Brian J Raney

Brian J Raney

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Brian J Raney

Brian J Raney

Publications by authors named "Brian J Raney"

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Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Authors:
Coen M Adema LaDeana W Hillier Catherine S Jones Eric S Loker Matty Knight Patrick Minx Guilherme Oliveira Nithya Raghavan Andrew Shedlock Laurence Rodrigues do Amaral Halime D Arican-Goktas Juliana G Assis Elio Hideo Baba Olga L Baron Christopher J Bayne Utibe Bickham-Wright Kyle K Biggar Michael Blouin Bryony C Bonning Chris Botka Joanna M Bridger Katherine M Buckley Sarah K Buddenborg Roberta Lima Caldeira Julia Carleton Omar S Carvalho Maria G Castillo Iain W Chalmers Mikkel Christensens Sandra Clifton Celine Cosseau Christine Coustau Richard M Cripps Yesid Cuesta-Astroz Scott F Cummins Leon Di Stefano Nathalie Dinguirard David Duval Scott Emrich Cédric Feschotte Rene Feyereisen Peter FitzGerald Catrina Fronick Lucinda Fulton Richard Galinier Sandra G Gava Michael Geusz Kathrin K Geyer Gloria I Giraldo-Calderón Matheus de Souza Gomes Michelle A Gordy Benjamin Gourbal Christoph Grunau Patrick C Hanington Karl F Hoffmann Daniel Hughes Judith Humphries Daniel J Jackson Liana K Jannotti-Passos Wander de Jesus Jeremias Susan Jobling Bishoy Kamel Aurélie Kapusta Satwant Kaur Joris M Koene Andrea B Kohn Dan Lawson Scott P Lawton Di Liang Yanin Limpanont Sijun Liu Anne E Lockyer Ty Anna L Lovato Fernanda Ludolf Vince Magrini Donald P McManus Monica Medina Milind Misra Guillaume Mitta Gerald M Mkoji Michael J Montague Cesar Montelongo Leonid L Moroz Monica C Munoz-Torres Umar Niazi Leslie R Noble Francislon S Oliveira Fabiano S Pais Anthony T Papenfuss Rob Peace Janeth J Pena Emmanuel A Pila Titouan Quelais Brian J Raney Jonathan P Rast David Rollinson Izinara C Rosse Bronwyn Rotgans Edwin J Routledge Kathryn M Ryan Larissa L S Scholte Kenneth B Storey Martin Swain Jacob A Tennessen Chad Tomlinson Damian L Trujillo Emanuela V Volpi Anthony J Walker Tianfang Wang Ittiprasert Wannaporn Wesley C Warren Xiao-Jun Wu Timothy P Yoshino Mohammed Yusuf Si-Ming Zhang Min Zhao Richard K Wilson

Nat Commun 2017 08 23;8:16153. Epub 2017 Aug 23.

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http://dx.doi.org/10.1038/ncomms16153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569240PMC
August 2017

Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Authors:
Coen M Adema LaDeana W Hillier Catherine S Jones Eric S Loker Matty Knight Patrick Minx Guilherme Oliveira Nithya Raghavan Andrew Shedlock Laurence Rodrigues do Amaral Halime D Arican-Goktas Juliana G Assis Elio Hideo Baba Olga L Baron Christopher J Bayne Utibe Bickham-Wright Kyle K Biggar Michael Blouin Bryony C Bonning Chris Botka Joanna M Bridger Katherine M Buckley Sarah K Buddenborg Roberta Lima Caldeira Julia Carleton Omar S Carvalho Maria G Castillo Iain W Chalmers Mikkel Christensens Sandra Clifton Celine Cosseau Christine Coustau Richard M Cripps Yesid Cuesta-Astroz Scott F Cummins Leon di Stephano Nathalie Dinguirard David Duval Scott Emrich Cédric Feschotte Rene Feyereisen Peter FitzGerald Catrina Fronick Lucinda Fulton Richard Galinier Sandra G Gava Michael Geusz Kathrin K Geyer Gloria I Giraldo-Calderón Matheus de Souza Gomes Michelle A Gordy Benjamin Gourbal Christoph Grunau Patrick C Hanington Karl F Hoffmann Daniel Hughes Judith Humphries Daniel J Jackson Liana K Jannotti-Passos Wander de Jesus Jeremias Susan Jobling Bishoy Kamel Aurélie Kapusta Satwant Kaur Joris M Koene Andrea B Kohn Dan Lawson Scott P Lawton Di Liang Yanin Limpanont Sijun Liu Anne E Lockyer TyAnna L Lovato Fernanda Ludolf Vince Magrini Donald P McManus Monica Medina Milind Misra Guillaume Mitta Gerald M Mkoji Michael J Montague Cesar Montelongo Leonid L Moroz Monica C Munoz-Torres Umar Niazi Leslie R Noble Francislon S Oliveira Fabiano S Pais Anthony T Papenfuss Rob Peace Janeth J Pena Emmanuel A Pila Titouan Quelais Brian J Raney Jonathan P Rast David Rollinson Izinara C Rosse Bronwyn Rotgans Edwin J Routledge Kathryn M Ryan Larissa L S Scholte Kenneth B Storey Martin Swain Jacob A Tennessen Chad Tomlinson Damian L Trujillo Emanuela V Volpi Anthony J Walker Tianfang Wang Ittiprasert Wannaporn Wesley C Warren Xiao-Jun Wu Timothy P Yoshino Mohammed Yusuf Si-Ming Zhang Min Zhao Richard K Wilson

Nat Commun 2017 05 16;8:15451. Epub 2017 May 16.

The McDonnell Genome Institute, Washington University, Saint Louis, Missouri 63108 USA.

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http://dx.doi.org/10.1038/ncomms15451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440852PMC
May 2017

Navigating protected genomics data with UCSC Genome Browser in a Box.

Bioinformatics 2015 Mar 27;31(5):764-6. Epub 2014 Oct 27.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341066PMC
March 2015

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Bioinformatics 2014 Dec 18;30(23):3293-301. Epub 2014 Aug 18.

Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145PMC
December 2014

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Bioinformatics 2014 Apr 13;30(7):1003-5. Epub 2013 Nov 13.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967101PMC
April 2014

The UCSC Genome Browser database: 2014 update.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D764-70. Epub 2013 Nov 21.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947PMC
January 2014

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

Three periods of regulatory innovation during vertebrate evolution.

Science 2011 Aug;333(6045):1019-24

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1126/science.1202702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511857PMC
August 2011

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Nucleic Acids Res 2011 Jan 30;39(Database issue):D871-5. Epub 2010 Oct 30.

Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkq1017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645PMC
January 2011

ENCODE whole-genome data in the UCSC Genome Browser.

Nucleic Acids Res 2010 Jan 17;38(Database issue):D620-5. Epub 2009 Nov 17.

Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkp961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808953PMC
January 2010

DUPCAR: reconstructing contiguous ancestral regions with duplications.

J Comput Biol 2008 Oct;15(8):1007-27

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1089/cmb.2008.0069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822PMC
October 2008

The infinite sites model of genome evolution.

Proc Natl Acad Sci U S A 2008 Sep 11;105(38):14254-61. Epub 2008 Sep 11.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1073/pnas.0805217105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533685PMC
September 2008

The ENCODE Project at UC Santa Cruz.

Nucleic Acids Res 2007 Jan 13;35(Database issue):D663-7. Epub 2006 Dec 13.

Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkl1017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781110PMC
January 2007

Reconstructing contiguous regions of an ancestral genome.

Genome Res 2006 Dec 18;16(12):1557-65. Epub 2006 Sep 18.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5383506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665639PMC
December 2006