Chad Nusbaum

Chad Nusbaum

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Chad Nusbaum

Publications by authors named "Chad Nusbaum"

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Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq.

Epigenetics Chromatin 2016 4;9:49. Epub 2016 Nov 4.

Broad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ; Department of Medicine, University of California San Diego, La Jolla, CA 92093 USA.

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http://epigeneticsandchromatin.biomedcentral.com/articles/10
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http://dx.doi.org/10.1186/s13072-016-0100-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097419PMC
January 2018

Genome Sequence of Spizellomyces punctatus.

Genome Announc 2016 Aug 18;4(4). Epub 2016 Aug 18.

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

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http://dx.doi.org/10.1128/genomeA.00849-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991717PMC
August 2016

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

PLoS One 2014 9;9(5):e96094. Epub 2014 May 9.

Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096094PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015934PMC
October 2015

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Cell 2015 Jun;161(7):1516-26

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503805PMC
June 2015

Regulated aggregative multicellularity in a close unicellular relative of metazoa.

Elife 2013 Dec 24;2:e01287. Epub 2013 Dec 24.

Department of Functional Genomics and Evolution, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.

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http://dx.doi.org/10.7554/eLife.01287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870316PMC
December 2013

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

BMC Genomics 2012 Dec 27;13:734. Epub 2012 Dec 27.

Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/1471-2164-13-734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543199PMC
December 2012

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.

Proc Natl Acad Sci U S A 2012 Dec;109(52):E3629-30

Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535640PMC
http://dx.doi.org/10.1073/pnas.1209419110DOI Listing
December 2012

Pacific biosciences sequencing technology for genotyping and variation discovery in human data.

BMC Genomics 2012 Aug 5;13:375. Epub 2012 Aug 5.

Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1186/1471-2164-13-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443046PMC
August 2012

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Genome Biol 2011 21;12(2):R18. Epub 2011 Feb 21.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-2-r18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188800PMC
February 2012

High-resolution description of antibody heavy-chain repertoires in humans.

PLoS One 2011 4;6(8):e22365. Epub 2011 Aug 4.

Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022365PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150326PMC
December 2011

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

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

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate.

J Bacteriol 2011 Mar 23;193(6):1485-6. Epub 2010 Dec 23.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA.

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http://jb.asm.org/cgi/doi/10.1128/JB.01421-10
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http://dx.doi.org/10.1128/JB.01421-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067637PMC
March 2011

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Nat Methods 2010 Sep 15;7(9):709-15. Epub 2010 Aug 15.

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

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http://dx.doi.org/10.1038/nmeth.1491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005310PMC
September 2010

Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota).

New Phytol 2010 Jul 6;187(2):494-507. Epub 2010 May 6.

Institute of Arctic Biology, 311 Irving I Building, 902 N Koyukuk Drive, PO Box 757000, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA.

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http://dx.doi.org/10.1111/j.1469-8137.2010.03283.xDOI Listing
July 2010

A catalog of reference genomes from the human microbiome.

Science 2010 May;328(5981):994-9

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http://dx.doi.org/10.1126/science.1183605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224PMC
May 2010

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Genome Biol 2009 16;10(10):R115. Epub 2009 Oct 16.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1186/gb-2009-10-10-r115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784330PMC
January 2010

A cellular memory of developmental history generates phenotypic diversity in C. elegans.

Curr Biol 2010 Jan 14;20(2):149-55. Epub 2010 Jan 14.

Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA.

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http://dx.doi.org/10.1016/j.cub.2009.11.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990539PMC
January 2010

Closing gaps in the human genome using sequencing by synthesis.

Genome Biol 2009 2;10(6):R60. Epub 2009 Jun 2.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/gb-2009-10-6-r60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718494PMC
September 2009

DNA sequence analysis of the conserved region around the SOD1 gene locus in recessively inherited ALS.

Neurosci Lett 2009 Sep 9;463(1):64-9. Epub 2009 Jul 9.

Massachusetts General Hospital, 114 16th Street, Navy Yard, Charlestown, MA 02129, USA.

