerman, Marco A Marra, David L Baillie, Steven J M Jones
BMC biology
·
08 Jul 2008
·
pubmed:18611272
Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.
Elizabeth D Wederell, Mikhail Bilenky, Rebecca Cullum, Nina Thiessen, Melis Dagpinar, ..., Martin Hirst, Gordon Robertson, Marco A Marra, Steven Jones, Pamela A Hoodless
Nucleic acids research
·
08 Jul 2008
·
pubmed:18611952
Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process
Afshin Raouf, Yun Zhao, Karen To, John Stingl, Allen Delaney, ..., Steven McKinney, Joanne Emerman, Samuel Aparicio, Marco Marra, Connie Eaves
Cell Stem Cell
·
01 Jul 2008
·
doi:10.1016/J.STEM.2008.05.018
Profiling the HeLa S3 Transcriptome using Randomly Primed cDNA and Massively Parallel Short-Read Sequencing
Ryan D. Morin, Matthew Bainbridge, Anthony Fejes, Martin Hirst, Martin Krzywinski, Trevor J. Pugh, Helen McDonald, Richard Varhol, Steven J.M. Jones, Marco A. Marra
BioTechniques
·
01 Jul 2008
·
doi:10.2144/000112900
Identification of transcripts with enriched expression in the developing and adult pancreas.
Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven J M Jones, Marco A Marra, Cheryl D Helgason
Genome biology
·
14 Jun 2008
·
pubmed:18554416
From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors.
Olena Morozova, Marco A Marra
Biochemistry and cell biology = Biochimie et biologie cellulaire
·
01 Apr 2008
·
pubmed:18443621
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
Ryan D. Morin, Michael D. O’Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, ..., Helen McDonald, Thomas Zeng, Martin Hirst, Connie J. Eaves, Marco A. Marra
Genome Research
·
19 Feb 2008
·
doi:10.1101/GR.7179508
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.
Ryan D Morin, Michael D O'Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, ..., Helen McDonald, Thomas Zeng, Martin Hirst, Connie J Eaves, Marco A Marra
Genome research
·
19 Feb 2008
·
pubmed:18285502
ALEXA: a microarray design platform for alternative expression analysis
Malachi Griffith, Michelle J Tang, Obi L Griffith, Ryan D Morin, Susanna Y Chan, ..., Martin Hirst, Steven J M Jones, Gregg B Morin, Isabella T Tai, Marco A Marra
Nature Methods
·
01 Feb 2008
·
doi:10.1038/NMETH0208-118
ALEXA: a microarray design platform for alternative expression analysis.
Malachi Griffith, Michelle J Tang, Obi L Griffith, Ryan D Morin, Susanna Y Chan, ..., Martin Hirst, Steven J M Jones, Gregg B Morin, Isabella T Tai, Marco A Marra
Nature methods
·
01 Feb 2008
·
pubmed:18235430
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding
Steven G Ralph, Hye Jung E Chun, Dawn Cooper, Robert Kirkpatrick, Natalia Kolosova, ..., Carl J Douglas, Robert A Holt, Steven JM Jones, Marco A Marra, Jörg Bohlmann
BMC Genomics
·
29 Jan 2008
·
doi:10.1186/1471-2164-9-57
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.
Steven G Ralph, Hye Jung E Chun, Dawn Cooper, Robert Kirkpatrick, Natalia Kolosova, ..., Carl J Douglas, Robert A Holt, Steven J M Jones, Marco A Marra, Jörg Bohlmann
BMC genomics
·
29 Jan 2008
·
pubmed:18230180
2007
A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1
F R Zahir, A Baross, A D Delaney, P Eydoux, N D Fernandes, T Pugh, M A Marra, J M Friedman
Journal of Medical Genetics
·
21 Dec 2007
·
doi:10.1136/JMG.2007.054437
A BAC clone fingerprinting approach to the detection of human genome rearrangements
Martin Krzywinski, Ian Bosdet, Carrie Mathewson, Natasja Wye, Jay Brebner, ..., Asim Siddiqui, Steven Jones, Jacquie Schein, Collin Collins, Marco Marra
Genome Biology
·
22 Oct 2007
·
doi:10.1186/GB-2007-8-10-R224
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data
Ágnes Baross, Allen D Delaney, H Irene Li, Tarun Nayar, Stephane Flibotte, ..., Giulia Kennedy, Sylvie Langlois, Patrice Eydoux, JM Friedman, Marco A Marra
BMC Bioinformatics
·
02 Oct 2007
·
doi:10.1186/1471-2105-8-368
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.
Agnes Baross, Allen D Delaney, H Irene Li, Tarun Nayar, Stephane Flibotte, ..., Giulia Kennedy, Sylvie Langlois, Patrice Eydoux, J M Friedman, Marco A Marra
BMC bioinformatics
·
02 Oct 2007
·
pubmed:17910767
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans.
Rebecca Hunt-Newbury, Ryan Viveiros, Robert Johnsen, Allan Mah, Dina Anastas, ..., Ralf Schnabel, Steven J Jones, Marco A Marra, David L Baillie, Donald G Moerman
PLoS biology
·
01 Sep 2007
·
pubmed:17850180
Identification and analysis of internal promoters in Caenorhabditis elegans operons.
Peiming Huang, Erin D Pleasance, Jason S Maydan, Rebecca Hunt-Newbury, Nigel J O'Neil, Allan Mah, David L Baillie, Marco A Marra, Donald G Moerman, Steven J M Jones
Genome research
·
21 Aug 2007
·
pubmed:17712020
A physical map of the bovine genome
Warren M Snelling, Readman Chiu, Jacqueline E Schein, Matthew Hobbs, Colette A Abbey, ..., John L Williams, James E Womack, Natasja H Wye, George Yang, Shaying Zhao
Genome Biology
·
14 Aug 2007
·
doi:10.1186/GB-2007-8-8-R165
A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)
Juan Hou, Anita M Charters, Sam C Lee, Yongjun Zhao, Mona K Wu, Steven JM Jones, Marco A Marra, Pamela A Hoodless
BMC Developmental Biology
·
02 Aug 2007
·
doi:10.1186/1471-213X-7-92
A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE).
Juan Hou, Anita M Charters, Sam C Lee, Yongjun Zhao, Mona K Wu, Steven J M Jones, Marco A Marra, Pamela A Hoodless
BMC developmental biology
·
02 Aug 2007
·
pubmed:17683524
Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.
