Robert Gentleman

Robert Gentleman

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Robert Gentleman

Publications by authors named "Robert Gentleman"

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Addressing the accuracy of direct-to-consumer genetic testing.

Genet Med 2019 03 29;21(3):758-759. Epub 2018 Jun 29.

23andMe, Mountain View California, USA.

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http://dx.doi.org/10.1038/s41436-018-0094-5DOI Listing
March 2019

Prediction and Quantification of Splice Events from RNA-Seq Data.

PLoS One 2016 24;11(5):e0156132. Epub 2016 May 24.

Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156132PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878813PMC
July 2017

Complex regulation of ADAR-mediated RNA-editing across tissues.

BMC Genomics 2016 Jan 15;17:61. Epub 2016 Jan 15.

Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.

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http://dx.doi.org/10.1186/s12864-015-2291-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714477PMC
January 2016

Discriminative motif analysis of high-throughput dataset.

Bioinformatics 2014 Mar 25;30(6):775-83. Epub 2013 Oct 25.

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Pediatrics, School of Medicine, Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Computer Science and Engineering, Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957073PMC
March 2014

Software for computing and annotating genomic ranges.

PLoS Comput Biol 2013 8;9(8):e1003118. Epub 2013 Aug 8.

Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738458PMC
February 2014

gCMAP: user-friendly connectivity mapping with R.

Bioinformatics 2014 Jan 15;30(1):127-8. Epub 2013 Oct 15.

Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt592DOI Listing
January 2014

Genetic and epigenetic determinants of neurogenesis and myogenesis.

Dev Cell 2012 Apr 22;22(4):721-35. Epub 2012 Mar 22.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/j.devcel.2012.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331915PMC
April 2012

Analyzing biological data using R: methods for graphs and networks.

Methods Mol Biol 2012 ;804:343-73

IRISA, Equipe Symbiose, Université de Rennes I, Rennes, France.

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http://dx.doi.org/10.1007/978-1-61779-361-5_19DOI Listing
March 2012

Querying genomic databases: refining the connectivity map.

Stat Appl Genet Mol Biol 2012 Jan 6;11(2). Epub 2012 Jan 6.

University of California-San Francisco, CA, USA.

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http://dx.doi.org/10.2202/1544-6115.1715DOI Listing
January 2012

iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor.

Adv Bioinformatics 2009 12:103839. Epub 2009 Nov 12.

Program in Computational Biology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N M2-B876, P.O. Box 19024, Seattle, WA 98109-1024, USA.

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http://dx.doi.org/10.1155/2009/103839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798115PMC
July 2011

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages.

EMBO J 2011 Feb 21;30(3):494-509. Epub 2010 Dec 21.

The Sprott Center for Stem Cell Research, Department of Regenerative Medicine, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1038/emboj.2010.342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034015PMC
February 2011

Independent filtering increases detection power for high-throughput experiments.

Proc Natl Acad Sci U S A 2010 May 11;107(21):9546-51. Epub 2010 May 11.

European Bioinformatics Institute, Cambridge CB10 1SD, UK.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0914005107
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http://dx.doi.org/10.1073/pnas.0914005107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906865PMC
May 2010

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.

Bioinformatics 2009 Oct 3;25(19):2607-8. Epub 2009 Aug 3.

Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752612PMC
October 2009

Knowledge based identification of essential signaling from genome-scale siRNA experiments.

BMC Syst Biol 2009 Aug 5;3:80. Epub 2009 Aug 5.

Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co,, Inc, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1186/1752-0509-3-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731733PMC
August 2009

rtracklayer: an R package for interfacing with genome browsers.

Bioinformatics 2009 Jul 25;25(14):1841-2. Epub 2009 May 25.

Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, 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/btp328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705236PMC
July 2009

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.

Bioinformatics 2009 Jun 5;25(11):1447-8. Epub 2009 Apr 5.

Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682516PMC
June 2009

flowCore: a Bioconductor package for high throughput flow cytometry.

BMC Bioinformatics 2009 Apr 9;10:106. Epub 2009 Apr 9.

Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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http://www.biomedcentral.com/1471-2105/10/106
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http://dx.doi.org/10.1186/1471-2105-10-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684747PMC
April 2009

DATABASE: A new forum for biological databases and curation.

Database (Oxford) 2009 16;2009:bap002. Epub 2009 Mar 16.

Potomac, MD, USA, Seattle, WA, USA, Leipzig, Germany and Toronto, ON, Canada.

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http://dx.doi.org/10.1093/database/bap002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790300PMC
March 2009

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.

Bioinformatics 2009 Feb 23;25(3):415-6. Epub 2008 Dec 23.

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639074PMC
February 2009

Modeling synthetic lethality.

Genome Biol 2008 12;9(9):R135. Epub 2008 Sep 12.

Division of Public Health Sciences, Fred Hutchinson Cancer Center Research, Program in Computational Biology, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1186/gb-2008-9-9-r135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592713PMC
January 2009

Gene set enrichment analysis using linear models and diagnostics.

