EECS500 Fall 2016 Department Colloquium

Vinay Varadan
Robust Integrative Modeling of Multi-omics Tumor Profiles to Decode Disease Mechanisms
Case Comprehensive Cancer Center
White 411
September 6, 2016

The etiology and progression of cancer involves the coordinated deregulation of cellular processes due to genomic aberrations and transcriptional or epigenetic alterations. While high-throughput profiling and next generation sequencing technologies have enabled genome-scale measurements of molecular deregulations in tumor samples, robust analytics that integrate these measurements into a systems-level mechanistic portrait of a given tumor have yet to fully mature. In this talk, I will outline some of the key challenges in detecting genomic aberrations and inferring signaling network deregulations on a genome-scale in tumor samples. I will then detail a novel systems biology framework, InFlo, which integrates multi-dimensional molecular measurements to robustly characterize global signaling pathway activities on a per-sample basis. Additionally, I will outline how we used InFlo to model disease-causing mechanisms in unique clinical paradigms, ranging from platinum-resistance in ovarian cancer to molecular drivers of Barrett's esophageal adenocarcinoma pathogenesis. I will end by detailing how we plan to expand our systems biology approach to achieve multi-scale integration of molecular and radiologic profiles to identify novel biomarkers of therapy response in breast cancer.


The overarching theme of Dr. Varadan’s translational research is to discover novel biomarkers and therapeutic targets through integrative analysis of large-scale molecular profiling of tumors. Thus, his research interests span statistical signal processing, machine learning, big data analytics, computational systems biology, functional genomics and genomics-enabled clinical trial development. During his graduate studies in Electrical Engineering at Columbia University, he focused on developing robust computational algorithms for the analysis of high-throughput genomic data, for which he was awarded a PhD with Distinction, an honor reserved for the top 10% of all doctoral candidates. He then joined Philips Healthcare as a Senior Member of Research Staff, focusing on platform technologies that integrate next-generation sequencing profiles with patient clinical data for oncology clinical decision support. His work at Philips resulted in a $5 million venture that is now commercializing the platform through evaluations across cancer centers. Since joining the Case Comprehensive Cancer Center in 2013, Dr. Varadan has developed an independent research program in cancer genomics and computational systems biology, with substantial contributions across breast, ovarian and GI cancers. His collaborations span academic and industrial research groups within the clinical, translational and engineering fields at Case Western Reserve University, University Hospitals, Cleveland Clinic, National cancer Institute, Yale University, Brown University and the Dana-Farber Cancer Institute.