Trevor J Pugh, Gwyn Bebb, Lorena Barclay, Margaret Sutcliffe, John Fee, ..., John English, Jeurgen Vielkind, Doug Horsman, Janessa J Laskin, Marco A Marra
BMC cancer
·
13 Jul 2007
·
pubmed:17626639
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron
John F. Etchberger, Adam Lorch, Monica C. Sleumer, Richard Zapf, Steven J. Jones, Marco A. Marra, Robert A. Holt, Donald G. Moerman, Oliver Hobert
Genes & Development
·
01 Jul 2007
·
doi:10.1101/GAD.1560107
A Modified Polymerase Chain Reaction‐Long Serial Analysis of Gene Expression Protocol Identifies Novel Transcripts in Human CD34
+
Bone Marrow Cells
Yun Zhao, Afshin Raouf, David Kent, Jaswinder Khattra, Allen Delaney, ..., Helen McDonald, Christina Chan, Steven Jones, Marco A. Marra, Connie J. Eaves
STEM CELLS
·
01 Jul 2007
·
doi:10.1634/STEMCELLS.2006-0794
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron.
John F Etchberger, Adam Lorch, Monica C Sleumer, Richard Zapf, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman, Oliver Hobert
Genes & development
·
01 Jul 2007
·
pubmed:17606643
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Elliott H. Margulies, Gregory M. Cooper, George Asimenos, Daryl J. Thomas, Colin N. Dewey, ..., David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow
Genome Research
·
01 Jun 2007
·
doi:10.1101/GR.6034307
Novel deletions of 14q11.2 associated with developmental delay, cognitive impairment and similar minor anomalies in three children.
Farah Zahir, Helen V Firth, Agnes Baross, Allen D Delaney, Patrice Eydoux, ..., Sylvie Langlois, Howard Martin, Lionel Willatt, Marco A Marra, Jan M Friedman
Journal of medical genetics
·
01 Jun 2007
·
pubmed:17545556
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Elliott H Margulies, Gregory M Cooper, George Asimenos, Daryl J Thomas, Colin N Dewey, ..., David Haussler, Webb Miller, Lior Pachter, Eric D Green, Arend Sidow
Genome research
·
01 Jun 2007
·
pubmed:17567995
A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation
Colin T. Kelleher, Readman Chiu, Heesun Shin, Ian E. Bosdet, Martin I. Krzywinski, ..., Jörg Bohlmann, Brian E. Ellis, Kermit Ritland, Carl J. Douglas, Jacqueline E. Schein
The Plant Journal
·
23 May 2007
·
doi:10.1111/J.1365-313X.2007.03112.X
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.
Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, ..., Chris P Ponting, Matthew Breen, Paul B Samollow, Eric S Lander, Kerstin Lindblad-Toh
Nature
·
10 May 2007
·
pubmed:17495919
A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.
Colin T Kelleher, Readman Chiu, Heesun Shin, Ian E Bosdet, Martin I Krzywinski, ..., Jörg Bohlmann, Brian E Ellis, Kermit Ritland, Carl J Douglas, Jacqueline E Schein
The Plant journal : for cell and molecular biology
·
03 May 2007
·
pubmed:17488239
Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults.
Peter Ruzanov, Donald L Riddle, Marco A Marra, Sheldon J McKay, Steven M Jones
Experimental gerontology
·
21 Apr 2007
·
pubmed:17543485
Evolutionary and biomedical insights from the rhesus macaque genome.
Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, ..., Donna Karolchik, Andy D Kern, Robert M Kuhn, Kayla E Smith, Ann S Zwieg
Science (New York, N.Y.)
·
13 Apr 2007
·
pubmed:17431167
A modified polymerase chain reaction-long serial analysis of gene expression protocol identifies novel transcripts in human CD34+ bone marrow cells.
Yun Zhao, Afshin Raouf, David Kent, Jaswinder Khattra, Allen Delaney, ..., Helen McDonald, Christina Chan, Steven Jones, Marco A Marra, Connie J Eaves
Stem cells (Dayton, Ohio)
·
05 Apr 2007
·
pubmed:17412892
Large-scale BAC clone restriction digest fingerprinting.
Carrie A Mathewson, Jacqueline E Schein, Marco A Marra
Current protocols in human genetics
·
01 Apr 2007
·
pubmed:18428413
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine
James D. McGhee, Monica C. Sleumer, Mikhail Bilenky, Kim Wong, Sheldon J. McKay, ..., Yuji Kohara, Marco A. Marra, Steven J.M. Jones, Donald G. Moerman, A. Gordon Robertson
Developmental Biology
·
01 Feb 2007
·
doi:10.1016/J.YDBIO.2006.10.024
Novel expressed sequences identified in a model of androgen independent prostate cancer.
Steven N Quayle, Heidi Hare, Allen D Delaney, Martin Hirst, Dorothy Hwang, Jacqueline E Schein, Steven J M Jones, Marco A Marra, Marianne D Sadar
BMC genomics
·
26 Jan 2007
·
pubmed:17257419
Osteopoikilosis, short stature and mental retardation as key features of a new microdeletion syndrome on 12q14.
Björn Menten, Karen Buysse, Farah Zahir, Jan Hellemans, Sara J Hamilton, ..., Barbara C McGillivray, Marco A Marra, Jan M Friedman, Frank Speleman, Geert Mortier
Journal of medical genetics
·
12 Jan 2007
·
pubmed:17220210
LongSAGE profiling of nine human embryonic stem cell lines.
Martin Hirst, Allen Delaney, Sean A Rogers, Angelique Schnerch, Deryck R Persaud, ..., Steven Jones, Daniela S Gerhard, James A Thomson, Connie J Eaves, Marco A Marra
Genome biology
·
01 Jan 2007
·
pubmed:17570852
A physical map of the bovine genome.