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http://dx.doi.org/10.1016/j.neulet.2009.07.010DOI Listing
September 2009

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Authors:
Brian J Haas Sophien Kamoun Michael C Zody Rays H Y Jiang Robert E Handsaker Liliana M Cano Manfred Grabherr Chinnappa D Kodira Sylvain Raffaele Trudy Torto-Alalibo Tolga O Bozkurt Audrey M V Ah-Fong Lucia Alvarado Vicky L Anderson Miles R Armstrong Anna Avrova Laura Baxter Jim Beynon Petra C Boevink Stephanie R Bollmann Jorunn I B Bos Vincent Bulone Guohong Cai Cahid Cakir James C Carrington Megan Chawner Lucio Conti Stefano Costanzo Richard Ewan Noah Fahlgren Michael A Fischbach Johanna Fugelstad Eleanor M Gilroy Sante Gnerre Pamela J Green Laura J Grenville-Briggs John Griffith Niklaus J Grünwald Karolyn Horn Neil R Horner Chia-Hui Hu Edgar Huitema Dong-Hoon Jeong Alexandra M E Jones Jonathan D G Jones Richard W Jones Elinor K Karlsson Sridhara G Kunjeti Kurt Lamour Zhenyu Liu Lijun Ma Daniel Maclean Marcus C Chibucos Hayes McDonald Jessica McWalters Harold J G Meijer William Morgan Paul F Morris Carol A Munro Keith O'Neill Manuel Ospina-Giraldo Andrés Pinzón Leighton Pritchard Bernard Ramsahoye Qinghu Ren Silvia Restrepo Sourav Roy Ari Sadanandom Alon Savidor Sebastian Schornack David C Schwartz Ulrike D Schumann Ben Schwessinger Lauren Seyer Ted Sharpe Cristina Silvar Jing Song David J Studholme Sean Sykes Marco Thines Peter J I van de Vondervoort Vipaporn Phuntumart Stephan Wawra Rob Weide Joe Win Carolyn Young Shiguo Zhou William Fry Blake C Meyers Pieter van West Jean Ristaino Francine Govers Paul R J Birch Stephen C Whisson Howard S Judelson Chad Nusbaum

Nature 2009 Sep 9;461(7262):393-8. Epub 2009 Sep 9.

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

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http://dx.doi.org/10.1038/nature08358DOI Listing
September 2009

High-resolution profiling and discovery of planarian small RNAs.

Proc Natl Acad Sci U S A 2009 Jul 29;106(28):11546-51. Epub 2009 Jun 29.

Max Delbrück Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.

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http://dx.doi.org/10.1073/pnas.0905222106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703670PMC
July 2009

Model-based analysis of ChIP-Seq (MACS).

Genome Biol 2008 17;9(9):R137. Epub 2008 Sep 17.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2008-9-9-r137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592715PMC
January 2009

High-resolution mapping of copy-number alterations with massively parallel sequencing.

Nat Methods 2009 Jan 30;6(1):99-103. Epub 2008 Nov 30.

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

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http://dx.doi.org/10.1038/nmeth.1276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630795PMC
January 2009

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.

Nat Methods 2009 Jan 14;6(1):67-9. Epub 2008 Dec 14.

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

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http://dx.doi.org/10.1038/nmeth.1286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613166PMC
January 2009

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.

Mol Ecol Resour 2008 Jul;8(4):742-52

Institute of Arctic Biology, 311 Irving I Building, University of Alaska, Fairbanks, AK 99775, USA, Broad Institute, Massachusetts Institute of Technology, 320 Charles Street, Cambridge, MA 02141, USA.

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http://www.lter.uaf.edu/dev2009/pdf/1311_Taylor_Booth_2008.p
Web Search
http://doi.wiley.com/10.1111/j.1755-0998.2008.02094.x
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http://dx.doi.org/10.1111/j.1755-0998.2008.02094.xDOI Listing
July 2008

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Genome Res 2008 May 13;18(5):810-20. Epub 2008 Mar 13.

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

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http://dx.doi.org/10.1101/gr.7337908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336810PMC
May 2008

Genome sequence of Aedes aegypti, a major arbovirus vector.

Science 2007 Jun 17;316(5832):1718-23. Epub 2007 May 17.

Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1138878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868357PMC
June 2007

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.

Nature 2006 Nov;444(7115):97-101

Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, D-35043 Marburg, Germany.

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http://dx.doi.org/10.1038/nature05248DOI Listing
November 2006

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

Genome Res 2006 Oct 5;16(10):1299-309. Epub 2006 Sep 5.

Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-0103, USA.

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http://dx.doi.org/10.1101/gr.5571506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581439PMC
October 2006

Structure and architecture of the maize genome.

Plant Physiol 2005 Dec;139(4):1612-24

Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D-85764 Neuherberg, Germany.

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http://dx.doi.org/10.1104/pp.105.068718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310546PMC
December 2005

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002