Jaime Huerta-Cepas

Jaime Huerta-Cepas

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Jaime Huerta-Cepas

Jaime Huerta-Cepas

Publications by authors named "Jaime Huerta-Cepas"

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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Microbiome 2019 06 3;7(1):84. Epub 2019 Jun 3.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1186/s40168-019-0684-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547473PMC
June 2019

Subspecies in the global human gut microbiome.

Mol Syst Biol 2017 12 14;13(12):960. Epub 2017 Dec 14.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740502PMC
http://dx.doi.org/10.15252/msb.20177589DOI Listing
December 2017

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Mol Biol Evol 2017 08;34(8):2115-2122

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1093/molbev/msx148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850834PMC
August 2017

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.

Mol Biol Evol 2017 06;34(6):1535-1542

Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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http://dx.doi.org/10.1093/molbev/msx055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435079PMC
June 2017

Metabolic anchor reactions for robust biorefining.

Metab Eng 2017 03 21;40:1-4. Epub 2017 Feb 21.

European Molecular Biology Laboratory, Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2017.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5368410PMC
March 2017

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Nucleic Acids Res 2017 01 24;45(D1):D529-D534. Epub 2016 Oct 24.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany

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http://dx.doi.org/10.1093/nar/gkw989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210662PMC
January 2017

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Bioinformatics 2016 08 8;32(16):2520-3. Epub 2016 Apr 8.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978931PMC
August 2016

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Mol Biol Evol 2016 06 26;33(6):1635-8. Epub 2016 Feb 26.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.

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http://dx.doi.org/10.1093/molbev/msw046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116PMC
June 2016

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Science 2016 Apr;352(6285):586-9

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.

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http://dx.doi.org/10.1126/science.aad8852DOI Listing
April 2016

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res 2016 Jan 17;44(D1):D286-93. Epub 2015 Nov 17.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg 69117, Germany Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany

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http://nar.oxfordjournals.org/content/early/2015/11/17/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1248
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http://dx.doi.org/10.1093/nar/gkv1248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702882PMC
January 2016

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evv121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524488PMC
July 2015

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Nucleic Acids Res 2015 Jan 28;43(Database issue):D447-52. Epub 2014 Oct 28.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland

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http://dx.doi.org/10.1093/nar/gku1003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383874PMC
January 2015

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Nucleic Acids Res 2015 Jan 31;43(Database issue):D494-502. Epub 2014 Oct 31.

European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany

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http://dx.doi.org/10.1093/nar/gku1081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383916PMC
January 2015

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

Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery.

Biochim Biophys Acta 2014 Sep 20;1843(9):1886-98. Epub 2014 May 20.

Biochemistry Department, Veterinary Faculty, Complutense University of Madrid, Institute of Neurochemistry (IUIN), Madrid, Spain; Health Research Institute of the Hospital Clinico San Carlos (IdISSC), Spain.

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http://dx.doi.org/10.1016/j.bbamcr.2014.05.004DOI Listing
September 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

eggNOG v4.0: nested orthology inference across 3686 organisms.

Nucleic Acids Res 2014 Jan 1;42(Database issue):D231-9. Epub 2013 Dec 1.

European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), C/Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark and Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkt1253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964997PMC
January 2014

Comparative transcriptomics of early dipteran development.

BMC Genomics 2013 Feb 24;14:123. Epub 2013 Feb 24.

EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2164-14-123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616871PMC
February 2013

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

Brief Bioinform 2011 Sep 22;12(5):442-8. Epub 2011 Apr 22.

Centre for Genomic Regulation, Barcelona, Spain.

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http://dx.doi.org/10.1093/bib/bbr022DOI Listing
September 2011

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Database (Oxford) 2011 7;2011:bar008. Epub 2011 Apr 7.

UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA-Lyon, Université de Lyon, 20 av. A. Einstein, F-69621 Villeurbanne, France.

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http://dx.doi.org/10.1093/database/bar008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072769PMC
July 2011

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

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

Nucleic Acids Res 2011 Mar 11;39(5):e32. Epub 2010 Dec 11.

Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkq953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061081PMC
March 2011

Assigning duplication events to relative temporal scales in genome-wide studies.

Bioinformatics 2011 Jan 11;27(1):38-45. Epub 2010 Nov 11.

Centre for Genomic Regulation (CRG), Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btq609DOI Listing
January 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

ETE: a python Environment for Tree Exploration.

BMC Bioinformatics 2010 Jan 13;11:24. Epub 2010 Jan 13.

Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2105-11-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820433PMC
January 2010

The human phylome.

Genome Biol 2007 ;8(6):R109

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain.

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http://genomebiology.com/2007/8/6/R109
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http://dx.doi.org/10.1186/gb-2007-8-6-r109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394744PMC
February 2008

PhylomeDB: a database for genome-wide collections of gene phylogenies.

Nucleic Acids Res 2008 Jan 25;36(Database issue):D491-6. Epub 2007 Oct 25.

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler, 13 Valencia 46013, Spain.

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http://dx.doi.org/10.1093/nar/gkm899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238872PMC
January 2008

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W38-42. Epub 2007 Apr 22.

Bioinformatics Department, Centro de Investigación Príncipe Felipe, INB, CIPF, Valencia 46013, Spain.

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http://dx.doi.org/10.1093/nar/gkm224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933211PMC
July 2007

Evidence for systems-level molecular mechanisms of tumorigenesis.

BMC Genomics 2007 Jun 20;8:185. Epub 2007 Jun 20.

Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2164-8-185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929080PMC
June 2007

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

Nucleic Acids Res 2007 Jan 28;35(Database issue):D815-22. Epub 2006 Nov 28.

Centre de Genètica Mèdica i Molecular, Institut d'Investigació Biomèdica de Bellvitge-Institut de Recerca Oncològica (IDIBELL-IRO) Hospital Duran i Reynals, Granvia Km 2,7. 08907 Hospitalet de Llobregat, Barcelona, Spain.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1747181PMC
January 2007

Next station in microarray data analysis: GEPAS.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W486-91

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E46013, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkl197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538867PMC
July 2006