Simon Kasif

Simon Kasif

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Simon Kasif

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Membrane metallo-endopeptidase (Neprilysin) regulates inflammatory response and insulin signaling in white preadipocytes.

Mol Metab 2019 04 25;22:21-36. Epub 2019 Jan 25.

Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molmet.2019.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437599PMC
April 2019

One for all and all for One: Improving replication of genetic studies through network diffusion.

PLoS Genet 2018 04 23;14(4):e1007306. Epub 2018 Apr 23.

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933817PMC
April 2018

Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes.

Cell Rep 2017 Dec;21(11):3040-3048

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Bioinformatics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247173171
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http://dx.doi.org/10.1016/j.celrep.2017.11.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841536PMC
December 2017

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

Nucleic Acids Res 2016 Jan 3;44(D1):D330-5. Epub 2015 Dec 3.

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA

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http://dx.doi.org/10.1093/nar/gkv1324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702925PMC
January 2016

Identification of rare germline copy number variations over-represented in five human cancer types.

Mol Cancer 2015 Feb 3;14:25. Epub 2015 Feb 3.

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s12943-015-0292-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381456PMC
February 2015

To supplement or not to supplement: a metabolic network framework for human nutritional supplements.

PLoS One 2013 5;8(8):e68751. Epub 2013 Aug 5.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068751PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740736PMC
September 2014

Objective: biochemical function.

Front Genet 2014 8;5:210. Epub 2014 Jul 8.

Department of Biomedical Engineering, Boston University Boston, MA, USA ; Department of Pathology and Laboratory Medicine, Boston University School of Medicine Boston, MA, USA.

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http://dx.doi.org/10.3389/fgene.2014.00210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085566PMC
July 2014

Hypermutable DNA chronicles the evolution of human colon cancer.

Proc Natl Acad Sci U S A 2014 May 21;111(18):E1889-98. Epub 2014 Apr 21.

Edwin L. Steele Laboratory for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.

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http://dx.doi.org/10.1073/pnas.1400179111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020055PMC
May 2014

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.

Cell 2014 Apr 10;157(3):580-94. Epub 2014 Apr 10.

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.02.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004670PMC
April 2014

Systems biology characterization of engineered tissues.

Annu Rev Biomed Eng 2013 ;15:55-70

Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24060, USA.

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http://dx.doi.org/10.1146/annurev-bioeng-071811-150120DOI Listing
February 2014

A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease.

Diabetes 2010 Nov 16;59(11):2960-71. Epub 2010 Aug 16.

Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.2337/db10-0367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963557PMC
November 2010

Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle.

Artif Intell Med 2010 Jul 26;49(3):167-76. Epub 2010 Jun 26.

Computer Science Department, Courant Institute of Mathematical Sciences, New York University, 715 Broadway, New York, NY 10003, USA.

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http://dx.doi.org/10.1016/j.artmed.2010.04.013DOI Listing
July 2010

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.

Bioinformatics 2009 Dec 28;25(23):3121-7. Epub 2009 Sep 28.

Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Center of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778339PMC
December 2009

A predictive phosphorylation signature of lung cancer.

PLoS One 2009 Nov 25;4(11):e7994. Epub 2009 Nov 25.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007994PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777383PMC
November 2009

Triplet repeat length bias and variation in the human transcriptome.

Proc Natl Acad Sci U S A 2009 Oct 17;106(40):17095-100. Epub 2009 Sep 17.

Department of Biomedical Engineering and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.0907112106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746125PMC
October 2009

Biological process linkage networks.

PLoS One 2009 23;4(4):e5313. Epub 2009 Apr 23.

Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005313PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669181PMC
July 2009

Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering.

Bioinformatics 2009 Jul 3;25(14):1789-95. Epub 2009 Jun 3.

Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel 84105.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705235PMC
July 2009

Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers.

Genome Biol 2008 8;9(7):R108. Epub 2008 Jul 8.

Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2008-9-7-r108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2530866PMC
October 2008

Context specific protein function prediction.

Genome Inform 2007 ;18:173-82

Boston University, Boston, MA 02215, USA.

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August 2008

Integration of relational and hierarchical network information for protein function prediction.

