Projects

Example Research Projects:

1. Single-cell Multi-omic Analyses To Identify And Characterize Cell Populations In Patients With Primary And Relapsed Pediatric Acute Myeloid Leukemia.
2. Single-cell multi-omics analysis of primary/recurrent GBM pairs and matched organoid models to investigate mechanisms of treatment resistance.
3. HPV- and EBV-associated genomic, transcriptomic and epigenomic dysregulation in cancer.
4. Effect of HPV integration on 3D genome structure and function in cervical cancer.
5. Pan-cancer analysis of extrachromosomal DNA structure and regulation.
6. The Personalized Approaches in the Treatment of Head and Neck Cancers (PATH) study.
7. Single nucleus multi-omics for precision cancer genomic medicine.

To see which team member is associated with the above projects, please check out our Team page

Featured

GRETTA Genetic inteRaction and EssenTiality neTwork mApper

An R package for mapping genetic interaction and essentiality networks. Takemon and Marra. Bioinformatics. 2023..

TMBur

A distributable tumor mutation burden approach for whole genome sequencing. Titmuss, et al. BMC Medical Genomics. 2022..

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HPV integration caller workflow

A collection of workflows for calling HPV integration with long and short-read sequencing.

RICO Rna-seq Immune COntainer

Immune profiling from RNA-seq data. Uses STAR/RSEM, and immunedeconv to provide estimates of cell populations in short read RNA-Seq data.