Publications by authors named "Jill Mesirov"

100Publications

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays.

F1000Res 2018 5;7. Epub 2018 Dec 5.

Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.12688/f1000research.16338.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498745PMC
September 2019

Precision Medicine: Improving health through high-resolution analysis of personal data.

Pac Symp Biocomput 2019 ;24:220-223

University of California, Berkeley, USA†Supported by U41 HG007346 and U19 HD077627.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526370PMC
January 2019

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.

Cell Syst 2018 Feb 7;6(2):256-258.e1. Epub 2018 Feb 7.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047755PMC
February 2018

Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2.

Cell Rep 2017 Dec;21(10):2688-2695

Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.11.018DOI Listing
December 2017

Variant Review with the Integrative Genomics Viewer.

Cancer Res 2017 11;77(21):e31-e34

School of Medicine, University of California San Diego, La Jolla, California.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678989PMC
November 2017

The GenePattern Notebook Environment.

Cell Syst 2017 08 16;5(2):149-151.e1. Epub 2017 Aug 16.

School of Medicine, University of California, San Diego, La Jolla, CA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1016/j.cels.2017.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572818PMC
August 2017

Leveraging premalignant biology for immune-based cancer prevention.

Proc Natl Acad Sci U S A 2016 09 16;113(39):10750-8. Epub 2016 Sep 16.

Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047191PMC
http://dx.doi.org/10.1073/pnas.1608077113DOI Listing
September 2016

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

Cell Syst 2016 07;3(1):99-101

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596920PMC
July 2016

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels.

Cell Rep 2016 07 30;16(3):672-83. Epub 2016 Jun 30.

Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics and Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972030PMC
July 2016

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Immunity 2016 Jan 12;44(1):194-206. Epub 2016 Jan 12.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613150053
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http://dx.doi.org/10.1016/j.immuni.2015.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330663PMC
January 2016

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Cell Syst 2015 Dec;1(6):417-425

Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cels.2015.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707969PMC
December 2015

Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation.

Neuron 2016 Jan 17;89(1):100-12. Epub 2015 Dec 17.

Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2015.11.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707072PMC
January 2016

Constellation Map: Downstream visualization and interpretation of gene set enrichment results.

F1000Res 2015 24;4:167. Epub 2015 Jun 24.

Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.12688/f1000research.6644.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648224PMC
November 2015

A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation.

PLoS One 2015 19;10(3):e0116096. Epub 2015 Mar 19.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, United States of America; Diabetes Unit, Medical Services, Massachusetts General Hospital, Boston, MA, 02114, United States of America, 617-726-6909; Department of Medicine, Harvard Medical School, Boston, MA, 02115, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116096PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366019PMC
April 2016

Quantitative visualization of alternative exon expression from RNA-seq data.

Bioinformatics 2015 Jul 22;31(14):2400-2. Epub 2015 Jan 22.

Department of Biology, MIT, Cambridge, MA, Department of Biological Engineering, MIT, Cambridge, MA.

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http://dx.doi.org/10.1093/bioinformatics/btv034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542614PMC
July 2015

Plasmodium falciparum gene expression measured directly from tissue during human infection.

Genome Med 2014 29;6(11):110. Epub 2014 Nov 29.

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA USA ; Broad Institute, Cambridge, MA USA ; University of Malawi College of Medicine, Blantyre, Malawi ; The Blantyre Malaria Project, Blantyre, Malawi ; Brigham and Women's Hospital, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-014-0110-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269068PMC
December 2014

Cytoscape: the network visualization tool for GenomeSpace workflows.

F1000Res 2014 1;3:151. Epub 2014 Jul 1.

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, USA.

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http://f1000research.com/articles/3-151/v2
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133763PMC
http://dx.doi.org/10.12688/f1000research.4492.2DOI Listing
October 2014

Molecular adaptations of striatal spiny projection neurons during levodopa-induced dyskinesia.

Proc Natl Acad Sci U S A 2014 Mar 5;111(12):4578-83. Epub 2014 Mar 5.

Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065.

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http://dx.doi.org/10.1073/pnas.1401819111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970487PMC
March 2014

Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit.

Cancer Discov 2014 Apr 20;4(4):452-65. Epub 2014 Jan 20.

Departments of 1Medical Oncology and 2Cancer Biology, Dana-Farber Cancer Institute; 3Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston; 4Broad Institute of Harvard and MIT, Cambridge; 5MGH Cancer Center, 6Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, Massachusetts; and 7Department of Surgery, Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980023PMC
April 2014

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies.

Sci Data 2014 30;1:140035. Epub 2014 Sep 30.

Broad Institute of Harvard and MIT, 7 Cambridge Center , Cambridge, Massachusetts 02142, USA ; Department of Medical, Dana-Farber Cancer Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, USA ; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, USA ; Departments of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/sdata201435
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http://dx.doi.org/10.1038/sdata.2014.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432652PMC
February 2016

Compression of structured high-throughput sequencing data.

PLoS One 2013 18;8(11):e79871. Epub 2013 Nov 18.

The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, New York, United States of America ; Department of Physiology and Biophysics, The Weill Cornell Medical College, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079871PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832420PMC
July 2014

Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration.

BMC Med 2013 Oct 17;11:220. Epub 2013 Oct 17.

Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 5W130, MSC 9735, 9609 Medical Center Drive, Bethesda, MD 20892-9735, USA.

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http://dx.doi.org/10.1186/1741-7015-11-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852338PMC
October 2013

Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response.

Eur J Immunol 2014 Jan 29;44(1):285-95. Epub 2013 Nov 29.

Broad Institute of MIT and Harvard, Cambridge, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA.

