We are a team of Cancer Researchers and Computational Biologists working on Cancer Classification, Target Discovery and Precision Oncology.

Projects and Collaborations

Below are our many ongoing projects and collaborations around our general framework to functionally delineate oncogenic states. These are understood as a defined set of specific and coordinated patterns of aberrant activation/deregulation of signaling pathways, and downstream effectors and transcriptional programs, including the tumor stroma and immune microenvironment, which result in similar phenotypic characteristics and cell vulnerabilities to genetic or pharmacological perturbations. Following this functional approach we use computational and experimental methodologies to define oncogenic states and provide a more accurate biological context, and molecular phenotypes, to guide cancer modeling, classification and to more effectively match therapies to individual cancer samples using a novel functional evidence-based paradigm for Precision Oncology. As part of our work we develop computational algorithms, tools, and software environment and make them available to the Cancer Research community.

UCSD Center for Cancer Target Discovery and Development (CTD2)

California Initiative to Advance Precision Medicine (CIAPM) UCSD Celsus Project

GSEA/MSigDB and GenePattern Development (Mesirov Lab Collaboration)

Moores Cancer Center Genomics and Computational Biology Shared Resource (GCBSR)

Prostate Cancer Precision Medicine Project

Oncogenic State Projects

Immuno-Oncology Projects

Computational Method Development Projects

Cancer Cell Map Initiative Collaboration

Functional Characterisation of Circular RNA (UCSD/Monash University Collaboration)