Publications by authors named "Salvador Capella-Gutiérrez"

31Publications

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.

Nucleic Acids Res 2017 07;45(W1):W484-W489

Biological Text Mining Unit, Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

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http://dx.doi.org/10.1093/nar/gkx462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570141PMC
July 2017

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.

Dev Cell 2016 10 13;39(2):186-197. Epub 2016 Oct 13.

Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2016.09.019DOI Listing
October 2016

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

Genome Res 2015 Sep 20;25(9):1256-67. Epub 2015 Jul 20.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain; Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1101/gr.190538.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561486PMC
September 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Authors:
Ariel D Chipman David E K Ferrier Carlo Brena Jiaxin Qu Daniel S T Hughes Reinhard Schröder Montserrat Torres-Oliva Nadia Znassi Huaiyang Jiang Francisca C Almeida Claudio R Alonso Zivkos Apostolou Peshtewani Aqrawi Wallace Arthur Jennifer C J Barna Kerstin P Blankenburg Daniela Brites Salvador Capella-Gutiérrez Marcus Coyle Peter K Dearden Louis Du Pasquier Elizabeth J Duncan Dieter Ebert Cornelius Eibner Galina Erikson Peter D Evans Cassandra G Extavour Liezl Francisco Toni Gabaldón William J Gillis Elizabeth A Goodwin-Horn Jack E Green Sam Griffiths-Jones Cornelis J P Grimmelikhuijzen Sai Gubbala Roderic Guigó Yi Han Frank Hauser Paul Havlak Luke Hayden Sophie Helbing Michael Holder Jerome H L Hui Julia P Hunn Vera S Hunnekuhl LaRonda Jackson Mehwish Javaid Shalini N Jhangiani Francis M Jiggins Tamsin E Jones Tobias S Kaiser Divya Kalra Nathan J Kenny Viktoriya Korchina Christie L Kovar F Bernhard Kraus François Lapraz Sandra L Lee Jie Lv Christigale Mandapat Gerard Manning Marco Mariotti Robert Mata Tittu Mathew Tobias Neumann Irene Newsham Dinh N Ngo Maria Ninova Geoffrey Okwuonu Fiona Ongeri William J Palmer Shobha Patil Pedro Patraquim Christopher Pham Ling-Ling Pu Nicholas H Putman Catherine Rabouille Olivia Mendivil Ramos Adelaide C Rhodes Helen E Robertson Hugh M Robertson Matthew Ronshaugen Julio Rozas Nehad Saada Alejandro Sánchez-Gracia Steven E Scherer Andrew M Schurko Kenneth W Siggens DeNard Simmons Anna Stief Eckart Stolle Maximilian J Telford Kristin Tessmar-Raible Rebecca Thornton Maurijn van der Zee Arndt von Haeseler James M Williams Judith H Willis Yuanqing Wu Xiaoyan Zou Daniel Lawson Donna M Muzny Kim C Worley Richard A Gibbs Michael Akam Stephen Richards

PLoS Biol 2014 Nov 25;12(11):e1002005. Epub 2014 Nov 25.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043PMC
November 2014

Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation.

BMC Genomics 2014 Oct 7;15:872. Epub 2014 Oct 7.

Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.

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http://dx.doi.org/10.1186/1471-2164-15-872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459065PMC
October 2014

A phylogenomics approach for selecting robust sets of phylogenetic markers.

Nucleic Acids Res 2014 Apr 29;42(7):e54. Epub 2014 Jan 29.

Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG) and UPF. Doctor Aiguader, 88. 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF). 08003 Barcelona, Spain, University of Kaiserslautern, Molecular Phylogenetics, Postfach 3049, 67653 Kaiserslautern, Germany and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gku071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985644PMC
April 2014

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

Nature 2014 Jan 18;505(7484):546-9. Epub 2013 Dec 18.

1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nature12817DOI Listing
January 2014

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.

Nucleic Acids Res 2014 Jan 25;42(Database issue):D897-902. Epub 2013 Nov 25.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkt1177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964985PMC
January 2014

Measuring guide-tree dependency of inferred gaps in progressive aligners.

Bioinformatics 2013 Apr 23;29(8):1011-7. Epub 2013 Feb 23.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88 and Universitat Pompeu Fabra, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btt095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624810PMC
April 2013

The genome of melon (Cucumis melo L.).

Proc Natl Acad Sci U S A 2012 Jul 2;109(29):11872-7. Epub 2012 Jul 2.

Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.1205415109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406823PMC
July 2012

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi.

BMC Biol 2012 May 31;10:47. Epub 2012 May 31.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1186/1741-7007-10-47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586952PMC
May 2012

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

Nucleic Acids Res 2011 Jul 6;39(Web Server issue):W470-4. Epub 2011 Jun 6.

Evolutionary Genomics Lab, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 16-3, 46013 Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkr408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125789PMC
July 2011

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.

Nucleic Acids Res 2011 Jan 12;39(Database issue):D556-60. Epub 2010 Nov 12.

Bioinformatics and Genomics Programme, Centre de Regulació Genòmica, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkq1109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013701PMC
January 2011

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.

Bioinformatics 2009 Aug 8;25(15):1972-3. Epub 2009 Jun 8.

Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btp348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712344PMC
August 2009