Simon Kasif, Ph.D.

photo of Dr. KasifProfessor, Biomedical Engineering

Computational Genomics Laboratory
Curriculum Vitae

M.S. & Ph.D., Computer Science, University of Maryland
B.Sc., Mathematics, Tel Aviv University
Phone: (617) 358-1845
Fax: (617) 353-6766
Office: LSEB 902

Research Interests

Prof. Kasif is a co-founder of the Center for Advanced Genomic Technology (CAGT) with Charles DeLisi, co-founder of COMBREX: COMPUTATIONAL BRIDGES TO EXPERIMENTS PROJECT with Rich Roberts and Martin Steffen,, and a member of the I2B2 Center (Informatics for Integrating Biology and Bedside). He was a participant in the Human Genome Consortium that produced the first public draft of the human genome. His contributions to Computational Biology include the co-development of Glimmer, one of the most widely used gene finders in the community (with Steven Salzberg and Art Delcher), Mummer, the first whole genome comparative alignment system (with Salzberg and Delcher), early advocacy of the use of Bayesian probabilistic networks (graphical models) in Computational Biology (1992), introduction of probabilistic functional linkage networks for gene function prediction , (with Stan Letovsky), and an early deployment of network signatures of disease (with Zak Kohane and Manway Liu) for diabetes as part of I2B2 activities. Prof. Kasif systems and genomic biology/medicine group has been using advanced network and general predictive methodologies for modeling and analysis of metabolic and signaling networks and their dis-regulation in diabetes, obesity, cancer and inflammation. His group also develops new technologies and frameworks and their applications in genomic and biomedical sciences.

Selected Recent Publications

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S. “COMBREX: a project to accelerate the functional annotation of prokaryotic genomes” Nucleic Acids Res. (2011)

Mori M, Liu M, Kasif S, Kahn CR. “A Systems Biology Approach Links Inflammation to the Predisposition to Metabolic Diseases in Mouse Strains” Diabetes. (2010)

Kasif S, Steffen M. “Biochemical networks: The evolution of gene annotation” Nat Chem Biol. Jan, 6(1):4-5. (2010)

Molla M, Delcher A, Sunyaev S, Cantor C, Kasif S. “Triplet repeat length bias and variation in the human transcriptome” Proc Natl Acad Sci U S A. Oct 6,106(40):17095-100. (2009)

Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M, Kasif S, Zavacki AM, Leshan RL, Myers MG, Patti ME. “Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice” Diabetes. May, 58(5):1192-200. (Epub: 2009 Feb 10) PMID: 19208909

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. “Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains” PLoS Genet. Oct, 4(10):e1000242. (Epub: 2008 Oct 31)

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. “Integration of relational and hierarchical network information for protein function prediction” BMC Bioinformatics. Aug 22, 9:350. (2008)

Anton B, Kasif S, Roberts R. “RimO, a MiaB-Like Enzyme, Methylthiolates the Universally Conserved Asp88 Residue of Ribosomal Protein S12 in Escherichia coli” Proc. Natl. Acad Sci USA. (2008)

Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. “Network-based analysis of affected biological processes in type 2 diabetes models” PLoS Genet. Jun 15, 3(6):e96. (2007) PMID: 17571924

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS “Large-scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles” PLoS Biology. (2007)

Tullai JW, Chen J, Schaffer ME, Kamenetsky E, Kasif S, Cooper GM. “Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells” J Biol Chem. Mar 30, 282(13):9482-91. (Epub: 2007 Feb 3) PMID: 17277356

Rachlin J, Cohen DD, Cantor C, Kasif S. “Biological context networks: a mosaic view of the interactome” Nature/Embo. Mol Syst Biol. 2:66. (Epub: 2006 Nov 28)

Murali TM, Wu CJ, Kasif S. “The art of gene function prediction” Nat Biotechnol. Dec, 24(12):1474-5. (2006)

Zheng Y., R. Roberts and S. Kasif. “Segmentally Variable Genes: A New Perspective on Adaptation” Public Library of Science PloS Biology. (2004)

Karaoz U., Murali, T.M., Letovsky, S., Zheng, Y., Ding, C.M., Cantor, C.R. Kasif S., “Whole Genome Annotation Using Evidence Integration in Functional Linkage Networks” PNAS. (2004)