Warren M Snelling, Readman Chiu, Jacqueline E Schein, Matthew Hobbs, Colette A Abbey, ..., John L Williams, James E Womack, Natasja H Wye, George Yang, Shaying Zhao
Genome biology
·
01 Jan 2007
·
pubmed:17697342
2006
Identification of ciliary and ciliopathy genes in Caenorhabditis elegansthrough comparative genomics
Nansheng Chen, Allan Mah, Oliver E Blacque, Jeffrey Chu, Kiran Phgora, ..., Marco Marra, Donald G Moerman, Michel R Leroux, David L Baillie, Lincoln D Stein
Genome Biology
·
22 Dec 2006
·
doi:10.1186/GB-2006-7-12-R126
Identification of Novel Lung Genes in Bronchial Epithelium by Serial Analysis of Gene Expression
Kim M. Lonergan, Raj Chari, Ronald J. deLeeuw, Ashleen Shadeo, Bryan Chi, ..., Victor Ling, Raymond Ng, Calum MacAulay, Stephen Lam, Wan L. Lam
American Journal of Respiratory Cell and Molecular Biology
·
01 Dec 2006
·
doi:10.1165/RCMB.2006-0056OC
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
Jaswinder Khattra, Allen D Delaney, Yongjun Zhao, Asim Siddiqui, Jennifer Asano, ..., Steven Jones, Robert Holt, Martin Hirst, Pamela A Hoodless, Marco A Marra
Genome research
·
29 Nov 2006
·
pubmed:17135571
The Genome of the Sea Urchin
Strongylocentrotus purpuratus
Erica Sodergren, George M. Weinstock, Eric H Davidson, R. Andrew Cameron, Richard A. Gibbs, ..., Geoffrey Okwuonu, David Parker, Ling-Ling Pu, Rachel Thorn, Rita Wright
Science
·
10 Nov 2006
·
doi:10.1126/SCIENCE.1133609
The genome of the sea urchin Strongylocentrotus purpuratus.
Erica Sodergren, George M Weinstock, Eric H Davidson, R Andrew Cameron, Richard A Gibbs, ..., Geoffrey Okwuonu, David Parker, Ling-Ling Pu, Rachel Thorn, Rita Wright
Science (New York, N.Y.)
·
10 Nov 2006
·
pubmed:17095691
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine.
James D McGhee, Monica C Sleumer, Mikhail Bilenky, Kim Wong, Sheldon J McKay, ..., Yuji Kohara, Marco A Marra, Steven J M Jones, Donald G Moerman, A Gordon Robertson
Developmental biology
·
21 Oct 2006
·
pubmed:17113066
The complete genome of
Rhodococcus
sp. RHA1 provides insights into a catabolic powerhouse
Michael P. McLeod, René L. Warren, William W. L. Hsiao, Naoto Araki, Matthew Myhre, ..., Keisuke Miyauchi, Masao Fukuda, Julian E. Davies, William W. Mohn, Lindsay D. Eltis
Proceedings of the National Academy of Sciences
·
17 Oct 2006
·
doi:10.1073/PNAS.0607048103
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
Michael P McLeod, René L Warren, William W L Hsiao, Naoto Araki, Matthew Myhre, ..., Keisuke Miyauchi, Masao Fukuda, Julian E Davies, William W Mohn, Lindsay D Eltis
Proceedings of the National Academy of Sciences of the United States of America
·
09 Oct 2006
·
pubmed:17030794
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
Matthew N Bainbridge, René L Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, ..., Elaine R Mardis, Marianne D Sadar, Asim S Siddiqui, Marco A Marra, Steven JM Jones
BMC Genomics
·
29 Sep 2006
·
doi:10.1186/1471-2164-7-246
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.
Matthew N Bainbridge, René L Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, ..., Elaine R Mardis, Marianne D Sadar, Asim S Siddiqui, Marco A Marra, Steven J M Jones
BMC genomics
·
29 Sep 2006
·
pubmed:17010196
The Genome of Black Cottonwood,
Populus trichocarpa
(Torr. & Gray)
G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, ..., C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer, D. Rokhsar
Science
·
15 Sep 2006
·
doi:10.1126/SCIENCE.1128691
Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation
J.M. Friedman, Ágnes Baross, Allen D. Delaney, Adrian Ally, Laura Arbour, ..., Gary Wilson, Siu-Li Yong, Farah Zahir, Patrice Eydoux, Marco A. Marra
The American Journal of Human Genetics
·
01 Sep 2006
·
doi:10.1086/507471
Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals
Guus Bakkeren, Guoqiao Jiang, René L. Warren, Yaron Butterfield, Heesun Shin, ..., Yuhong Tang, Bruce A. Roe, Steven Jones, Marco Marra, James W. Kronstad
Fungal Genetics and Biology
·
01 Sep 2006
·
doi:10.1016/J.FGB.2006.04.002
Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome.
Steven G Ralph, Hesther Yueh, Michael Friedmann, Dana Aeschliman, Jeffrey A Zeznik, ..., Steven J M Jones, Marco A Marra, Carl J Douglas, Kermit Ritland, Jörg Bohlmann
Plant, cell & environment
·
01 Aug 2006
·
pubmed:16898017
Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.
J M Friedman, Agnes Baross, Allen D Delaney, Adrian Ally, Laura Arbour, ..., Gary Wilson, Siu-Li Yong, Farah Zahir, Patrice Eydoux, Marco A Marra
American journal of human genetics
·
25 Jul 2006
·
pubmed:16909388
Sequence biases in large scale gene expression profiling data
A. S. Siddiqui
Nucleic Acids Research
·
19 Jul 2006
·
doi:10.1093/NAR/GKL404
Sequence biases in large scale gene expression profiling data.
Asim S Siddiqui, Allen D Delaney, Angelique Schnerch, Obi L Griffith, Steven J M Jones, Marco A Marra
Nucleic acids research
·
13 Jul 2006
·
pubmed:16840527
Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells
G Wang, S J M Jones, M A Marra, M D Sadar
Oncogene
·
05 Jun 2006
·
doi:10.1038/SJ.ONC.1209715
Physical map-assisted whole-genome shotgun sequence assemblies
René L. Warren, Dmitry Varabei, Darren Platt, Xiaoqiu Huang, David Messina, ..., Jacqueline E. Schein, Asim S. Siddiqui, Marco A. Marra, Richard K. Wilson, Steven J.M. Jones
Genome Research
·
01 Jun 2006
·
doi:10.1101/GR.5090606
Physical map-assisted whole-genome shotgun sequence assemblies.
René L Warren, Dmitry Varabei, Darren Platt, Xiaoqiu Huang, David Messina, ..., Jacqueline E Schein, Asim S Siddiqui, Marco A Marra, Richard K Wilson, Steven J M Jones
Genome research
·
01 Jun 2006
·
pubmed:16741162
Sequencing and analysis of 10,967 full-length cDNA clones fromXenopus laevisandXenopus tropicalisreveals post-tetraploidization transcriptome remodeling
Ryan D. Morin, Elbert Chang, Anca Petrescu, Nancy Liao, Malachi Griffith, ..., Lukas Wagner, Daniela S. Gerhard, Marco A. Marra, Steven J.M. Jones, Robert A. Holt
Genome Research
·
03 May 2006
·
doi:10.1101/GR.4871006
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.
