Jose M Duarte

Jose M Duarte

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Jose M Duarte

Jose M Duarte

Publications by authors named "Jose M Duarte"

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RCSB Protein Data Bank: Enabling biomedical research and drug discovery.

Protein Sci 2020 Jan 29;29(1):52-65. Epub 2019 Nov 29.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey.

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http://dx.doi.org/10.1002/pro.3730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933845PMC
January 2020

Assessment of protein assembly prediction in CASP13.

Proteins 2019 12 27;87(12):1190-1199. Epub 2019 Aug 27.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, California.

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http://dx.doi.org/10.1002/prot.25795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851419PMC
December 2019

Azaperone and xylazine: A pharmacological combination to facilitate captive deer management for red brocket deer (Mazama americana).

PLoS One 2019 2;14(8):e0220288. Epub 2019 Aug 2.

Department of Animal Science-Deer Research and Conservation Center (NUPECCE), Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220288PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677384PMC
August 2019

BioJava 5: A community driven open-source bioinformatics library.

PLoS Comput Biol 2019 02 8;15(2):e1006791. Epub 2019 Feb 8.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.plos.org/10.1371/journal.pcbi.1006791
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http://dx.doi.org/10.1371/journal.pcbi.1006791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383946PMC
February 2019

Investigation of protein quaternary structure via stoichiometry and symmetry information.

PLoS One 2018 4;13(6):e0197176. Epub 2018 Jun 4.

RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197176PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986128PMC
November 2018

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution.

Mol Syst Biol 2018 09 10;14(9):e8102. Epub 2018 Sep 10.

Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129954PMC
http://dx.doi.org/10.15252/msb.20178102DOI Listing
September 2018

Intrapopulation Chromosomal Polymorphism in Mazama gouazoubira (Cetartiodactyla; Cervidae): The Emergence of a New Species?

Cytogenet Genome Res 2018 14;154(3):147-152. Epub 2018 Apr 14.

Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil.

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https://www.karger.com/Article/FullText/488377
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http://dx.doi.org/10.1159/000488377DOI Listing
May 2018

Automated evaluation of quaternary structures from protein crystals.

PLoS Comput Biol 2018 04 30;14(4):e1006104. Epub 2018 Apr 30.

Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1006104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945228PMC
April 2018

Assessment of protein assembly prediction in CASP12.

Proteins 2018 03 8;86 Suppl 1:247-256. Epub 2017 Nov 8.

Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, PSI, 5232, Switzerland.

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http://dx.doi.org/10.1002/prot.25408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949145PMC
March 2018

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America.

Authors:
Fernando Gonçalves Ricardo S Bovendorp Gabrielle Beca Carolina Bello Raul Costa-Pereira Renata L Muylaert Raisa R Rodarte Nacho Villar Rafael Souza Maurício E Graipel Jorge J Cherem Deborah Faria Julio Baumgarten Martín R Alvarez Emerson M Vieira Nilton Cáceres Renata Pardini Yuri L R Leite Leonora P Costa Marco A R Mello Erich Fischer Fernando C Passos Luiz H Varzinczak Jayme A Prevedello Ariovaldo P Cruz-Neto Fernando Carvalho Alexandre R Percequillo Agustin Paviolo Alessandra Nava José M B Duarte Noé U de la Sancha Enrico Bernard Ronaldo G Morato Juliana F Ribeiro Rafael G Becker Gabriela Paise Paulo S Tomasi Felipe Vélez-Garcia Geruza L Melo Jonas Sponchiado Felipe Cerezer Marília A S Barros Albérico Q S de Souza Cinthya C Dos Santos Gastón A F Giné Patricia Kerches-Rogeri Marcelo M Weber Guilherme Ambar Lucía V Cabrera-Martinez Alan Eriksson Maurício Silveira Carolina F Santos Lucas Alves Eder Barbier Gabriela C Rezende Guilherme S T Garbino Élson O Rios Adna Silva Alexandre Túlio A Nascimento Rodrigo S de Carvalho Anderson Feijó Juan Arrabal Ilaria Agostini Daniela Lamattina Sebastian Costa Ezequiel Vanderhoeven Fabiano R de Melo Plautino de Oliveira Laroque Leandro Jerusalinsky Mônica M Valença-Montenegro Amely B Martins Gabriela Ludwig Renata B de Azevedo Agustin Anzóategui Marina X da Silva Marcela Figuerêdo Duarte Moraes Alexandre Vogliotti Andressa Gatti Thomas Püttker Camila S Barros Thais K Martins Alexine Keuroghlian Donald P Eaton Carolina L Neves Marcelo S Nardi Caryne Braga Pablo R Gonçalves Ana Carolina Srbek-Araujo Poliana Mendes João A de Oliveira Fábio A M Soares Patrício A Rocha Peter Crawshaw Milton C Ribeiro Mauro Galetti

