Simon Kasif | Profiles RNS

Simon Kasif, PhD

Professor

Boston University College of Engineering

Biomedical Engineering

PhD, University of Maryland
MS, University of Maryland
BS, Tel Aviv University

Websites

	BU College of Engineering
	Google Scholar
	ResearchGate
	Genomic Systems Biology Laboratory

Dr. 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.

BU Research
NIH RePORTER Research

Billing Agreement for Alfred Ramirez
06/01/2017 - 05/31/2018 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
4T32DK007260-40

Expansion of the Diabetes Research Center's Pilot and Feasibility Program
07/01/2016 - 06/30/2017 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
4P30DK036836-30

Diabetes Research Center-Genomics Core
07/01/2016 - 06/30/2017 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
4P30DK036836-30

Billing Agreement for Jonathan Dreyfuss
07/01/2016 - 06/30/2017 (PI)
Joslin Diabetes Center

Billing Agreement for Hui Pan
07/01/2016 - 06/30/2017 (PI)
Joslin Diabetes Center

Billing Agreement for Alfred Ramirez
06/01/2016 - 05/31/2017 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
5T32DK007260-39

Billing Agreement for Jonathan Dreyfuss
07/01/2015 - 06/30/2016 (PI)
Joslin Diabetes Center

Diabetes Research Center-Genomics Core
09/14/2012 - 06/30/2016 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
5P30DK036836-29

Expansion of the Diabetes Research Center's Pilot and Feasibility Program
09/14/2012 - 06/30/2016 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
5P30DK036836-29

Billing Agreement for Alfred Ramirez
06/01/2015 - 05/31/2016 (Subcontract PI)
Joslin Diabetes Center NIH NIDDK
5T32DK007260-38

Showing 10 of 16 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs
2016	BU Joslin regional Computational (BUJRC) Regional/national Shared Resources Core	4P30DK036836-30-7127	1279
2015	BU Joslin regional Computational (BUJRC) Regional/national Shared Resources Core	5P30DK036836-29-7127	1279
2014	BU Joslin regional Computational (BUJRC) Regional/national Shared Resources Core	5P30DK036836-28-7127	1279
2013	BU Joslin regional Computational (BUJRC) Regional/national Shared Resources Core	5P30DK036836-27-7127	1279
2012	BU Joslin regional Computational (BUJRC) Regional/national Shared Resources Core	2P30DK036836-26A1-7127	1279
2010	SciBay: A New Methodology for Scientific Collaboration and Gene Function Determi	5RC2GM092602-02	24
2009	SciBay: A New Methodology for Scientific Collaboration and Gene Function Determi	1RC2GM092602-01	24
2007	Gene Annotation Using Evidence Integration &Propagation in Functional Linkage	5R01HG003367-03	14
2006	Gene Annotation Using Edvidence Integration &Propagati.	5R01HG003367-02	14
2006	Comparative Cross-Species Genomic Analysis System	5R33HG002850-03	14

Showing 10 of 13 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Rep Methods. 2023 May 22; 3(5):100467. PMID: 37323575; PMCID: PMC10261907; DOI: 10.1016/j.crmeth.2023.100467;

Law JN, Akers K, Tasnina N, Santina CMD, Deutsch S, Kshirsagar M, Klein-Seetharaman J, Crovella M, Rajagopalan P, Kasif S, Murali TM. Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2. Gigascience. 2021 12 29; 10(12). PMID: 34966926; PMCID: PMC8716363; DOI: 10.1093/gigascience/giab082;

Dreyfuss JM, Yuchi Y, Dong X, Efthymiou V, Pan H, Simonson DC, Vernon A, Halperin F, Aryal P, Konkar A, Sebastian Y, Higgs BW, Grimsby J, Rondinone CM, Kasif S, Kahn BB, Foster K, Seeley R, Goldfine A, Djordjilovic V, Patti ME. High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control. Nat Commun. 2021 11 29; 12(1):6951. PMID: 34845204; PMCID: PMC8630169; DOI: 10.1038/s41467-021-27289-2;

Kasif S, Roberts RJ. We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data. PLoS Biol. 2020 11; 18(11):e3000999. PMID: 33253151; PMCID: PMC7728211; DOI: 10.1371/journal.pbio.3000999;

Lancour D, Dupuis J, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GC, Crovella M, Farrer LA, Kasif S. Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease. Alzheimers Res Ther. 2020 09 02; 12(1):103.View Related Profiles.