Ryan D Morin, Elbert Chang, Anca Petrescu, Nancy Liao, Malachi Griffith, ..., Lukas Wagner, Daniela S Gerhard, Marco A Marra, Steven J M Jones, Robert A Holt
Genome research
·
03 May 2006
·
pubmed:16672307
Genomics of hybrid poplar (Populus trichocarpa× deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full‐length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect‐induced defences in poplar
STEVEN RALPH, CLAIRE ODDY, DAWN COOPER, HESTHER YUEH, SHARON JANCSIK, ..., MARCO A. MARRA, BRIAN E. ELLIS, CARL J. DOUGLAS, KERMIT RITLAND, JÖRG BOHLMANN
Molecular Ecology
·
01 Apr 2006
·
doi:10.1111/J.1365-294X.2006.02824.X
Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar.
Steven Ralph, Claire Oddy, Dawn Cooper, Hesther Yueh, Sharon Jancsik, ..., Marco A Marra, Brian E Ellis, Carl J Douglas, Kermit Ritland, Jörg Bohlmann
Molecular ecology
·
01 Apr 2006
·
pubmed:16626454
2005
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla
Gary M. Wilson, Stephane Flibotte, Perseus I. Missirlis, Marco A. Marra, Steven Jones, Kevin Thornton, Andrew G. Clark, Robert A. Holt
Genome Research
·
19 Dec 2005
·
doi:10.1101/GR.4456006
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.
Gary M Wilson, Stephane Flibotte, Perseus I Missirlis, Marco A Marra, Steven Jones, Kevin Thornton, Andrew G Clark, Robert A Holt
Genome research
·
19 Dec 2005
·
pubmed:16365383
A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells
Asim S. Siddiqui, Jaswinder Khattra, Allen D. Delaney, Yongjun Zhao, Caroline Astell, ..., Steven J. M. Jones, Cheryl D. Helgason, Elizabeth M. Simpson, Pamela A. Hoodless, Marco A. Marra
Proceedings of the National Academy of Sciences
·
13 Dec 2005
·
doi:10.1073/PNAS.0509455102
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells.
Asim S Siddiqui, Jaswinder Khattra, Allen D Delaney, Yongjun Zhao, Caroline Astell, ..., Steven J M Jones, Cheryl D Helgason, Elizabeth M Simpson, Pamela A Hoodless, Marco A Marra
Proceedings of the National Academy of Sciences of the United States of America
·
13 Dec 2005
·
pubmed:16352711
A high-resolution whole-genome cattle–human comparative map reveals details of mammalian chromosome evolution
Annelie Everts-van der Wind, Denis M. Larkin, Cheryl A. Green, Janice S. Elliott, Colleen A. Olmstead, Readman Chiu, Jacqueline E. Schein, Marco A. Marra, James E. Womack, Harris A. Lewin
Proceedings of the National Academy of Sciences
·
09 Dec 2005
·
doi:10.1073/PNAS.0509285102
A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution.
Annelie Everts-van der Wind, Denis M Larkin, Cheryl A Green, Janice S Elliott, Colleen A Olmstead, Readman Chiu, Jacqueline E Schein, Marco A Marra, James E Womack, Harris A Lewin
Proceedings of the National Academy of Sciences of the United States of America
·
09 Dec 2005
·
pubmed:16339895
Serial Analysis of Gene Expression Reveals Conserved Links between Protein Kinase A, Ribosome Biogenesis, and Phosphate Metabolism in
Ustilago maydis
Luis M. Larraya, Kylie J. Boyce, Austin So, Barbara R. Steen, Steven Jones, Marco Marra, James W. Kronstad
Eukaryotic Cell
·
01 Dec 2005
·
doi:10.1128/EC.4.12.2029-2043.2005
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters
Nathalie Pavy, Charles Paule, Lee Parsons, John A Crow, Marie-Josee Morency, ..., Marco Marra, Armand Seguin, Ernest Retzel, Jean Bousquet, John MacKay
BMC Genomics
·
19 Oct 2005
·
doi:10.1186/1471-2164-6-144
A physical map of the genome of Atlantic salmon, Salmo salar
Siemon H.S. Ng, Carlo G. Artieri, Ian E. Bosdet, Readman Chiu, Roy G. Danzmann, ..., Asim Siddiqui, Jim Thorsen, Natasja Wye, George Yang, Baoli Zhu
Genomics
·
01 Oct 2005
·
doi:10.1016/J.YGENO.2005.06.001
A physical map of the genome of Atlantic salmon, Salmo salar.
Siemon H S Ng, Carlo G Artieri, Ian E Bosdet, Readman Chiu, Roy G Danzmann, ..., Asim Siddiqui, Jim Thorsen, Natasja Wye, George Yang, Baoli Zhu
Genomics
·
01 Oct 2005
·
pubmed:16026963
Simple, robust methods for high-throughput nanoliter-scale DNA sequencing
Duane E. Smailus, Andre Marziali, Philip Dextras, Marco A. Marra, Robert A. Holt
Genome Research
·
16 Sep 2005
·
doi:10.1101/GR.4221805
Simple, robust methods for high-throughput nanoliter-scale DNA sequencing.
Duane E Smailus, Andre Marziali, Philip Dextras, Marco A Marra, Robert A Holt
Genome research
·
16 Sep 2005
·
pubmed:16169928
The Genome of the Kinetoplastid Parasite,
Leishmania major
Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwal, ..., Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrell, Peter J. Myler
Science
·
15 Jul 2005
·
doi:10.1126/SCIENCE.1112680
Functional genomics of the cilium, a sensory organelle.
Oliver E Blacque, Elliot A Perens, Keith A Boroevich, Peter N Inglis, Chunmei Li, ..., Marco A Marra, David L Baillie, Donald G Moerman, Shai Shaham, Michel R Leroux
Current biology : CB
·
24 May 2005
·
pubmed:15916950
Management and Visualization of Whole Genome Shotgun Assemblies Using SAM
René L. Warren, Yaron S. Butterfield, Ryan D. Morin, Asim S. Siddiqui, Marco A. Marra, Steven J.M. Jones
BioTechniques
·
01 May 2005
·
doi:10.2144/05385ST01
Functional Genomics of the Cilium, a Sensory Organelle
Oliver E. Blacque, Elliot A. Perens, Keith A. Boroevich, Peter N. Inglis, Chunmei Li, ..., Marco A. Marra, David L. Baillie, Donald G. Moerman, Shai Shaham, Michel R. Leroux
Current Biology
·
01 May 2005
·
doi:10.1016/J.CUB.2005.04.059
Management and visualization of whole genome shotgun assemblies using SAM.
