The overarching theme of the Varadan laboratory is the development and application of systems biology approaches to delineate mechanisms of disease progression and discover novel biomarkers of therapy response:
Systems Biology of Cancer
We are developing multidimensional frameworks that delineate complex cellular processes underlying disease progression through the integration of transcriptomic, genomic and/or epigenomic profiles for any given biological sample. Our goal is to develop computational methods based on information theory, Bayesian inference and deep learning to robustly infer genomic aberrations and network-level deregulations in cancer tissues. These methods are being applied to genomic profiles derived from primary cancer samples, single-cell sequencing data and genome-scale functional genomic screens.
Development of novel biomarkers of therapy response in breast cancer
We recently identified novel transcriptional and immune signatures predictive of preoperative therapy response using large-scale RNA sequencing of breast tumor biopsies. Ongoing studies are focused on integrative analysis of DNA and RNA sequencing profiles to discover signaling pathways and immune mechanisms underlying therapy response in HER2-positive breast cancers.
Integrative genomics to discover disease mechanisms in cancers
Our ongoing collaboration with members of the Case GI SPORE has already resulted in the characterization of genome-wide mutation and copy-number landscapes in African American colon cancers. Current efforts involve applying our systems biology approach to discover molecular drivers of tumorigenesis in distinct pathologic subtypes of gastrointestinal cancers.
Systems Biology of Cancer
We are developing multidimensional frameworks that delineate complex cellular processes underlying disease progression through the integration of transcriptomic, genomic and/or epigenomic profiles for any given biological sample. Our goal is to develop computational methods based on information theory, Bayesian inference and deep learning to robustly infer genomic aberrations and network-level deregulations in cancer tissues. These methods are being applied to genomic profiles derived from primary cancer samples, single-cell sequencing data and genome-scale functional genomic screens.
Development of novel biomarkers of therapy response in breast cancer
We recently identified novel transcriptional and immune signatures predictive of preoperative therapy response using large-scale RNA sequencing of breast tumor biopsies. Ongoing studies are focused on integrative analysis of DNA and RNA sequencing profiles to discover signaling pathways and immune mechanisms underlying therapy response in HER2-positive breast cancers.
Integrative genomics to discover disease mechanisms in cancers
Our ongoing collaboration with members of the Case GI SPORE has already resulted in the characterization of genome-wide mutation and copy-number landscapes in African American colon cancers. Current efforts involve applying our systems biology approach to discover molecular drivers of tumorigenesis in distinct pathologic subtypes of gastrointestinal cancers.