Dupuis, Josee
Farrer, Lindsay
Kasif, Simon

PMID: 32878640; PMCID: PMC7469336; DOI: 10.1186/s13195-020-00674-7;

Ramirez AK, Dankel SN, Rastegarpanah B, Cai W, Xue R, Crovella M, Tseng YH, Kahn CR, Kasif S. Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity. Nat Commun. 2020 04 30; 11(1):2117. PMID: 32355218; PMCID: PMC7192917; DOI: 10.1038/s41467-020-16019-9;

Ramirez AK, Dankel S, Cai W, Sakaguchi M, Kasif S, Kahn CR. Membrane metallo-endopeptidase (Neprilysin) regulates inflammatory response and insulin signaling in white preadipocytes. Mol Metab. 2019 04; 22:21-36. PMID: 30795914; PMCID: PMC6437599; DOI: 10.1016/j.molmet.2019.01.006;

Lancour D, Naj A, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Crovella M, Farrer LA, Kasif S. One for all and all for One: Improving replication of genetic studies through network diffusion. PLoS Genet. 2018 04; 14(4):e1007306.View Related Profiles.

Farrer, Lindsay
Kasif, Simon

PMID: 29684019; PMCID: PMC5933817; DOI: 10.1371/journal.pgen.1007306;

Ramirez AK, Lynes MD, Shamsi F, Xue R, Tseng YH, Kahn CR, Kasif S, Dreyfuss JM. Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes. Cell Rep. 2017 Dec 12; 21(11):3040-3048. PMID: 29241534; PMCID: PMC5841536; DOI: 10.1016/j.celrep.2017.11.065;

Lerin C, Goldfine AB, Boes T, Liu M, Kasif S, Dreyfuss JM, De Sousa-Coelho AL, Daher G, Manoli I, Sysol JR, Isganaitis E, Jessen N, Goodyear LJ, Beebe K, Gall W, Venditti CP, Patti ME. Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism. Mol Metab. 2016 Oct; 5(10):926-936. PMID: 27689005

Showing 10 of 86 results. Show More

Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Nucleic Acids Res. 2016 Jan 4; 44(D1):D330-5.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 26635392; PMCID: PMC4702925; DOI: 10.1093/nar/gkv1324;

Park RW, Kim TM, Kasif S, Park PJ. Identification of rare germline copy number variations over-represented in five human cancer types. Mol Cancer. 2015 Feb 03; 14:25. PMID: 25644941

Nogiec C, Burkart A, Dreyfuss JM, Lerin C, Kasif S, Patti ME. Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. Mol Metab. 2015 Mar; 4(3):151-63. PMID: 25737951

Anton BP, Kasif S, Roberts RJ, Steffen M. Objective: biochemical function. Front Genet. 2014; 5:210.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 25071837; DOI: 10.3389/fgene.2014.00210;

Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang S, Kasif S, Jain RK. Hypermutable DNA chronicles the evolution of human colon cancer. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):E1889-98. PMID: 24753616

Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24; 157(3):580-94. PMID: 24726434

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. The COMBREX project: design, methodology, and initial results. PLoS Biol. 2013; 11(8):e1001638.View Related Profiles.

Choi, Han-Pil
Steffen, Martin
Kasif, Simon

PMID: 24013487; PMCID: PMC3754883; DOI: 10.1371/journal.pbio.1001638;

Nogiec CD, Kasif S. To supplement or not to supplement: a metabolic network framework for human nutritional supplements. PLoS One. 2013; 8(8):e68751. PMID: 23967053

Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PLoS One. 2013; 8(6):e66605.View Related Profiles.

Choi, Han-Pil
Steffen, Martin
Kasif, Simon

PMID: 23825549; PMCID: PMC3688963; DOI: 10.1371/journal.pone.0066605;

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. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep. 2013 May 30; 3(5):1567-79. PMID: 23707066

Rajagopalan P, Kasif S, Murali TM. Systems biology characterization of engineered tissues. Annu Rev Biomed Eng. 2013; 15:55-70. PMID: 23862675

Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biol Direct. 2012; 7:37.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 23111013; PMCID: PMC3534567; DOI: 10.1186/1745-6150-7-37;

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012; 7(6):e37919.View Related Profiles.