BMC Bioinformatics 2008 Aug 22;9:350. Epub 2008 Aug 22.

Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2535605PMC
August 2008

Hierarchical tree snipping: clustering guided by prior knowledge.

Bioinformatics 2007 Dec 7;23(24):3335-42. Epub 2007 Nov 7.

Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btm526DOI Listing
December 2007

Immediate-early and delayed primary response genes are distinct in function and genomic architecture.

J Biol Chem 2007 Aug 15;282(33):23981-95. Epub 2007 Jun 15.

Department of Biology, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1074/jbc.M702044200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2039722PMC
August 2007

Network-based analysis of affected biological processes in type 2 diabetes models.

PLoS Genet 2007 Jun;3(6):e96

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0030096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904360PMC
June 2007

Biological context networks: a mosaic view of the interactome.

Mol Syst Biol 2006 28;2:66. Epub 2006 Nov 28.

Department of Computer Science, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1038/msb4100103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693461PMC
March 2007

Probabilistic protein function prediction from heterogeneous genome-wide data.

PLoS One 2007 Mar 28;2(3):e337. Epub 2007 Mar 28.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000337PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828618PMC
March 2007

Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy.

Proc Natl Acad Sci U S A 2007 Feb 20;104(9):3061-6. Epub 2007 Feb 20.

Center for Advanced Biotechnology, Department of Biomedical Engineering, Bioinformatics Program, and Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.0611075104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805538PMC
February 2007

The art of gene function prediction.

Nat Biotechnol 2006 Dec;24(12):1474-5; author reply 1475-6

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http://dx.doi.org/10.1038/nbt1206-1474DOI Listing
December 2006

Multi-node graphs: a framework for multiplexed biological assays.

J Comput Biol 2006 Dec;13(10):1659-72

Department of Mathematics, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1089/cmb.2006.13.1659DOI Listing
December 2006

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

BMC Genomics 2006 Oct 19;7:265. Epub 2006 Oct 19.

Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA.

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http://dx.doi.org/10.1186/1471-2164-7-265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624830PMC
October 2006

The complete genome sequence of a dog: a perspective.

Bioessays 2006 Jun;28(6):569-73

Bioinformatics Program, Boston University, MA 02215, USA.

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http://dx.doi.org/10.1002/bies.20421DOI Listing
June 2006

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.

BMC Genomics 2005 Nov 27;6:168. Epub 2005 Nov 27.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1186/1471-2164-6-168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310621PMC
November 2005

Phylogenetic detection of conserved gene clusters in microbial genomes.

BMC Bioinformatics 2005 Oct 3;6:243. Epub 2005 Oct 3.

Bioinformatics Graduate Program, Boston University, Boston, MA, USA.

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http://dx.doi.org/10.1186/1471-2105-6-243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1266350PMC
October 2005

Less is more: towards an optimal universal description of protein folds.

Bioinformatics 2005 Sep;21 Suppl 2:ii66-71

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.

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http://bioinformatics.oxfordjournals.org/content/21/suppl_2/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bti1111DOI Listing
September 2005

MuPlex: multi-objective multiplex PCR assay design.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W544-7

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gki377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160138PMC
July 2005

GEMS: a web server for biclustering analysis of expression data.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W596-9

Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gki469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160230PMC
July 2005

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

BMC Genomics 2005 Jul 25;6:102. Epub 2005 Jul 25.

Bioinformatics program, Boston University, MA 02215, USA.

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http://dx.doi.org/10.1186/1471-2164-6-102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1190169PMC
July 2005

Characterization of two new aminopeptidases in Escherichia coli.

J Bacteriol 2005 Jun;187(11):3671-7

Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA.

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http://dx.doi.org/10.1128/JB.187.11.3671-3677.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1112042PMC
June 2005

Gene expression module discovery using gibbs sampling.

Genome Inform 2004 ;15(1):239-48

Boston University Bioinformatics Program, Boston, MA 02215, USA.

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May 2005

Identification of genes with fast-evolving regions in microbial genomes.

Nucleic Acids Res 2004 2;32(21):6347-57. Epub 2004 Dec 2.

Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC535660PMC
December 2004

GC/AT-content spikes as genomic punctuation marks.

Proc Natl Acad Sci U S A 2004 Nov 17;101(48):16855-60. Epub 2004 Nov 17.

Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.0407821101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534751PMC
November 2004

Predicting protein function from protein/protein interaction data: a probabilistic approach.

Bioinformatics 2003 ;19 Suppl 1:i197-204

Bioinformatics Program and Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1026DOI Listing
October 2004

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 9;279(19):20167-77. Epub 2004 Feb 9.

Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1074/jbc.M309260200DOI Listing
May 2004

Segmentally variable genes: a new perspective on adaptation.

PLoS Biol 2004 Apr 13;2(4):E81. Epub 2004 Apr 13.

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA.

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http://dx.plos.org/10.1371/journal.pbio.0020081
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http://dx.doi.org/10.1371/journal.pbio.0020081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387263PMC
April 2004

Whole-genome annotation by using evidence integration in functional-linkage networks.

Proc Natl Acad Sci U S A 2004 Mar 23;101(9):2888-93. Epub 2004 Feb 23.

Bioinformatics Program, Boston University, 48 Cummington Street, Boston, MA 02215, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0307326101
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http://dx.doi.org/10.1073/pnas.0307326101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC365715PMC
March 2004

topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association.

Nucleic Acids Res 2004 Jan;32(Database issue):D520-2

Department of Bioengineering, University of Illinois at Chicago, M/C 063, 851 S. Morgan Street, Chicago, IL 60607, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkh104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308838PMC
January 2004

Extracting conserved gene expression motifs from gene expression data.

Pac Symp Biocomput 2003 :77-88

Bioinformatics Program, 48 Cummington St., Boston University, Boston, MA 02152, USA.

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August 2003

Identification of functional links between genes using phylogenetic profiles.

Bioinformatics 2003 Aug;19(12):1524-30

Department of Biomedical Engineering, USA Bioinformatics Graduate Program, Boston University, 44 Cummington St., Boston, MA, 02215, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg187DOI Listing
August 2003

RankGene: identification of diagnostic genes based on expression data.

Bioinformatics 2003 Aug;19(12):1578-9

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg179DOI Listing
August 2003

Human-mouse gene identification by comparative evidence integration and evolutionary analysis.

Genome Res 2003 Jun 12;13(6A):1190-202. Epub 2003 May 12.

Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1101/gr.703903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403647PMC
June 2003

On the normalization of RNA equilibrium free energy to the length of the sequence.

Nucleic Acids Res 2003 May;31(9):e49

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC154237PMC
http://dx.doi.org/10.1093/nar/gng049DOI Listing
May 2003

Structural location of disease-associated single-nucleotide polymorphisms.

J Mol Biol 2003 Apr;327(5):1021-30

Department of Bioengineering SEO, MC-063, University of Illinois at Chicago, Room 218, 851, S. Morgan Street, Chicago, IL 60607-7052, USA.

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http://dx.doi.org/10.1016/s0022-2836(03)00240-7DOI Listing
April 2003

A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.

Nucleic Acids Res 2002 Oct;30(20):e106

Center for Advanced Genomic Technology, Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137150PMC
http://dx.doi.org/10.1093/nar/gnf105DOI Listing
October 2002

Genomic functional annotation using co-evolution profiles of gene clusters.

Genome Biol 2002 Oct 10;3(11):RESEARCH0060. Epub 2002 Oct 10.

Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC133444PMC
http://dx.doi.org/10.1186/gb-2002-3-11-research0060DOI Listing
October 2002

Computational identification of operons in microbial genomes.

Genome Res 2002 Aug;12(8):1221-30

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1101/gr.200602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186635PMC
August 2002

A comparative genomic method for computational identification of prokaryotic translation initiation sites.

Nucleic Acids Res 2002 Jul;30(14):3181-91

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135744PMC
http://dx.doi.org/10.1093/nar/gkf423DOI Listing
July 2002

A Bayesian framework for combining gene predictions.

Bioinformatics 2002 Jan;18(1):19-27

Bioinformatics Program, Department of Bioengineering, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/bioinformatics/18.1.19DOI Listing
January 2002