Ecology 2018 Feb;99(2):498

Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, 13506, Brasil.

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http://dx.doi.org/10.1002/ecy.2106DOI Listing
February 2018

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

Protein Sci 2018 01 11;27(1):316-330. Epub 2017 Nov 11.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.

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http://dx.doi.org/10.1002/pro.3331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734314PMC
January 2018

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

ACS Synth Biol 2017 11 21;6(11):1988-1995. Epub 2017 Aug 21.

Department of Evolutionary Biology and Environmental Studies, University of Zurich , Winterthurerstrasse 190, 8057 Zürich, Switzerland.

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http://dx.doi.org/10.1021/acssynbio.7b00111DOI Listing
November 2017

The Effects of Cryopreservation on Different Passages of Fibroblast Cell Culture in Brown Brocket Deer (Mazama gouazoubira).

Biopreserv Biobank 2017 Oct 18;15(5):463-468. Epub 2017 Sep 18.

1 Laboratory of Physiology and Control of Reproduction, Faculty of Veterinary, Ceará State University , Fortaleza, Brazil .

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http://dx.doi.org/10.1089/bio.2017.0060DOI Listing
October 2017

Towards an efficient compression of 3D coordinates of macromolecular structures.

PLoS One 2017 31;12(3):e0174846. Epub 2017 Mar 31.

Structural Bioinformatics Laboratory, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174846PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376293PMC
August 2017

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

PLoS Comput Biol 2017 Jun 2;13(6):e1005575. Epub 2017 Jun 2.

Structural Bioinformatics Laboratory, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473584PMC
June 2017

Ovarian cycle of southern brown howler monkey (Alouatta guariba clamitans) through fecal progestin measurement.

Primates 2017 Jan 19;58(1):131-139. Epub 2016 Aug 19.

Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil.

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http://dx.doi.org/10.1007/s10329-016-0561-zDOI Listing
January 2017

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.

Bioinformatics 2016 Feb 27;32(4):481-9. Epub 2015 Oct 27.

Laboratory of Biomolecular Research, Paul Scherrer Institute, OFLC/110, 5232 Villigen PSI, Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btv622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743631PMC
February 2016

Donation after cardiac death: results of the SUMMA 112 - Hospital 12 de Octubre Program.

Clin Transplant 2013 Mar-Apr;27(2):283-8. Epub 2013 Jan 27.

Department of Urology, Hospital Universitario 12 de Octubre, Madrid, Spain.

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http://dx.doi.org/10.1111/ctr.12071DOI Listing
October 2013

An analysis of oligomerization interfaces in transmembrane proteins.

BMC Struct Biol 2013 Oct 17;13:21. Epub 2013 Oct 17.

Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, 5232, Switzerland.

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http://dx.doi.org/10.1186/1472-6807-13-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015793PMC
October 2013

Protein interface classification by evolutionary analysis.

BMC Bioinformatics 2012 Dec 22;13:334. Epub 2012 Dec 22.

Paul Scherrer Institut, Villigen, CH-5232, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-13-334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556496PMC
December 2012

Cryopreservation of red brocket deer semen (Mazama americana): comparison between three extenders.

J Zoo Wildl Med 2012 Dec;43(4):820-7

Núcleo de Pesquisa e Conservação de Cervídeos, Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Universidade Estadual Paulista, SP, 14884-900, Brasil.

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http://dx.doi.org/10.1638/2011-0195R1.1DOI Listing
December 2012

CMView: interactive contact map visualization and analysis.

Bioinformatics 2011 Jun 5;27(11):1573-4. Epub 2011 Apr 5.

Department of Simulations and Graphics, O.v.G. University Magdeburg, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr163DOI Listing
June 2011

The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors.

