Computational Systems Biology
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.
Mechanisms underlying therapy resistance and metastatic spread in breast cancer
We previously identified transcriptional and immune signatures predictive of preoperative therapy response across major subtypes of breast cancer. Ongoing studies include a multi-scale mechanism of chemotherapy resistance in Triple-Negative Breast Cancer, mechanisms underlying resistance to anti-HER2 therapy, and pathways associated with breast cancer brain metastases.
Systems models of tumorigenesis and disease progression in gastrointestinal malignancies
In collaboration with members of the Case GI SPORE and BETRNet programs we recently applied systems biology approaches to discover molecular dependencies with therapeutic implications in esophageal adenocarcinoma. We are currently building on these efforts to discover molecular drivers of tumorigenesis in distinct pathologic subtypes of gastrointestinal cancers.
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.
Mechanisms underlying therapy resistance and metastatic spread in breast cancer
We previously identified transcriptional and immune signatures predictive of preoperative therapy response across major subtypes of breast cancer. Ongoing studies include a multi-scale mechanism of chemotherapy resistance in Triple-Negative Breast Cancer, mechanisms underlying resistance to anti-HER2 therapy, and pathways associated with breast cancer brain metastases.
Systems models of tumorigenesis and disease progression in gastrointestinal malignancies
In collaboration with members of the Case GI SPORE and BETRNet programs we recently applied systems biology approaches to discover molecular dependencies with therapeutic implications in esophageal adenocarcinoma. We are currently building on these efforts to discover molecular drivers of tumorigenesis in distinct pathologic subtypes of gastrointestinal cancers.