Our lab’s mission is to discover genetic alterations relevant to human disease - particularly in cancer - and translate these findings into treatments and cures.

Principal Themes

  • Genomic and epigenomic alterations involved in initiation, progression, and metastasis of cancer

  • Regulation of gene expression and splicing and their association with cancer

  • Expression and post-translational regulation of proteins in the context of tumor development and treatment

We develop software that uses state-of-the-art sequencing technology to identify variants that contribute to disease, including small mutations, structural variations, epigenetic modifications, and gene-protein-phosphoprotein expression changes. We then validate computational predictions using cell-based assays and high throughput screenings. By looking at thousands of tumors across many forms of cancer, we gain novel insight into the initiation, progression, metastasis, and treatment of cancer at the gene, pathway, and cell level. Ultimately, our work contributes to a deeper understanding cancer and more effective treatments.

Cancer Genomics and Proteomics Projects

Collaboration projects our group participates in:

Tools in Active Development

  • VarScan: Detect viruses from next-generation sequencing data [github]
  • MiSplice: Discover mutation-induced splice sites from integration of DNA and RNA sequence data [github]
  • MSIsensor: Microsatellite instability detection using paired tumor-normal sequence data [pubmed] [github]
  • SciClone: Infer the subclonal architecture of tumors [github] 
  • Hotspot3D: Identify mutation-mutation and mutation-drug clusters using 3D protein structures and correlate them with known or potentially interacting functional variants, domains, and proteins [pubmed] [github]
  • GenomeVIP: Cloud-enabled variant discovery [github]
  • PepScan: Protein quantification and peptide identification from mass spectra data [github]
  • CharGer:  Characterization of the clinical significance of germline variants [github]
  • Breakpoint Surveyor:  Visualization of breakpoints and copy-number variation

For more information on all of our tools, see Tools page.