Brad Chapman

Brad Chapman

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Brad Chapman

Brad Chapman

Publications by authors named "Brad Chapman"

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43Publications

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Bioconda: sustainable and comprehensive software distribution for the life sciences.

Nat Methods 2018 07;15(7):475-476

Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.

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http://dx.doi.org/10.1038/s41592-018-0046-7DOI Listing
July 2018

Silencing of the Drosophila ortholog of SOX5 leads to abnormal neuronal development and behavioral impairment.

Hum Mol Genet 2017 04;26(8):1472-1482

Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, MassGeneral Institute for Neurodegenerative Diseases, Charlestown, MA 02129, USA.

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https://academic.oup.com/hmg/article/26/8/1472/2982369
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http://dx.doi.org/10.1093/hmg/ddx051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075463PMC
April 2017

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PLoS Comput Biol 2016 Feb 25;12(2):e1004691. Epub 2016 Feb 25.

Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767331PMC
February 2016

The Bioinformatics Open Source Conference (BOSC) 2013.

Bioinformatics 2015 Jan 14;31(2):299-300. Epub 2014 Jul 14.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS 972R525, Berkeley, CA 94720, USA, Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK, Bioinformatics Core, Harvard School of Public Health, Boston, MA 02115, USA, The Computational Biology Institute, George Washington University, Washington, DC 20052, USA, Bioinformatics Department, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland and National Evolutionary Synthesis Center (NESCent), Durham, NC 27705, 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/btu413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287938PMC
January 2015

Clonal dynamics of native haematopoiesis.

Nature 2014 Oct 5;514(7522):322-7. Epub 2014 Oct 5.

1] Stem Cell Program, Children's Hospital, Boston, Massachusetts 02115, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA [3] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature13824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408613PMC
October 2014

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Nat Biotechnol 2014 Mar 16;32(3):246-51. Epub 2014 Feb 16.

Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.2835DOI Listing
March 2014

GEMINI: integrative exploration of genetic variation and genome annotations.

PLoS Comput Biol 2013 18;9(7):e1003153. Epub 2013 Jul 18.

Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1003153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715403PMC
February 2014

CloudMan as a platform for tool, data, and analysis distribution.

BMC Bioinformatics 2012 Nov 27;13:315. Epub 2012 Nov 27.

Center for Informatics and Computing (CIR), Ruđer Bošković Institute (RBI), Zagreb, Croatia.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-13-315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556322PMC
November 2012

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

BMC Bioinformatics 2012 Aug 21;13:209. Epub 2012 Aug 21.

Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602, USA.

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http://dx.doi.org/10.1186/1471-2105-13-209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468381PMC
August 2012

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

Curr Protoc Bioinformatics 2012 Jun;Chapter 11:Unit11.9

Center for Informatics and Computing, Ruder Bošković Institute (RBI), Zagreb, Croatia.

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http://dx.doi.org/10.1002/0471250953.bi1109s38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412548PMC
June 2012

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

BMC Bioinformatics 2012 Mar 19;13:42. Epub 2012 Mar 19.

J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1186/1471-2105-13-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372431PMC
March 2012

The genomic binding sites of a noncoding RNA.

Proc Natl Acad Sci U S A 2011 Dec 5;108(51):20497-502. Epub 2011 Dec 5.

Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.

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http://dx.doi.org/10.1073/pnas.1113536108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251105PMC
December 2011

Galaxy CloudMan: delivering cloud compute clusters.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S4. Epub 2010 Dec 21.

Department of Biology, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S12-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040530PMC
December 2010

Beneficial effects of oxygen addition and hybrid poplar phytoremediation of petroleum-contaminated soils.

J Environ Sci Health A Tox Hazard Subst Environ Eng 2010 Oct;45(12):1492-503

Department of Environmental Engineering, Institute of Environmental Studies and Research, Ain Shams University, Abbassia, Cairo, Egypt.

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http://www.tandfonline.com/doi/abs/10.1080/10934529.2010.506
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http://dx.doi.org/10.1080/10934529.2010.506095DOI Listing
October 2010

Pairwise selection assembly for sequence-independent construction of long-length DNA.

Nucleic Acids Res 2010 May 1;38(8):2594-602. Epub 2010 Mar 1.

Codon Devices, Inc., One Kendall Square, Building 300, Cambridge, MA 02139, 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/gkq123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860126PMC
May 2010

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon.

Trends Genet 2006 Nov 18;22(11):597-602. Epub 2006 Sep 18.

Plant Genome Mapping Laboratory and Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S016895250600296
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http://dx.doi.org/10.1016/j.tig.2006.09.003DOI Listing
November 2006

Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.

Proc Natl Acad Sci U S A 2006 Feb 8;103(8):2730-5. Epub 2006 Feb 8.

Plant Genome Mapping Laboratory and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0507782103
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http://dx.doi.org/10.1073/pnas.0507782103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413778PMC
February 2006

A comparative phylogenetic approach for dating whole genome duplication events.

Bioinformatics 2004 Jan;20(2):180-5

Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth022DOI Listing
January 2004

Structure and evolution of cereal genomes.

Curr Opin Genet Dev 2003 Dec;13(6):644-50

Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1016/j.gde.2003.10.002DOI Listing
December 2003

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice ( Oryza sativa L.).

Theor Appl Genet 2003 Jun 3;107(1):62-73. Epub 2003 Apr 3.

Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA.

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http://link.springer.com/10.1007/s00122-003-1231-2
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http://dx.doi.org/10.1007/s00122-003-1231-2DOI Listing
June 2003

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.

Nature 2003 Mar;422(6930):433-8

Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1038/nature01521DOI Listing
March 2003