Pablo Tamayo

Pablo Tamayo

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Pablo Tamayo

Publications by authors named "Pablo Tamayo"

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The multikinase inhibitor RXDX-105 is effective against neuroblastoma and .

Oncotarget 2019 Oct 29;10(59):6323-6333. Epub 2019 Oct 29.

Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.18632/oncotarget.27259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824878PMC
October 2019

Cyclin E Overexpression in Human Mammary Epithelial Cells Promotes Epithelial Cancer-Specific Copy Number Alterations.

iScience 2019 Sep 27;19:850-859. Epub 2019 Aug 27.

Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.08.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739637PMC
September 2019

Modelling bistable tumour population dynamics to design effective treatment strategies.

J Theor Biol 2019 Aug 9;474:88-102. Epub 2019 May 9.

Institute of Statistical Science, Academia Sinica, 128 Academia Rd, Sec 2, Nankang, 11529, Taipei, Taiwan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193019
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http://dx.doi.org/10.1016/j.jtbi.2019.05.005DOI Listing
August 2019

Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding.

Cell Syst 2018 12 5;7(6):656-666.e4. Epub 2018 Dec 5.

Department of Bioengineering, University of California, San Diego, San Diego, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311449PMC
December 2018

Comprehensive Genomic Profiling Reveals Diverse but Actionable Molecular Portfolios across Hematologic Malignancies: Implications for Next Generation Clinical Trials.

Cancers (Basel) 2018 Dec 21;11(1). Epub 2018 Dec 21.

Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.3390/cancers11010011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356731PMC
December 2018

APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy.

Oncoimmunology 2019 24;8(3):1550341. Epub 2018 Dec 24.

Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA.

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http://dx.doi.org/10.1080/2162402X.2018.1550341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350681PMC
December 2018

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Cell Syst 2018 Apr 28;6(4):484-495.e5. Epub 2018 Mar 28.

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cels.2018.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920724PMC
April 2018

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

Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers.

Cell Syst 2016 09;3(3):302-316.e4

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455996PMC
September 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

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

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

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

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

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

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

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

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

SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer.

Cancer Cell 2013 Dec;24(6):738-50

Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2013.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910168PMC
December 2013

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

Integrative functional genomics identifies RINT1 as a novel GBM oncogene.

Neuro Oncol 2012 Nov 16;14(11):1325-31. Epub 2012 Oct 16.

Department of Medical Oncology, Dana-Farber Cancer Institute, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/neuonc/nos246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480269PMC
November 2012

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

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

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

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

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

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

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

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

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

GeneCruiser: a web service for the annotation of microarray data.

Bioinformatics 2005 Sep 19;21(18):3681-2. Epub 2005 Jul 19.

Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti587DOI Listing
September 2005

Combining gene expression profiles and clinical parameters for risk stratification in medulloblastomas.

J Clin Oncol 2004 Mar 17;22(6):994-8. Epub 2004 Feb 17.

Division of Neuroscience, Department of Neurology, Department of Medicine, Children's Hospital, 300 Longwood Ave, Boston MA 02115, USA.

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http://dx.doi.org/10.1200/JCO.2004.03.036DOI Listing
March 2004

Metagenes and molecular pattern discovery using matrix factorization.

Proc Natl Acad Sci U S A 2004 Mar 11;101(12):4164-9. Epub 2004 Mar 11.

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1073/pnas.0308531101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384712PMC
March 2004

Estimating dataset size requirements for classifying DNA microarray data.

J Comput Biol 2003 ;10(2):119-42

Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1089/106652703321825928DOI Listing
July 2003

A strategy for oligonucleotide microarray probe reduction.

Genome Biol 2002 25;3(12):RESEARCH0073. Epub 2002 Nov 25.

Center for Genome Research, Whitehead Institute/Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151175PMC
http://dx.doi.org/10.1186/gb-2002-3-12-research0073DOI Listing
June 2003

Gene expression-based classification of malignant gliomas correlates better with survival than histological classification.

Cancer Res 2003 Apr;63(7):1602-7

Department of Pathology and Neurosurgical Service, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.

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April 2003