Bioinformatics 2008 Nov 11;24(22):2586-91. Epub 2008 Sep 11.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579710PMC
November 2008

Coverage and error models of protein-protein interaction data by directed graph analysis.

Genome Biol 2007 ;8(9):R186

EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2007-8-9-r186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375024PMC
May 2008

Making the most of high-throughput protein-interaction data.

Genome Biol 2007 ;8(10):112

Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1186/gb-2007-8-10-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246275PMC
May 2008

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.

Bioinformatics 2008 Apr 7;24(8):1100-1. Epub 2007 Nov 7.

EBI-EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm518DOI Listing
April 2008

Estimating node degree in bait-prey graphs.

Bioinformatics 2008 Jan 19;24(2):218-24. Epub 2007 Nov 19.

Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm565DOI Listing
January 2008

Graphs in molecular biology.

BMC Bioinformatics 2007 Sep 27;8 Suppl 6:S8. Epub 2007 Sep 27.

European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2105-8-S6-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995545PMC
September 2007

Extensions to gene set enrichment.

Bioinformatics 2007 Feb 24;23(3):306-13. Epub 2006 Nov 24.

Computational Biology, 1100 Fairview Avenue. N. M2-B876, PO Box 19024, Seattle, WA 98109-1024, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl599DOI Listing
February 2007

GGtools: analysis of genetics of gene expression in bioconductor.

Bioinformatics 2007 Feb 8;23(4):522-3. Epub 2006 Dec 8.

Channing Laboratory, Brigham and Women's Hospital, 75 Francis Street, Boston 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl628DOI Listing
February 2007

Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery.

J Proteome Res 2006 Nov;5(11):2947-55

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

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http://pubs.acs.org/doi/abs/10.1021/pr060099u
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http://dx.doi.org/10.1021/pr060099uDOI Listing
November 2006

Making sense of high-throughput protein-protein interaction data.

Stat Appl Genet Mol Biol 2004 3;3:Article39. Epub 2005 Jan 3.

Northwestern University.

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http://dx.doi.org/10.2202/1544-6115.1107DOI Listing
May 2006

Reproducible research: a bioinformatics case study.

Authors:
Robert Gentleman

Stat Appl Genet Mol Biol 2005 11;4:Article2. Epub 2005 Jan 11.

Harvard University, USA.

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http://dx.doi.org/10.2202/1544-6115.1034DOI Listing
May 2006

Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation.

Clin Cancer Res 2005 Oct;11(20):7209-19

Department of Medical Oncology and Biostatistical Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-04-2165DOI Listing
October 2005

Local modeling of global interactome networks.

Bioinformatics 2005 Sep 5;21(17):3548-57. Epub 2005 Jul 5.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti567DOI Listing
September 2005

Association of valproate-induced teratogenesis with histone deacetylase inhibition in vivo.

FASEB J 2005 Jul 18;19(9):1166-8. Epub 2005 May 18.

Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1096/fj.04-3425fjeDOI Listing
July 2005

Bayesian error-in-variable survival model for the analysis of GeneChip arrays.

Biometrics 2005 Jun;61(2):488-97

Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6021, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2005.00313.xDOI Listing
June 2005

Wavelet thresholding with bayesian false discovery rate control.

Biometrics 2005 Mar;61(1):25-35

Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1111/j.0006-341X.2005.031102.xDOI Listing
March 2005

Network structures and algorithms in Bioconductor.

Bioinformatics 2005 Jan 5;21(1):135-6. Epub 2004 Aug 5.

Channing Laboratory, Brigham and Women's Hospital 75 Francis Street, 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/bth458DOI Listing
January 2005

A graph-theoretic approach to testing associations between disparate sources of functional genomics data.

Bioinformatics 2004 Dec 15;20(18):3353-62. Epub 2004 Jul 15.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth405DOI Listing
December 2004

Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.

Nucleic Acids Res 2004 Aug 25;32(15):e121. Epub 2004 Aug 25.

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/nar/gnh120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC516078PMC
August 2004

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.

Bioinformatics 2004 Jul 26;20(10):1651-2. Epub 2004 Feb 26.

Department of Molecular Genome Analysis, German Cancer Research Center, INF 580, Heidelberg, 69120, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth133DOI Listing
July 2004

Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.

Blood 2004 Apr 18;103(7):2771-8. Epub 2003 Dec 18.

Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1182/blood-2003-09-3243DOI Listing
April 2004

The graft response to transplantation: a gene expression profile analysis.

Physiol Genomics 2003 Sep 29;15(1):52-64. Epub 2003 Sep 29.

Laboratory of Molecular Immunology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00139.2002DOI Listing
September 2003

Open source software for the analysis of microarray data.

Biotechniques 2003 Mar;Suppl:45-51

University of California, Berkeley, CA, USA.

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March 2003

An extensible application for assembling annotation for genomic data.

Bioinformatics 2003 Jan;19(1):155-6

Department of Biostatistical Science, Dana-Farber Cancer Institute, Harvard School of Public Health, and Channing Laboratory, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/19.1.155DOI Listing
January 2003