Amar, Salomon
Kasif, Simon

PMID: 22675498; PMCID: PMC3366996; DOI: 10.1371/journal.pone.0037919;

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 Jan; 39(Database issue):D11-4.View Related Profiles.

Choi, Han-Pil
Steffen, Martin
Kasif, Simon

PMID: 21097892; PMCID: PMC3013729; DOI: 10.1093/nar/gkq1168;

Mori MA, Liu M, Bezy O, Almind K, Shapiro H, Kasif S, Kahn CR. A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. Diabetes. 2010 Nov; 59(11):2960-71. PMID: 20713682

Mitrofanova A, Kleinberg S, Carlton J, Kasif S, Mishra B. Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. Artif Intell Med. 2010 Jul; 49(3):167-76. PMID: 20580212

Anton BP, Russell SP, Vertrees J, Kasif S, Raleigh EA, Limbach PA, Roberts RJ. Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res. 2010 Oct; 38(18):6195-205. PMID: 20472640

Kasif S, Steffen M. Biochemical networks: the evolution of gene annotation. Nat Chem Biol. 2010 Jan; 6(1):4-5.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 20016491; PMCID: PMC2907659; DOI: 10.1038/nchembio.288;

Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M. A predictive phosphorylation signature of lung cancer. PLoS One. 2009; 4(11):e7994.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 19946374; PMCID: PMC2777383; DOI: 10.1371/journal.pone.0007994;

Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 01; 25(23):3121-7. PMID: 19786482

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. 2009 Oct 06; 106(40):17095-100. PMID: 19805156

Dotan-Cohen D, Kasif S, Melkman AA. Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering. Bioinformatics. 2009 Jul 15; 25(14):1789-95. PMID: 19497934

Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S. Biological process linkage networks. PLoS One. 2009; 4(4):e5313. PMID: 19390589

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. 2009 May; 58(5):1192-200. PMID: 19208909

Lee S, Kasif S, Weng Z, Cantor CR. Quantitative analysis of single nucleotide polymorphisms within copy number variation. PLoS One. 2008; 3(12):e3906. PMID: 19093001

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. 2008 Oct; 4(10):e1000242. PMID: 18974828

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics. 2008; 9:350.View Related Profiles.

Steffen, Martin
Kasif, Simon

PMID: 18721473; PMCID: PMC2535605; DOI: 10.1186/1471-2105-9-350;

Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol. 2008; 9(7):R108. PMID: 18611264

Anton BP, Saleh L, Benner JS, Raleigh EA, Kasif S, Roberts RJ. RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A. 2008 Feb 12; 105(6):1826-31. PMID: 18252828

Dotan-Cohen D, Melkman AA, Kasif S. Hierarchical tree snipping: clustering guided by prior knowledge. Bioinformatics. 2007 Dec 15; 23(24):3335-42. PMID: 17989094

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 Aug 17; 282(33):23981-95. PMID: 17575275

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; 3(6):e96. PMID: 17571924

Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS One. 2007 Mar 28; 2(3):e337. PMID: 17396164

Zhang L, Kasif S, Cantor AC. Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A. 2007 Feb 27; 104(9):3061-6. PMID: 17360609

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. 2007 Mar 30; 282(13):9482-9491. PMID: 17277356

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; 5(1):e8. PMID: 17214507

Nariai N, Kasif S. Context specific protein function prediction. Genome Inform. 2007; 18:173-82. PMID: 18546485

Alon N, Asodi V, Cantor C, Kasif S, Rachlin J. Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol. 2006 Dec; 13(10):1659-72. PMID: 17238837

Murali TM, Wu CJ, Kasif S. The art of gene function prediction. Nat Biotechnol. 2006 Dec; 24(12):1474-5; author reply 1475-6. PMID: 17160037

Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome. Mol Syst Biol. 2006; 2:66. PMID: 17130868

Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics. 2006 Oct 19; 7:265. PMID: 17052348

