General Medical Sciences (Oncology)

Vinay Varadan

VINAY VARADAN, PhD

Assistant Professor
General Medical Sciences (Oncology)

Phone: 216.368.2194
email: vxv89@case.edu


Keywords

Bioinformatics
Genomics
Breast Cancer


Research Interests

My academic training is in bioinformatics, machine learning, statistics and genomics with a focus on integrative computational analysis of high throughput genomic data. My recent work has focused on integrative analysis of RNA and DNA sequencing to identify genomic changes associated with benefit to targeted therapy. Previously I developed methods to identify prognostic association of genome wide DNA methylation changes in breast cancer in collaboration with clinical and bench scientists. I also developed a computational framework (InFlo) that integrates genome-wide copy-number and gene expression data with biological pathway definitions to identify dysregulated pathways in individual patient tumors that are associated with clinical outcomes in breast and ovarian cancer.


Recent Publications

Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie R, Dimitrova N, Harris LN. Translating Next Generation Sequencing to practice: opportunities and necessary steps. Molecular Oncology, 2013. [PMID: 23769412]

Wang S, Wang L, Bayaxi N, Li J, Verhaegh W, Janevski A, Varadan V, et al. A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue. Gut, 62(2):280-9, 2013.[ PMID: 22535378]

Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. “Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Frontiers in Oncology, 2:197, 2012. [PMID: 23293768]

Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N. Effective normalization for copy number variation detection from whole genome sequencing. BMC Genomics, 13 Suppl 6:S16, 2012. [PMID: 23134596]

Varadan V, Mittal P, Vaske CJ, Benz SC. The integration of biological pathway knowledge in cancer genomics: a review of existing computational approaches. IEEE Signal Processing, 29(1):35-50, 2012.

Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, et al. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One, 6(12):e28503, 2011. [PMID: 22174824]

Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A et al. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables, Molecular Oncology, 2011. [PMID: 21169070]

Kim H, Watkinson J, Varadan V, Anastassiou D. “Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1. BMC Medical Genomics, 3:51, 2010. [PMID: 21047417]

Janevski A, Kamalakaran S, Banerjee N, Varadan V, and Dimitrova N. “PAPAyA: a platform for breast cancer biomarker discovery, evaluation and assessment. BMC Bioinformatics, 10(Suppl 9):S7, 2009. [PMID: 19761577]

Varadan V, Miller DM 3rd, Anastassiou D. "Computational Inference of the molecular logic for synaptic connectivity in C. elegan. Bioinformatics, 22(14):e497-506, 2006. [PMID: 16873513]

Varadan V, Anastassiou D. Inference of disease-related molecular logic from systems-based microarray analysis. PLoS Computational Biology, 2(6):e68, 2006. [PMID: 16789819]

Anastassiou D, Liu H, Varadan V. "Variable window binding for mutually exclusive alternative splicing. Genome Biology, 7(1):R2, 2006. (Highly Accessed) [PMID: 16507134]