René L Warren, Yaron S Butterfield, Ryan D Morin, Asim S Siddiqui, Marco A Marra, Steven J M Jones
BioTechniques
·
01 May 2005
·
pubmed:15945370
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
Julius Halaschek-Wiener, Jaswinder S. Khattra, Sheldon McKay, Anatoli Pouzyrev, Jeff M. Stott, ..., Robert A. Holt, Steven J.M. Jones, Marco A. Marra, Angela R. Brooks-Wilson, Donald L. Riddle
Genome Research
·
18 Apr 2005
·
doi:10.1101/GR.3274805
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression.
Julius Halaschek-Wiener, Jaswinder S Khattra, Sheldon McKay, Anatoli Pouzyrev, Jeff M Stott, ..., Robert A Holt, Steven J M Jones, Marco A Marra, Angela R Brooks-Wilson, Donald L Riddle
Genome research
·
18 Apr 2005
·
pubmed:15837805
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Ladeana W Hillier, Tina A Graves, Robert S Fulton, Lucinda A Fulton, Kymberlie H Pepin, ..., Peer Bork, Mikita Suyama, David Torrents, Robert H Waterston, Richard K Wilson
Nature
·
07 Apr 2005
·
pubmed:15815621
Generation and annotation of the DNA sequences of human chromosomes 2 and 4
LaDeana W. Hillier, Tina A. Graves, Robert S. Fulton, Lucinda A. Fulton, Kymberlie H. Pepin, ..., Peer Bork, Mikita Suyama, David Torrents, Robert H. Waterston, Richard K. Wilson
Nature
·
01 Apr 2005
·
doi:10.1038/NATURE03466
Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans.
Tianshun Lian, Megan I Simmer, Cletus A D'Souza, Barbara R Steen, Scott D Zuyderduyn, Steven J M Jones, Marco A Marra, James W Kronstad
Molecular microbiology
·
01 Mar 2005
·
pubmed:15720553
The Genome of the Basidiomycetous Yeast and Human Pathogen
Cryptococcus neoformans
Brendan J. Loftus, Eula Fung, Paola Roncaglia, Don Rowley, Paolo Amedeo, ..., Jennifer K. Lodge, Joseph Heitman, Ronald W. Davis, Claire M. Fraser, Richard W. Hyman
Science
·
25 Feb 2005
·
doi:10.1126/SCIENCE.1103773
Iron‐regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans
Tianshun Lian, Megan I. Simmer, Cletus A. D’Souza, Barbara R. Steen, Scott D. Zuyderduyn, Steven J. M. Jones, Marco A. Marra, James W. Kronstad
Molecular Microbiology
·
04 Feb 2005
·
doi:10.1111/J.1365-2958.2004.04474.X
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
Brendan J Loftus, Eula Fung, Paola Roncaglia, Don Rowley, Paolo Amedeo, ..., Jennifer K Lodge, Joseph Heitman, Ronald W Davis, Claire M Fraser, Richard W Hyman
Science (New York, N.Y.)
·
13 Jan 2005
·
pubmed:15653466
High-throughput sequencing: a failure mode analysis
George S Yang, Jeffery M Stott, Duane Smailus, Sarah A Barber, Miruna Balasundaram, Marco A Marra, Robert A Holt
BMC Genomics
·
04 Jan 2005
·
doi:10.1186/1471-2164-6-2
High-throughput sequencing: a failure mode analysis.
George S Yang, Jeffery M Stott, Duane Smailus, Sarah A Barber, Miruna Balasundaram, Marco A Marra, Robert A Holt
BMC genomics
·
04 Jan 2005
·
pubmed:15631628
2004
Novel Avian Influenza H7N3 Strain Outbreak, British Columbia
Martin Hirst, Caroline R. Astell, Malachi Griffith, Shaun M. Coughlin, Michelle Moksa, ..., Sean K. Byrne, Yan Li, Darwyn Kobasa, Tim Booth, Mark Paetzel
Emerging Infectious Diseases
·
01 Dec 2004
·
doi:10.3201/EID1012.040743
Novel avian influenza H7N3 strain outbreak, British Columbia.
Martin Hirst, Caroline R Astell, Malachi Griffith, Shaun M Coughlin, Michelle Moksa, ..., Sean K Byrne, Yan Li, Darwyn Kobasa, Tim Booth, Mark Paetzel
Emerging infectious diseases
·
01 Dec 2004
·
pubmed:15663859
Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading
Rhodococcus
sp. Strain RHA1
René Warren, William W. L. Hsiao, Hisashi Kudo, Matt Myhre, Manisha Dosanjh, ..., William W. Mohn, Fiona S. L. Brinkman, Masao Fukuda, Julian Davies, Lindsay D. Eltis
Journal of Bacteriology
·
15 Nov 2004
·
doi:10.1128/JB.186.22.7783-7795.2004
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
René Warren, William W L Hsiao, Hisashi Kudo, Matt Myhre, Manisha Dosanjh, ..., William W Mohn, Fiona S L Brinkman, Masao Fukuda, Julian Davies, Lindsay D Eltis
Journal of bacteriology
·
01 Nov 2004
·
pubmed:15516593
The ENCODE (ENCyclopedia Of DNA Elements) Project
[no author info]
Science
·
22 Oct 2004
·
doi:10.1126/SCIENCE.1105136
The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)
[no author info]
Genome Research
·
15 Oct 2004
·
doi:10.1101/GR.2596504
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
Ágnes Baross, Yaron S.N. Butterfield, Shaun M. Coughlin, Thomas Zeng, Malachi Griffith, ..., Helen L. McDonald, Sheldon J. McKay, Michelle Moksa, Robert A. Holt, Marco A. Marra
Genome Research
·
15 Oct 2004
·
doi:10.1101/GR.2473704
Systematic recovery and analysis of full-ORF human cDNA clones.
Agnes Baross, Yaron S N Butterfield, Shaun M Coughlin, Thomas Zeng, Malachi Griffith, ..., Helen L McDonald, Sheldon J McKay, Michelle Moksa, Robert A Holt, Marco A Marra
Genome research
·
01 Oct 2004
·
pubmed:15489330
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
Daniela S Gerhard, Lukas Wagner, Elise A Feingold, Carolyn M Shenmen, Lynette H Grouse, ..., Marco A Marra, Sandra Clifton, Kathryn A Makowski, Stephanie Bosak, Joel Malek
Genome research
·
01 Oct 2004
·
pubmed:15489334
Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilms' tumor versus normal kidney
Michael S. Anglesio, Valentina Evdokimova, Nataliya Melnyk, Liyong Zhang, Conrad V. Fernandez, ..., Stephen Leach, Marco A. Marra, Angela R. Brooks-Wilson, Josef Penninger, Poul H.B. Sorensen
Human Molecular Genetics
·
14 Jul 2004
·
doi:10.1093/HMG/DDH215
Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilms' tumor versus normal kidney.
