Publications by authors named "Genis Parra"

27Publications

Using geneid to Identify Genes.

Curr Protoc Bioinformatics 2018 12 17;64(1):e56. Epub 2018 Oct 17.

Centre de Regulació Genòmica (CRG), Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpbi.56DOI Listing
December 2018

Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.

Mol Biol Evol 2016 08 24;33(8):2135-50. Epub 2016 May 24.

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msw098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948712PMC
August 2016

Recent Selection Changes in Human Genes under Long-Term Balancing Selection.

Mol Biol Evol 2016 06 1;33(6):1435-47. Epub 2016 Feb 1.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msw023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909129PMC
June 2016

Genetic adaptation to levels of dietary selenium in recent human history.

Mol Biol Evol 2015 Jun 3;32(6):1507-18. Epub 2015 Mar 3.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msv043DOI Listing
June 2015

WISCOD: a statistical web-enabled tool for the identification of significant protein coding regions.

Biomed Res Int 2014 15;2014:282343. Epub 2014 Sep 15.

Department of Statistics, University of Barcelona, Avenida Diagonal 643, 08028 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1155/2014/282343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181902PMC
July 2015

SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D437-43. Epub 2013 Nov 4.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt1045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965025PMC
January 2014

Assessing the gene space in draft genomes.

Nucleic Acids Res 2009 Jan 28;37(1):289-97. Epub 2008 Nov 28.

UC Davis Genome Center, University of California Davis, Davis, CA, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkn916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615622PMC
January 2009

Using geneid to identify genes.

Curr Protoc Bioinformatics 2007 Jun;Chapter 4:Unit 4.3

Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/0471250953.bi0403s18
Publisher Site
http://dx.doi.org/10.1002/0471250953.bi0403s18DOI Listing
June 2007

Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression.

Plant Cell 2008 Mar 4;20(3):543-51. Epub 2008 Mar 4.

Molecular and Cellular Biology, University of California, Davis, California 95616, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1105/tpc.107.057190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329928PMC
March 2008

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.

Bioinformatics 2007 May 1;23(9):1061-7. Epub 2007 Mar 1.

UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btm071DOI Listing
May 2007

Tandem chimerism as a means to increase protein complexity in the human genome.

Genome Res 2006 Jan 12;16(1):37-44. Epub 2005 Dec 12.

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.4145906
Publisher Site
http://dx.doi.org/10.1101/gr.4145906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356127PMC
January 2006

Gene finding in the chicken genome.

BMC Bioinformatics 2005 May 30;6:131. Epub 2005 May 30.

Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-6-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174864PMC
May 2005

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

Nucleic Acids Res 2005 4;33(6):1935-9. Epub 2005 Apr 4.

Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra, Centre de Regulació Genòmica E08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gki328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074396PMC
April 2005

Are splicing mutations the most frequent cause of hereditary disease?

FEBS Lett 2005 Mar;579(9):1900-3

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.febslet.2005.02.047DOI Listing
March 2005

Gene organization features in A/T-rich organisms.

J Mol Evol 2005 Jan;60(1):90-8

Department of Genome Analysis, Institute for Molecular Biotechnology Jena, Beutenbergstr. 11, D-07745 Jena, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-004-0201-2DOI Listing
January 2005

Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.

Proc Natl Acad Sci U S A 2003 Feb 27;100(3):1140-5. Epub 2003 Jan 27.

Research Group in Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra/Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0337561100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298740PMC
February 2003

Comparative gene prediction in human and mouse.

Genome Res 2003 Jan;13(1):108-17

Grup de Recerca en Informàtica Biomèdica. Institut Municipal d'Investigació Medica / Universitat Pompeu Fabra / Centre de Regulació Genòmica 08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.871403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430976PMC
January 2003

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.

View Article

Download full-text PDF

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