Cancer

 

Selected publications are below.

 

  1. Hypermutable DNA chronicles the evolution of human colon cancer. Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang, S, Kasif S, Jain RK. Proc Natl Acad Sci U S A. 2014 PMID: 24753616
  2. Reconstructing and reprogramming the developmental hierarchy of glioblastoma, Mario L. Suvà*, Esther Rheinbay* et al, Cell, 2014.
  3. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. Cell Reports. 2013 May 30;3(5):1567-79.  2013.04.021. Epub 2013 May 23. PMID: 23707066
  4. Systems biology characterization of engineered tissues. Rajagopalan P, Kasif S, Murali TM. Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. PMID: 23862675
  5. To supplement or not to supplement: a metabolic network framework for human nutritional supplements. Nogiec CD, Kasif S. PLoS One. 2013;8(8):e68751. doi: 10.1371/journal.pone.0068751. PMID: 23967053
  6. Deep sequencing of the oral microbiome reveals s signatures of periodontal disease, Bo Liu1,2*, Lina Faller3*, Niels Klitgord3*, Varun Mazumdar3*, Mohammad Ghodsi1,2,Daniel D. Sommer1, Theodore R. Gibbons1,4, Todd J. Treangen1,10, Yi-Chien Chang3,Shan Li5, O. Colin Stine5, Hatice Hasturk8, Simon Kasif3,7,9, Daniel Segrè3,6,7#,  Mihai Pop1,2,4#, Salomon Amar3,8#,, PLOS One, 2012
  7. Network Signatures of Insulin Resistance and Life Span, M. Liu, M. Mori, IS. Kohane, ME Patti, A. Goldfine, CR Kahn, S. Kasif, in preparation.
  8. Chris Nogiec, Allison Burkhart, Jonathan Dreyfuss, Simon Kasif* and ME Patti*, Metabolic Analysis of Insulin Resistance, in revision (contributed equally authors), in review.
  9. Towards a Personal Repeatome: A Genome-Wide Survey of Length Variation in Short Tandem Repeats in Human Gene Transcripts, in preparation.
  10. A Critical Assessment of Genomic and Clinical Breast Cancer Biomarkers. Chang-Jiun Wu, Tianxi Cai, Zoltan Szallasi, Kamila Naxerova, Martin Steffen, L.J. Wei, Isaac S. Kohane*, Simon Kasif*, co-corresponding authors, in revision.
  11. Integrative Pheno-genomic module discovery with application to breast cancer, Chang-Jiun Wu, Tianxi Cai, Isaac S. Kohane*, Simon Kasif*, in revision.
  12. A Systems Biology Approach Links Inflammation to the Predisposition to Metabolic Diseases in Mouse Strains, Marcelo Mori*, Manway Liu*, Simon Kasif, Ron Kahn, Diabetes 2010.
  13. Transcriptome Analysis Reveals Parallel Dysregulation of Oxidative Metabolism and Inflammation in Muscle and Adipose Tissue With Progression of Insulin Resistance in Humans, Mary-Elizabeth Patti, Manway Liu, Wanzhu Jin, Carles Lerin, Jonathan Dreyfuss, Martha Vokes, Joshua Schroeder, Elizabeth Tatro, Peter Park, Isaac Kohane, Igor Leykin, Simon Kasif, and Allison Goldfine, in preparation.
  14. Drug Response Phosphorylation Signatures of Lung Cancer, Chang-Jiun Wu, Martin Steffen, Simon Kasif in preparation.
  15. A Predictive phosphorylation signature of lung cancer. Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif,* Martin Steffen*, co-corresponding authors,  PLoS ONE, Nov 2009.
  16. Triplet repeat length bias and variation in the human transcriptome,  Molla M*, Delcher A*, Cantor CR, Kasif S, Proc. of National Academy of Sciences, Oct. 2009, PMID: 19805156
  17. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Bioinformatics. 2009 Dec 1;25(23):3121-7. Epub 2009 Sep 28.PMID: 19786482
  18. Biological process linkage networks. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S. PLoS ONE. 2009;4(4):e5313. Epub 2009 Apr 23. PMID 19390589
  19. Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice. 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. Diabetes. 2009 May;58(5):1192-200. Epub 2009 Feb 10. PMID: 19208909
  20. Quantitative analysis of single nucleotide polymorphisms within copy number variation. Lee S, Kasif S, Weng Z, Cantor CR. PLoS ONE. 2008;3(12):e3906. Epub 2008 Dec 18. PMID: 19093001
  21. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. 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. PLoS Genet. 2008 Oct;4(10):e1000242. Epub 2008 Oct 31. PMID: 18974828
  22. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Genome Biol. 2008;9(7):R108. Epub 2008 Jul 8. PMID: 18611264
  23. Context specific protein function prediction. Nariai N, Kasif S. Genome Inform. 2007; 18:173-82. PMID: 18546485
  24. Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, Cooper GM. Immediate-early and delayed primary response genes are distinct in function and genomic architecture, J Biol Chem. 2007 Jun 15;
  25. 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. 2007 Jun 15;3(6):e96. PMID:17571924
  26. 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 Biol. 2007 Jan 9;5(1):e8 PMID: 17214507
  27. Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nature Biotechnology. 2006 Dec;24(12):1474-5. PMID: 17160037
  28. Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome. Nature/Embo. Mol Syst Biol. 2006;2:66. Epub 2006 Nov 28. PMID: 17130868
  29. Lee S, Kohane I, Kasif S. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics. 2005 Nov 27;6:168. PMID: 16309559
  30. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM. Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9. PMID: 14769801
  31. Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: identification of diagnostic genes based on expression data. Bioinformatics. 2003 Aug 12;19(12):1578-9. PMID: 12912841

 

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