Michael S Anglesio, Valentina Evdokimova, Nataliya Melnyk, Liyong Zhang, Conrad V Fernandez, ..., Stephen Leach, Marco A Marra, Angela R Brooks-Wilson, Josef Penninger, Poul H B Sorensen
Human molecular genetics
·
14 Jul 2004
·
pubmed:15254018
A set of BAC clones spanning the human genome.
Martin Krzywinski, Ian Bosdet, Duane Smailus, Readman Chiu, Carrie Mathewson, ..., Shaying Zhao, Pieter J de Jong, Jacqueline Schein, Steven Jones, Marco A Marra
Nucleic acids research
·
09 Jul 2004
·
pubmed:15247347
A set of BAC clones spanning the human genome
M. Krzywinski
Nucleic Acids Research
·
07 Jul 2004
·
doi:10.1093/NAR/GKH700
Serial Analysis of Gene Expression Profiles of Developmental Stages in Non-small Cell Lung Carcinoma
Calum MacAulay, Kim Lonergan, Bryan Chi, Scott Zuyderduyn, Jaquie Shein, ..., Jean LeRiche, Steven Jones, Marco Marra, Stephen Lam, Wan L. Lam
Chest
·
01 May 2004
·
doi:10.1378/CHEST.125.5_SUPPL.97S
Delineation of a minimal region of deletion at 6q16.3 in follicular lymphoma and construction of a bacterial artificial chromosome contig spanning a 6-megabase region of 6q16-q21.
Laura-Jane Henderson, Ichiro Okamoto, Valia S Lestou, Olga Ludkovski, Marc Robichaud, ..., Richard J Klasa, Joseph M Connors, Marco A Marra, Douglas E Horsman, Wan L Lam
Genes, chromosomes & cancer
·
01 May 2004
·
pubmed:15034870
Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
Martin Krzywinski, John Wallis, Claudia Gösele, Ian Bosdet, Readman Chiu, ..., Richard Wilson, Norbert Hübner, Steven Jones, Marco Marra, Jacqueline Schein
Genome Research
·
01 Apr 2004
·
doi:10.1101/GR.2336604
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Richard A. Gibbs, George M. Weinstock, Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, ..., Mark Guyer, Adam Felsenfeld, Susan Old, Stephen Mockrin, Francis Collins
Nature
·
01 Apr 2004
·
doi:10.1038/NATURE02426
Effect of TERT and ATM on gene expression profiles in human fibroblasts.
Agnes Baross, Mike Schertzer, Scott D Zuyderduyn, Steven J M Jones, Marco A Marra, Peter M Lansdorp
Genes, chromosomes & cancer
·
01 Apr 2004
·
pubmed:14978791
Delineation of a minimal region of deletion at 6q16.3 in follicular lymphoma and construction of a bacterial artificial chromosome contig spanning a 6‐megabase region of 6q16–q21
Laura‐Jane Henderson, Ichiro Okamoto, Valia S. Lestou, Olga Ludkovski, Marc Robichaud, ..., Richard J. Klasa, Joseph M. Connors, Marco A. Marra, Douglas E. Horsman, Wan L. Lam
Genes, Chromosomes and Cancer
·
26 Feb 2004
·
doi:10.1002/GCC.20013
A tiling resolution DNA microarray with complete coverage of the human genome
Adrian S Ishkanian, Chad A Malloff, Spencer K Watson, Ronald J deLeeuw, Bryan Chi, ..., Daniel Pinkel, Marco A Marra, Victor Ling, Calum MacAulay, Wan L Lam
Nature Genetics
·
15 Feb 2004
·
doi:10.1038/NG1307
A tiling resolution DNA microarray with complete coverage of the human genome.
Adrian S Ishkanian, Chad A Malloff, Spencer K Watson, Ronald J DeLeeuw, Bryan Chi, ..., Daniel Pinkel, Marco A Marra, Victor Ling, Calum MacAulay, Wan L Lam
Nature genetics
·
15 Feb 2004
·
pubmed:14981516
Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
Matthew L. Rise, Kristian R. von Schalburg, Gordon D. Brown, Melanie A. Mawer, Robert H. Devlin, ..., Yaron S.N. Butterfield, Jeff M. Stott, Siemon H.S. Ng, William S. Davidson, Ben F. Koop
Genome Research
·
12 Feb 2004
·
doi:10.1101/GR.1687304
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.
Matthew L Rise, Kristian R von Schalburg, Gordon D Brown, Melanie A Mawer, Robert H Devlin, ..., Yaron S N Butterfield, Jeff M Stott, Siemon H S Ng, William S Davidson, Ben F Koop
Genome research
·
12 Feb 2004
·
pubmed:14962987
Automated ordering of fingerprinted clones
Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E. Schein, Heesun Shin, Marco A. Marra
Bioinformatics
·
10 Feb 2004
·
doi:10.1093/BIOINFORMATICS/BTH079
Automated ordering of fingerprinted clones.
Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E Schein, Heesun Shin, Marco A Marra
Bioinformatics (Oxford, England)
·
10 Feb 2004
·
pubmed:14871860
Effect of TERT and ATM on gene expression profiles in human fibroblasts
Ágnes Baross, Mike Schertzer, Scott D. Zuyderduyn, Steven J. M. Jones, Marco A. Marra, Peter M. Lansdorp
Genes, Chromosomes and Cancer
·
22 Jan 2004
·
doi:10.1002/GCC.20006
New Genomic Tools for Molecular Studies of Evolutionary Change in Threespine Sticklebacks
William Talbot, Yee Man Cha, Jeremy Schmutz, Brian Friedlander, Jane Grimwood, ..., Marco Marra, Dolph Schluter, Jacqueline Schein, Chris Amemiya, Pieter de Jong
Behaviour
·
01 Jan 2004
·
doi:10.1163/1568539042948150
2003
Cryptococcus neoformans
Gene Expression during Experimental Cryptococcal Meningitis
B. R. Steen, S. Zuyderduyn, D. L. Toffaletti, M. Marra, S. J. M. Jones, J. R. Perfect, J. Kronstad
Eukaryotic Cell
·
01 Dec 2003
·
doi:10.1128/EC.2.6.1336-1349.2003
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, ..., Chaochun Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston
PLoS Biology
·
17 Nov 2003
·
doi:10.1371/JOURNAL.PBIO.0000045
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, ..., C Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston
PLoS biology
·
17 Nov 2003
·
pubmed:14624247
Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes
Kathy Boon, Jennifer B Edwards, I-Mei Siu, Deric Olschner, Charles G Eberhart, Marco A Marra, Robert L Strausberg, Gregory J Riggins
Oncogene
·
23 Oct 2003
·
doi:10.1038/SJ.ONC.1207043
Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes.