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http://dx.doi.org/10.1002/eji.201343657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973429PMC
January 2014

Integrative radiogenomic profiling of squamous cell lung cancer.

Cancer Res 2013 Oct 26;73(20):6289-98. Epub 2013 Aug 26.

Authors' Affiliations: Harvard Radiation Oncology Program; Division of Medical Sciences, Harvard University; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School; Department of Medical Oncology, Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute; Department of Pathology, Brigham and Women's Hospital, Boston; Chemical Biology Program; Howard Hughes Medical Institute, The Broad Institute of MIT and Harvard; Novartis Institute for Biomedical Research; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; and Department of Medicine, Baylor College of Medicine, Houston, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-1616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856255PMC
October 2013

Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers.

Cancer Discov 2013 Sep 13;3(9):1044-57. Epub 2013 Jun 13.

1Departments of Medical Oncology and 2Cancer Biology; 3Center for Cancer Genome Discovery, Dana-Farber Cancer Institute;4Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; 5Broad Institute of Harvard and MIT, Cambridge, Massachusetts; and 6Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina.

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http://dx.doi.org/10.1158/2159-8290.CD-12-0592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770815PMC
September 2013

The limitations of simple gene set enrichment analysis assuming gene independence.

Stat Methods Med Res 2016 Feb 14;25(1):472-87. Epub 2012 Oct 14.

The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA Boston University Bioinformatics Program, Boston University, Boston, MA, USA.

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http://dx.doi.org/10.1177/0962280212460441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758419PMC
February 2016

An RNA profile identifies two subsets of multiple sclerosis patients differing in disease activity.

Sci Transl Med 2012 Sep;4(153):153ra131

Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA.

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http://stm.sciencemag.org/cgi/doi/10.1126/scitranslmed.30041
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http://dx.doi.org/10.1126/scitranslmed.3004186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753678PMC
September 2012

AraPath: a knowledgebase for pathway analysis in Arabidopsis.

Bioinformatics 2012 Sep 3;28(17):2291-2. Epub 2012 Jul 3.

Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426845PMC
September 2012

Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome.

J Hematol Oncol 2012 May 6;5:20. Epub 2012 May 6.

Department of Medicine, Division of Hematology and Oncology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY 10032, USA.

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http://dx.doi.org/10.1186/1756-8722-5-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407785PMC
May 2012

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Brief Bioinform 2013 Mar 19;14(2):178-92. Epub 2012 Apr 19.

Broad Institute, 7 Cambridge Center 301B-5057, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bib/bbs017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603213PMC
March 2013

Molecular signatures database (MSigDB) 3.0.

Bioinformatics 2011 Jun 5;27(12):1739-40. Epub 2011 May 5.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106198PMC
June 2011

Computer science. Accessible reproducible research.

Authors:
Jill P Mesirov

Science 2010 Jan;327(5964):415-6

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.1179653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878063PMC
January 2010

Prediction of high-responding peptides for targeted protein assays by mass spectrometry.

Nat Biotechnol 2009 Feb 25;27(2):190-8. Epub 2009 Jan 25.

Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nbt.1524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753399PMC
February 2009

ISMB 2008 Toronto.

PLoS Comput Biol 2008 Jun 27;4(6):e1000094. Epub 2008 Jun 27.

International Society for Computational Biology, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427177PMC
June 2008

Using GenePattern for gene expression analysis.

Curr Protoc Bioinformatics 2008 Jun;Chapter 7:Unit 7.12

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://doi.wiley.com/10.1002/0471250953.bi0712s22
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http://dx.doi.org/10.1002/0471250953.bi0712s22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893799PMC
June 2008

Breast cancer stratification from analysis of micro-array data of micro-dissected specimens.

Genome Inform 2007 ;18:130-40

The Broad Institute of MIT and Harvard, Cambridge MA 02142, USA.

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August 2008

Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells.

Cancer Res 2008 Jun;68(11):4331-9

Department of Medicine, The Cancer Institute of New Jersey, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey 08903, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-08-0943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725025PMC
June 2008

Subclass mapping: identifying common subtypes in independent disease data sets.

PLoS One 2007 Nov 21;2(11):e1195. Epub 2007 Nov 21.

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001195PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2065909PMC
November 2007

Comment on "The consensus coding sequences of human breast and colorectal cancers".

Science 2007 Sep;317(5844):1500

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.1138764DOI Listing
September 2007

Portraits of breast cancer progression.

BMC Bioinformatics 2007 Aug 6;8:291. Epub 2007 Aug 6.

Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1186/1471-2105-8-291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1978212PMC
August 2007

GSEA-P: a desktop application for Gene Set Enrichment Analysis.

Bioinformatics 2007 Dec 20;23(23):3251-3. Epub 2007 Jul 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm369DOI Listing
December 2007

Metagene projection for cross-platform, cross-species characterization of global transcriptional states.

Proc Natl Acad Sci U S A 2007 Apr 27;104(14):5959-64. Epub 2007 Mar 27.

Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1073/pnas.0701068104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838404PMC
April 2007

Combo: a whole genome comparative browser.

Bioinformatics 2006 Jul 18;22(14):1782-3. Epub 2006 May 18.

The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl193DOI Listing
July 2006

Comparative gene marker selection suite.

Bioinformatics 2006 Aug 18;22(15):1924-5. Epub 2006 May 18.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl196DOI Listing
August 2006

GenePattern 2.0.

Nat Genet 2006 May;38(5):500-1

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http://dx.doi.org/10.1038/ng0506-500DOI Listing
May 2006

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Proc Natl Acad Sci U S A 2005 Oct 30;102(43):15545-50. Epub 2005 Sep 30.

Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1073/pnas.0506580102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239896PMC
October 2005