Simon Kasif, PhD
Professor
Boston University College of Engineering
Dept of Biomedical Engineering

PhD, University of Maryland
MS, University of Maryland




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.


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

  1. 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;
     
  2. 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;
     
  3. 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;
     
  4. 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. PMID: 32878640; PMCID: PMC7469336; DOI: 10.1186/s13195-020-00674-7;
     
  5. 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;
     
  6. 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;
     
  7. 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. PMID: 29684019; PMCID: PMC5933817; DOI: 10.1371/journal.pgen.1007306;
     
  8. 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;
     
  9. 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
     
  10. 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. PMID: 26635392; PMCID: PMC4702925; DOI: 10.1093/nar/gkv1324;
     
Showing 10 of 85 results. Show More

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

Bar chart showing 85 publications over 24 distinct years, with a maximum of 8 publications in 2004 and 2007

YearPublications
19931
19981
19993
20001
20011
20025
20037
20048
20057
20065
20078
20085
20096
20105
20122
20135
20143
20153
20161
20171
20181
20191
20203
20212

Contact for Mentoring:

44 Cummington St, Boston MA 02215
Boston MA 02215
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