Lee S, Kasif S. The complete genome sequence of a dog: a perspective. Bioessays. 2006 Jun; 28(6):569-73. PMID: 16700068

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

Zheng Y, Anton BP, Roberts RJ, Kasif S. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics. 2005 Oct 03; 6:243. PMID: 16202130

Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics. 2005 Sep 01; 21 Suppl 2:ii66-71. PMID: 16204127

Rachlin J, Ding C, Cantor C, Kasif S. Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics. 2005 Jul 25; 6:102. PMID: 16042802

Wu CJ, Kasif S. GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W596-9. PMID: 15980544

Rachlin J, Ding C, Cantor C, Kasif S. MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W544-7. PMID: 15980531

Zheng Y, Roberts RJ, Kasif S, Guan C. Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol. 2005 Jun; 187(11):3671-7. PMID: 15901689

Zheng Y, Roberts RJ, Kasif S. Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res. 2004; 32(21):6347-57. PMID: 15576679

Zhang L, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A. 2004 Nov 30; 101(48):16855-60. PMID: 15548610

Zheng Y, Roberts RJ, Kasif S. Segmentally variable genes: a new perspective on adaptation. PLoS Biol. 2004 Apr; 2(4):E81. PMID: 15094797

Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 02; 101(9):2888-93. PMID: 14981259

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 07; 279(19):20167-77. PMID: 14769801

Wu CJ, Fu Y, Murali TM, Kasif S. Gene expression module discovery using gibbs sampling. Genome Inform. 2004; 15(1):239-48. PMID: 15712126

Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D520-2. PMID: 14681472

Logan BT, Karaoz U, Moreno PJ, Weng Z, Kasif S. Protein seer: a Web server for protein homology detection. Conf Proc IEEE Eng Med Biol Soc. 2004; 2004:3064-7. PMID: 17270925

Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12; 19(12):1524-30. PMID: 12912833

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

Zhang L, Pavlovic V, Cantor CR, Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 2003 Jun; 13(6A):1190-202. PMID: 12743024

Pervouchine DD, Graber JH, Kasif S. On the normalization of RNA equilibrium free energy to the length of the sequence. Nucleic Acids Res. 2003 May 01; 31(9):e49. PMID: 12711694

Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003 Apr 11; 327(5):1021-30. PMID: 12662927

Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003; 77-88. PMID: 12603019

Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 2003; 19 Suppl 1:i197-204. PMID: 12855458

Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15; 30(20):e106. PMID: 12384608

Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 2002 Oct 10; 3(11):RESEARCH0060. PMID: 12429059

Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S. Computational identification of operons in microbial genomes. Genome Res. 2002 Aug; 12(8):1221-30. PMID: 12176930

Walker M, Pavlovic V, Kasif S. A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res. 2002 Jul 15; 30(14):3181-91. PMID: 12136100

Pavlovic V, Garg A, Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 2002 Jan; 18(1):19-27. PMID: 11836207

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921.View Related Profiles.

Galagan, James
Kasif, Simon

PMID: 11237011

Cai D, Delcher A, Kao B, Kasif S. Modeling splice sites with Bayes networks. Bioinformatics. 2000 Feb; 16(2):152-8. PMID: 10842737

Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics. 1999 Dec 15; 62(3):500-7. PMID: 10644449

Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999 Dec 01; 27(23):4636-41. PMID: 10556321

Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999 Jun 01; 27(11):2369-76. PMID: 10325427

Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998 Jan 15; 26(2):544-8. PMID: 9421513

Delcher AL, Kasif S, Goldberg HR, Hsu WH. Protein secondary structure modelling with probabilistic networks. Proc Int Conf Intell Syst Mol Biol. 1993; 1:109-17. PMID: 7584325

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 86 publications over 25 distinct years, with a maximum of 8 publications in 2004 and 2007

Bar chart showing 86 publications over 25 distinct years, with a maximum of 8 publications in 2004 and 2007

Year	Publications
1993	1
1998	1
1999	3
2000	1
2001	1
2002	5
2003	7
2004	8
2005	7
2006	5
2007	8
2008	5
2009	6
2010	5
2012	2
2013	5
2014	3
2015	3
2016	1
2017	1
2018	1
2019	1
2020	3
2021	2
2023	1

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