Mol Cancer 2011 May 16;10:54. Epub 2011 May 16.

Max-Planck Institute for Molecular Genetics, Structural Proteomics/Bioinformatics Group, Otto-Warburg Laboratory, Boltzmannstrasse 12, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1476-4598-10-54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123651PMC
May 2011

PDBWiki: added value through community annotation of the Protein Data Bank.

Database (Oxford) 2010 Jul 6;2010:baq009. Epub 2010 Jul 6.

Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/database/baq009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911844PMC
July 2010

Survey for foot-and-mouth disease in the endangered marsh deer (Blastocerus dichotomus) from marshlands of the Parana River Basin, Brazil.

J Wildl Dis 2010 Jul;46(3):939-43

Instituto de Biociências, Universidade Estadual Paulista (UNESP), Departamento de Microbiologia e Imunologia, 18618-000, Botucatu, São Paulo, Brazil.

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http://dx.doi.org/10.7589/0090-3558-46.3.939DOI Listing
July 2010

Optimal contact definition for reconstruction of contact maps.

BMC Bioinformatics 2010 May 27;11:283. Epub 2010 May 27.

Max Planck Institute for Molecular Genetics, Ihnestr, Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583236PMC
May 2010

Defining an essence of structure determining residue contacts in proteins.

PLoS Comput Biol 2009 Dec 4;5(12):e1000584. Epub 2009 Dec 4.

Structural Genomics/Bioinformatics Group, Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778133PMC
December 2009

Designing evolvable libraries using multi-body potentials.

Curr Opin Biotechnol 2009 Aug 26;20(4):437-46. Epub 2009 Aug 26.

Max-Planck-Institute for Molecular Genetics, Structural Proteomics/Bioinformatics Group, Ihnestrasse 63-73, Berlin 14195, Germany.

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http://dx.doi.org/10.1016/j.copbio.2009.07.008DOI Listing
August 2009

Ophthalmic patterns of captive brown brocket deer (Mazama gouazoubira).

J Zoo Wildl Med 2007 Dec;38(4):526-32

Ophthalmology Unit, Anaerobic Laboratory, Wild Animal Facilities, College of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Sao Paulo 14884-900, Brazil.

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http://dx.doi.org/10.1638/MS05-084.1DOI Listing
December 2007

Natural infection by Paramphistomoidea Stiles and Goldberger, 1910 trematodes in wild Marsh Deer (Blastocerus dichotomus Illiger, 1815) from Sérgio Mottas's hydroelectric power station flooding area.

Rev Bras Parasitol Vet 2006 Oct-Dec;15(4):133-7

Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, via de acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14887-900, Brazil.

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May 2007

Environmental effect on the occurrence of anti-Neospora caninum antibodies in pampas-deer (Ozotoceros bezoarticus).

Vet Parasitol 2005 Nov 19;134(1-2):73-6. Epub 2005 Aug 19.

Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Bzazil.

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http://dx.doi.org/10.1016/j.vetpar.2005.07.015DOI Listing
November 2005

Occurrence of anti-Neospora caninum antibodies in Brazilian cervids kept in captivity.

Vet Parasitol 2005 May;129(3-4):341-3

Depto. de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Orlando Marques de Paula, 87, Cidade Universitária, São Paulo CEP 05508-000, SP, Brazil.

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http://dx.doi.org/10.1016/j.vetpar.2004.12.016DOI Listing
May 2005

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Role of taurine uptake on the induction of long-term synaptic potentiation.

Eur J Neurosci 2004 Apr;19(7):1875-86

Departamento de Psicobiología, Facultad Psicología, UNED, Madrid, Spain.

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http://dx.doi.org/10.1111/j.1460-9568.2004.03309.xDOI Listing
April 2004

Tuberculosis survey of free-ranging marsh deer (Blastocerus dichotomus) in Brazil.

J Zoo Wildl Med 2003 Dec;34(4):414-5

Laboratório de Biologia Molecular Aplicada e Sorologia, Departamento de Medicina Veterinária Preventiva, Universidade de São Paulo, Av. Orlando Marques de Paiva, 87, São Paulo City, São Paulo, Brazil.

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http://dx.doi.org/10.1638/02-068DOI Listing
December 2003