Gyan Bhanot Professor Rutgers University Dept. of Molecular Biology and Biochemistry & Physics 271 Hill Center, BioMaPS Institute 610 Taylor Road Piscataway. NJ 08854 (732) 445-0091 FAX - gbhanot@rci.rutgers.edu

Computational biology, evolutionary genetics

My lab is focussed on two research areas. The first is computational biology related to cancer. Specifically, we are using microarray, mass spec and SNP polymorphism data to identify, quantify and explain cancer initiation, progression, and metastasis. The goal is to develop protocols for clinical use, participate in clinical trials and identify therapeutic strategies. This research involves collaborations with local clinicians and researchers at BME, CINJ, UMDNJ, CABM and BioMaPS as well as collaborators from the Institute for Advanced Study, Princeton, Broad Institute, IBM Research, Tokyo Gerontological Institute and Boston University.

My second focus area is Evolutionary Genetics including human migration, phylogeny, disease association studies and patterns of mutations correlated with longevity and complex disease phenotypes.

Selected Publications

Mathew R, Karp CM, Beaudoin B, Vuong N, Chen G, Chen HY, Bray K, Reddy A, Bhanot G, Gelinas C, Dipaola RS, Karantza-Wadsworth V, White E. (2009) Autophagy suppresses tumorigenesis through elimination of p62. Cell. 137(6):1062-75.

Lexe G, Monaco J, Doyle S, Basavanhally A, Reddy A, Seiler M, Ganesan S, Bhanot G, Madabhushi A. (2009) Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging. Exp Biol Med (Maywood). 234(8):860-79.

Alexe, G., Vijaya-Satya, R., Seiler, M., Platt, D., Bhanot,T., Hui, S., Tanaka, M., Levine, and Bhanot, G. (2008) PCA and clustering reveal alternate mtDNA phylogeny of N and M Clades J. Mol Evol 67 (5):465-487.

Bilal, E. Rabadan, R., Alexe, G., Fuku, N., Ueno, H., Nishigaki, Y., Fujita,Y., Ito, M., Arai, Y., Hirose, N., Ruckenstein, A., Bhanot, G., Tanaka, M. (2008) Mitochondrial DNA Haplogroup D4a is a marker for extreme longevity in Japan. PLoS ONE 3(6): 2421.

Alexe, G., Dalgin, G. S., Scanfeld, D., Tamayo, P., Mesirov, J., Delisi, C., Harris, L., Barnard, N., Martel, M., Levine, A., Ganesan, S., Bhanot, G. (2007) High expression of lymphocyte associated genes in node-negative HER2+ breast cancer correlates with lower recurrence rates. Cancer Research 67:10669-10676.

Dalgin, G. S., Alexe, G., Scanfeld, D., Tamayo, P., Mesirov, J., Ganesan, S., DeLisi, C., Bhanot, G. (2007) Portraits of breast cancer progression. BMC Bioinformatics 8:291.

Alexe G., Dalgin, G. S., Scanfeld, D., Tamayo, P., Mesirov, J., Ganesan,S., Bhanot, G., DeLisi, C. Breast cancer stratification from analysis of micro-array data of micro-dissected Specimens. In Proceedings of the IBSB 2007, Genome Informatics Series, Vol. 18, Jan 2008, World Scientific: ISBN 978-1-86094-991-3.

Alexe G., Dalgin, G. S., Ramaswamy, R, DeLisi, C., Bhanot, G. (2006) Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns. Cancer Informatics 2:243–274.

Alexe, G., Fuku, N., Bilal, E., Ueno, H., Nishigaki, Y., Fujita, Y., Ito, M., Arai, Y., Hirose, N., Bhanot, G., Tanaka, M. (2007) Enrichment of longevity phenotype in mtDNA haplogroups D4b2b, D4a and D5 in the Japanese population. Human Genetics (3-4):347-56.

Alexe, G., Bhanot, G., Climescu-Haulica A. (2006) A cross entropy algorithm for classification with delta-patterns. Fourth Colloquium on Mathematics and Computer Science DMTCS proc. AG. 399-402

Vijaya-Satya, R., Mukherjee, A., Alexe, G., Parida, L., Bhanot, G. (2006) Constructing near-perfect phylogenies with multiple homoplasy events. Bioinformatics 22(14):514-522.

Almasi, G. , Bhanot, G. (2006). et al, Scaling physics and material science applications on a massively arallel Blue Gene/L system. Comm. in App. Math. and Comp. Science 1:29-51.

Bhanot, G., Lawless, E., Gara, A., Sexton, J., Heidelberger, P., Walkup, R. (2005) Optimizing task layout on the Blue Gene/L Supercomputer IBM. Journal of R&D. V49 2/3: p 489.

Bhanot, G., Alexe, G., Levine, A. J., Stolovitzky, G. (2005) Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories. Genome Informatics 16(1): 233-244.

Bhanot, G., Alexe, G., Venkataraghavan, B., Levine, A. J. (2005) A robust meta-classification strategy for cancer detection from mass spectrometry data. Proteomics 6(2):592-604.

Bhanot, G. Chen, D., Gara, A., Sexton, J. C., Vranas, P. Lattice QCD on BlueGene/L, the Next Generation. Proceedings of Supercomputing 2005, Seattle, Nov. 2005. Nucl Physics B, Vol 140, 823-825.

Bhanot, G. (2004) Results from modeling of B-Cell receptors binding to antigen Prog. Biophysics and Mol. Bio. 85, 2-3:343-352.

Bhanot, G., Zhu,J., Louzoun, Y. and Delisi, C. (2003) The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophysical Journal 84:124-135.

Bhanot, G., Louzoun, Y, Weigert, M Dynamical analysis of a degenerate primary and secondary humoral immune response. Bulletin of Mathematical Biology 65 (2003) 535-545.