Brian J Haas

Brian J Haas

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Brian J Haas

Brian J Haas

Publications by authors named "Brian J Haas"

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Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution.

Nat Commun 2018 12 4;9(1):5153. Epub 2018 Dec 4.

Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-018-07604-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279788PMC
December 2018

Advances in Decoding Axolotl Limb Regeneration.

Trends Genet 2017 08 22;33(8):553-565. Epub 2017 Jun 22.

Harvard Medical School, Harvard Stem Cell Institute, and Brigham and Women's Hospital Department of Orthopedic Surgery, 60 Fenwood Road, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2017.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534018PMC
August 2017

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress.

Mol Ecol 2017 Jun 4;26(11):2978-2992. Epub 2017 Apr 4.

Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization (CSIRO), Floreat, 6014, Australia.

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http://dx.doi.org/10.1111/mec.14087DOI Listing
June 2017

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.

Genome Res 2015 Dec 1;25(12):1860-72. Epub 2015 Oct 1.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA.

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http://dx.doi.org/10.1101/gr.192237.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665007PMC
December 2015

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation.

Mol Cell 2015 Dec;60(5):816-827

Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765150090
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http://dx.doi.org/10.1016/j.molcel.2015.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720255PMC
December 2015

Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.

G3 (Bethesda) 2015 Sep 28;5(12):2539-45. Epub 2015 Sep 28.

Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27606 Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27606

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http://dx.doi.org/10.1534/g3.115.020057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683626PMC
September 2015

A universal genomic coordinate translator for comparative genomics.

BMC Bioinformatics 2014 Jun 30;15:227. Epub 2014 Jun 30.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1186/1471-2105-15-227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086997PMC
June 2014

Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.

Bioinformatics 2013 Oct 31;29(19):2387-94. Epub 2013 Jul 31.

Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA and Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777111PMC
October 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

'Next-generation' sequencing becomes 'now-generation'.

Genome Biol 2011 18;12(3):303. Epub 2011 Mar 18.

Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129669PMC
January 2012

Approaches to Fungal Genome Annotation.

Mycology 2011 Oct;2(3):118-141

Genome Sequencing and Analysis Program, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, U.S.A.

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http://dx.doi.org/10.1080/21501203.2011.606851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207268PMC
October 2011

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Proc Natl Acad Sci U S A 2010 Jul 21;107(27):12168-73. Epub 2010 Jun 21.

J Craig Venter Institute, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1073/pnas.1003379107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901460PMC
July 2010

Advancing RNA-Seq analysis.

Nat Biotechnol 2010 May;28(5):421-3

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http://www.nature.com/articles/nbt0510-421
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http://dx.doi.org/10.1038/nbt0510-421DOI Listing
May 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

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

DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.

Nat Struct Mol Biol 2008 May 13;15(5):515-22. Epub 2008 Apr 13.

Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4 La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nsmb.1414DOI Listing
May 2008

Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.

Nucleic Acids Res 2008 May 13;36(9):3150-61. Epub 2008 Apr 13.

Department of Botany, Miami University, Oxford, OH 45056, USA.

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http://dx.doi.org/10.1093/nar/gkn158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396415PMC
May 2008

Characterization of paralogous protein families in rice.

BMC Plant Biol 2008 Feb 19;8:18. Epub 2008 Feb 19.

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

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http://dx.doi.org/10.1186/1471-2229-8-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275729PMC
February 2008

Cross-talk of expression quantitative trait loci within 2 interacting blood pressure quantitative trait loci.

Hypertension 2007 Dec 15;50(6):1126-33. Epub 2007 Oct 15.

Department of Pharmacology and Physiology, George Washington University, Washington, DC, USA.

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http://dx.doi.org/10.1161/HYPERTENSIONAHA.107.093138DOI Listing
December 2007

Identification and characterization of lineage-specific genes within the Poaceae.

Plant Physiol 2007 Dec 19;145(4):1311-22. Epub 2007 Oct 19.

The Institute for Genomic Research and J. Craig Venter Institute, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1104/pp.107.104513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151710PMC
December 2007

Schistosoma mansoni genome: closing in on a final gene set.

Exp Parasitol 2007 Nov 21;117(3):225-8. Epub 2007 Jun 21.

The J.C. Venter Institute, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1016/j.exppara.2007.06.005DOI Listing
November 2007

Identification of Pax5 as a target of MTA1 in B-cell lymphomas.

Cancer Res 2007 Aug;67(15):7132-8

Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-07-0750DOI Listing
August 2007

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.

BMC Genomics 2006 Dec 28;7:327. Epub 2006 Dec 28.

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

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http://dx.doi.org/10.1186/1471-2164-7-327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1769492PMC
December 2006

Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.

BMC Genomics 2006 Oct 24;7:272. Epub 2006 Oct 24.

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

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http://dx.doi.org/10.1186/1471-2164-7-272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635983PMC
October 2006

Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome.

Plant J 2005 Jan;41(2):212-20

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

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http://dx.doi.org/10.1111/j.1365-313X.2004.02295.xDOI Listing
January 2005

DAGchainer: a tool for mining segmental genome duplications and synteny.

Bioinformatics 2004 Dec 9;20(18):3643-6. Epub 2004 Jul 9.

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

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http://dx.doi.org/10.1093/bioinformatics/bth397DOI Listing
December 2004

Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.

Plant J 2004 May;38(3):545-61

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

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http://dx.doi.org/10.1111/j.1365-313X.2004.02061.xDOI Listing
May 2004

Computational discovery of internal micro-exons.

Genome Res 2003 Jun;13(6A):1216-21

The Institute for Genomic Research, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1101/gr.677503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403649PMC
June 2003

Annotation of the Arabidopsis genome.

Plant Physiol 2003 Jun;132(2):461-8

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

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http://dx.doi.org/10.1104/pp.103.022251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166989PMC
June 2003

Kinetics and binding of the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates.

DNA Repair (Amst) 2003 Jan;2(1):107-20

Department of Biological Sciences, SUNY at Albany, Albany, NY 12222, USA.

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January 2003

Full-length messenger RNA sequences greatly improve genome annotation.

Genome Biol 2002 30;3(6):RESEARCH0029. Epub 2002 May 30.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC116726PMC
http://dx.doi.org/10.1186/gb-2002-3-6-research0029DOI Listing
August 2002

Proteome map of the chloroplast lumen of Arabidopsis thaliana.

J Biol Chem 2002 Mar 21;277(10):8354-65. Epub 2001 Nov 21.

Department of Medical Nutrition, Karolinska Institute, Novum, Huddinge SE-14186, Sweden.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M108575200
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http://dx.doi.org/10.1074/jbc.M108575200DOI Listing
March 2002