Kathy Boon, Jennifer B Edwards, I-Mei Siu, Deric Olschner, Charles G Eberhart, Marco A Marra, Robert L Strausberg, Gregory J Riggins
Oncogene
·
23 Oct 2003
·
pubmed:14576832
The DNA sequence of human chromosome 7.
Ladeana W Hillier, Robert S Fulton, Lucinda A Fulton, Tina A Graves, Kymberlie H Pepin, ..., Maynard V Olson, Evan E Eichler, Eric D Green, Robert H Waterston, Richard K Wilson
Nature
·
10 Jul 2003
·
pubmed:12853948
The DNA sequence of human chromosome 7
LaDeana W. Hillier, Robert S. Fulton, Lucinda A. Fulton, Tina A. Graves, Kymberlie H. Pepin, ..., Maynard V. Olson, Evan E. Eichler, Eric D. Green, Robert H. Waterston, Richard K. Wilson
Nature
·
01 Jul 2003
·
doi:10.1038/NATURE01782
Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
Christopher D. Fjell, Ian Bosdet, Jacqueline E. Schein, Steven J.M. Jones, Marco A. Marra
Genome Research
·
01 Jun 2003
·
doi:10.1101/GR.819303
Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Christopher D Fjell, Ian Bosdet, Jacqueline E Schein, Steven J M Jones, Marco A Marra
Genome research
·
01 Jun 2003
·
pubmed:12799356
The Genome Sequence of the SARS-Associated Coronavirus
Marco A. Marra, Steven J. M. Jones, Caroline R. Astell, Robert A. Holt, Angela Brooks-Wilson, ..., Mel Krajden, Martin Petric, Danuta M. Skowronski, Chris Upton, Rachel L. Roper
Science
·
30 May 2003
·
doi:10.1126/SCIENCE.1085953
Assessment of SAGE in Transcript Identification
Erin D. Pleasance, Marco A. Marra, Steven J.M. Jones
Genome Research
·
12 May 2003
·
doi:10.1101/GR.873003
Assessment of SAGE in transcript identification.
Erin D Pleasance, Marco A Marra, Steven J M Jones
Genome research
·
12 May 2003
·
pubmed:12743019
Software for Automated Analysis of DNA Fingerprinting Gels
Daniel R. Fuhrmann, Martin I. Krzywinski, Readman Chiu, Parvaneh Saeedi, Jacqueline E. Schein, ..., LaDeana W. Hillier, Robert H. Waterston, John D. McPherson, Steven J.M. Jones, Marco A. Marra
Genome Research
·
01 May 2003
·
doi:10.1101/GR.904303
Software for automated analysis of DNA fingerprinting gels.
Daniel R Fuhrmann, Martin I Krzywinski, Readman Chiu, Parvaneh Saeedi, Jacqueline E Schein, ..., LaDeana W Hillier, Robert H Waterston, John D McPherson, Steven J M Jones, Marco A Marra
Genome research
·
01 May 2003
·
pubmed:12727910
The Genome sequence of the SARS-associated coronavirus.
Marco A Marra, Steven J M Jones, Caroline R Astell, Robert A Holt, Angela Brooks-Wilson, ..., Mel Krajden, Martin Petric, Danuta M Skowronski, Chris Upton, Rachel L Roper
Science (New York, N.Y.)
·
01 May 2003
·
pubmed:12730501
A SAGE approach to discovery of genes involved in autophagic cell death.
Sharon M Gorski, Suganthi Chittaranjan, Erin D Pleasance, J D Freeman, Carrie L Anderson, Richard J Varhol, Shaun M Coughlin, Scott D Zuyderduyn, Steven J M Jones, Marco A Marra
Current biology : CB
·
18 Feb 2003
·
pubmed:12593804
A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death
Sharon M. Gorski, Suganthi Chittaranjan, Erin D. Pleasance, J.D. Freeman, Carrie L. Anderson, Richard J. Varhol, Shaun M. Coughlin, Scott D. Zuyderduyn, Steven J.M. Jones, Marco A. Marra
Current Biology
·
01 Feb 2003
·
doi:10.1016/S0960-9822(03)00082-4
Gene Expression Profiling of Cells, Tissues, and Developmental Stages of the Nematode C. elegans
S.J. MCKAY, R. JOHNSEN, J. KHATTRA, J. ASANO, D.L. BAILLIE, ..., G. VATCHER, A. WARNER, K. WONG, Z. ZHAO, D.G. MOERMAN
Cold Spring Harbor Symposia on Quantitative Biology
·
01 Jan 2003
·
doi:10.1101/SQB.2003.68.159
A comparative map of bovine chromosome 19 based on a combination of mapping on a bacterial artificial chromosome scaffold map, a whole genome radiation hybrid panel and the human draft sequence
S.S. Moore, C. Hansen, J.L. Williams, A. Fu, Y. Meng, ..., B. Benkel, P.J. de Jong, K. Osoegawa, B.W. Kirkpatrick, C.A. Gill
Cytogenetic and Genome Research
·
01 Jan 2003
·
doi:10.1159/000075721
2002
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
Robert L Strausberg, Elise A Feingold, Lynette H Grouse, Jeffery G Derge, Richard D Klausner, ..., Duane E Smailus, Angelique Schnerch, Jacqueline E Schein, Steven J M Jones, Marco A Marra
Proceedings of the National Academy of Sciences of the United States of America
·
11 Dec 2002
·
pubmed:12477932
Temperature-Regulated Transcription in the Pathogenic Fungus Cryptococcus neoformans
Barbara R. Steen, Tian Lian, Scott Zuyderduyn, William Kim MacDonald, Marco Marra, Steven J.M. Jones, James W. Kronstad
Genome Research
·
01 Sep 2002
·
doi:10.1101/GR.80202
Resuspension of DNA Sequencing Reaction Products in Agarose Increases Sequence Quality on an Automated Sequencer
G. Vatcher, D. Smailus, M. Krzywinski, R. Guin, J. Stott, ..., R. Coope, A. Marziali, J. Schein, S. Jones, M. Marra
BioTechniques
·
01 Sep 2002
·
doi:10.2144/02333ST03_11824A
Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.
Jacqueline E Schein, Kristin L Tangen, Readman Chiu, Heesun Shin, Klaus B Lengeler, ..., Ian Bosdet, Joseph Heitman, Steven J M Jones, Marco A Marra, James W Kronstad
Genome research
·
01 Sep 2002
·
pubmed:12213782
Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans
Jacqueline E. Schein, Kristin L. Tangen, Readman Chiu, Heesun Shin, Klaus B. Lengeler, ..., Ian Bosdet, Joseph Heitman, Steven J.M. Jones, Marco A. Marra, James W. Kronstad
Genome Research
·
21 Aug 2002
·
doi:10.1101/GR.81002
A physical map of the mouse genome
Simon G. Gregory, Mandeep Sekhon, Jacqueline Schein, Shaying Zhao, Kazutoyo Osoegawa, ..., Pieter J. de Jong, Claire M. Fraser, Marco Marra, John D. McPherson, David R. Bentley
Nature
·
01 Aug 2002
·
doi:10.1038/NATURE00957
Systematic sequencing of cDNA clones using the transposon Tn5
Y. Shevchenko
Nucleic Acids Research
·
01 Jun 2002
·
doi:10.1093/NAR/30.11.2469
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones
Y. S. N. Butterfield
Nucleic Acids Research
·
01 Jun 2002
·
doi:10.1093/NAR/30.11.2460
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.
Yaron S N Butterfield, Marco A Marra, Jennifer K Asano, Susanna Y Chan, Ranabir Guin, ..., Miranda I Tsai, George S Yang, Scott D Zuyderduyn, Jacqueline E Schein, Steven J M Jones
Nucleic acids research
·
01 Jun 2002
·
pubmed:12034834
Systematic sequencing of cDNA clones using the transposon Tn5.
Yuriy Shevchenko, Gerard G Bouffard, Yaron S N Butterfield, Robert W Blakesley, James L Hartley, Alice C Young, Marco A Marra, Steven J M Jones, Jeffrey W Touchman, Eric D Green
Nucleic acids research
·
01 Jun 2002
·
pubmed:12034835
Programmed cell death takes flight: genetic and genomic approaches to gene discovery inDrosophila
S. Gorski, M. Marra
Physiological Genomics
·
10 May 2002
·
doi:10.1152/PHYSIOLGENOMICS.00114.2001
Transferrin receptor 2 (TfR2) and HFE mutational analysis in non-C282Y iron overload: identification of a novel TfR2 mutation
A. Mattman
Blood
·
17 Apr 2002
·
doi:10.1182/BLOOD-2002-01-0133
Assembly of fingerprint contigs: parallelized FPC
S. R. Ness, W. Terpstra, M. Krzywinski, M. A. Marra, S. J. M. Jones
Bioinformatics
·
01 Mar 2002
·
doi:10.1093/BIOINFORMATICS/18.3.484
2001
An SSLP marker–anchored BAC framework map of the mouse genome
Wei-Wen Cai, Chi-Wan Chow, Shamsha Damani, Simon G. Gregory, Marco Marra, Allan Bradley
Nature Genetics
·
01 Oct 2001
·
doi:10.1038/NG1001-133
An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library
Matthew D. Clark, Steffen Hennig, Ralf Herwig, Sandy W. Clifton, Marco A. Marra, Hans Lehrach, Stephen L. Johnson, the WU-GSC EST Group
Genome Research
·
16 Aug 2001
·
doi:10.1101/GR.186901
Changes in Gene Expression Associated with Developmental Arrest and Longevity in Caenorhabditis elegans
Steven J.M. Jones, Donald L. Riddle, Anatoli T. Pouzyrev, Victor E. Velculescu, LaDeana Hillier, Sean R. Eddy, Shawn L. Stricklin, David L. Baillie, Robert Waterston, Marco A. Marra
Genome Research
·
12 Jul 2001
·
doi:10.1101/GR.184401
A physical map of the human genome
John D. McPherson, Marco Marra, LaDeana Hillier, Robert H. Waterston, Asif Chinwalla, ..., Peter Seranski, Celine Hoff, Annemarie Poustka, Richard Reinhardt, Hans Lehrach
Nature
·
15 Feb 2001
·
doi:10.1038/35057157
Theories and Applications for Sequencing Randomly Selected Clones
M. C. Wendl
Genome Research
·
18 Jan 2001
·
doi:10.1101/GR.GR-1339R
2000
Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana
[no author info]
Nature
·
01 Dec 2000
·
doi:10.1038/35048507
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
[no author info]
Nature
·
01 Dec 2000
·
doi:10.1038/35048692
The complete sequence of a heterochromatic island from a higher eukaryote
[no author info]
Current Opinion in Plant Biology
·
01 Jan 2000
·
doi:10.1016/S1369-5266(00)80014-X
1999
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
K. Mayer, C. Schüller, R. Wambutt, G. Murphy, G. Volckaert, ..., A. Johnson, E. Chen, M. Marra, R. Martienssen, W. R. McCombie
Nature
·
01 Dec 1999
·
doi:10.1038/47134
A complete BAC-based physical map of the Arabidopsis thaliana genome
Teresa Mozo, Ken Dewar, Pat Dunn, Joseph R. Ecker, Sabine Fischer, ..., Hans Lehrach, Marco Marra, Robert Martienssen, Sebastian Meier-Ewert, Thomas Altmann
Nature Genetics
·
01 Jul 1999
·
doi:10.1038/10334
An encyclopedia of mouse genes
Marco Marra, LaDeana Hillier, Tamara Kucaba, Melissa Allen, Robert Barstead, ..., Karen Underwood, Todd Wylie, Tamara Yount, Richard Wilson, Robert Waterston
Nature Genetics
·
01 Feb 1999
·
doi:10.1038/5976
1997
Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution
S. Chissoe
Nucleic Acids Research
·
01 Aug 1997
·
doi:10.1093/NAR/25.15.2960
1994
Recovery of duplications by drug resistance selection in Caenorhabditis elegans
Marco A. Marra, D. L. Baillie
Genome
·
01 Aug 1994
·
doi:10.1139/G94-098
The Caenorhabditis elegans unc-60 gene encodes proteins homologous to a family of actin-binding proteins
Kim S. McKim, Camela Matheson, Marco A. Marra, Marcia F. Wakarchuk, David L. Baillie
Molecular and General Genetics MGG
·
01 Feb 1994
·
doi:10.1007/BF00280425
1993
The use of deficiencies to determine essential gene content in the let-56–unc-22 region of Caenorhabditis elegans
Jacquie E. Schein, Marco A. Marra, Guy M. Benian, Chris Fields, David L. Baillie
Genome
·
01 Dec 1993
·
doi:10.1139/G93-153