Cedric Notredame

Cedric Notredame

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Cedric Notredame

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A field guide for the compositional analysis of any-omics data.

Gigascience 2019 Sep;8(9)

Poultry Hub Australia, University of New England, Elm Avenue, Armidale New South Wales 2351, Australia.

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http://dx.doi.org/10.1093/gigascience/giz107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755255PMC
September 2019

Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.

Nucleic Acids Res 2019 Jul;47(W1):W600-W604

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkz414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602478PMC
July 2019

Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability.

Bioinformatics 2019 Feb 6. Epub 2019 Feb 6.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz082DOI Listing
February 2019

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty.

Syst Biol 2018 11;67(6):997-1009

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/sysbio/syx096DOI Listing
November 2018

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.

iScience 2018 Nov 26;9:244-257. Epub 2018 Oct 26.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.10.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231116PMC
November 2018

[Nextflow, an efficient tool to improve computation numerical stability in genomic analysis].

Biol Aujourdhui 2017 7;211(3):233-237. Epub 2018 Feb 7.

Comparative Bioinformatics Group, Bioinformatics and Genomics Programme, Center for Genomic Regulation (CRG), Dr Aiguader, 88, 08003 Barcelona, Spain - Universitat Pompeu Fabra (UPF), Barcelona, Spain.

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http://dx.doi.org/10.1051/jbio/2017029DOI Listing
August 2018

Extinction and reinstatement of an operant responding maintained by food in different models of obesity.

Addict Biol 2018 03 28;23(2):544-555. Epub 2017 Dec 28.

Laboratori de Neurofarmacologia. Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.

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http://dx.doi.org/10.1111/adb.12597DOI Listing
March 2018

Time-course and dynamics of obesity-related behavioral changes induced by energy-dense foods in mice.

Addict Biol 2018 03 10;23(2):531-543. Epub 2018 Jan 10.

Cellular and Systems Neurobiology, Systems Biology Program, The Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Spain.

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http://dx.doi.org/10.1111/adb.12595DOI Listing
March 2018

Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani.

Nat Ecol Evol 2017 Dec 6;1(12):1961-1969. Epub 2017 Nov 6.

Institut Pasteur, INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, 75015, Paris, France.

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http://dx.doi.org/10.1038/s41559-017-0361-xDOI Listing
December 2017

Combined Treatment With Environmental Enrichment and (-)-Epigallocatechin-3-Gallate Ameliorates Learning Deficits and Hippocampal Alterations in a Mouse Model of Down Syndrome.

eNeuro 2016 Sep-Oct;3(5). Epub 2016 Nov 8.

Cellular and Systems Neurobiology, Systems Biology Program, the Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain; Human Pharmacology and Clinical Neurosciences Research Group, Neurosciences Research Program, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain; Centro De Investigación Biomédica En Red De Enfermedades Raras, Madrid, 28029, Spain.

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http://dx.doi.org/10.1523/ENEURO.0103-16.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099603PMC
October 2017

Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis.

Plant Cell 2017 Jun 26;29(6):1248-1261. Epub 2017 May 26.

Instituto de Biología Molecular y Celular de Rosario, CONICET, and Universidad Nacional de Rosario, Rosario 2000, Argentina

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http://dx.doi.org/10.1105/tpc.17.00272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502457PMC
June 2017

Nextflow enables reproducible computational workflows.

Nat Biotechnol 2017 04;35(4):316-319

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/nbt.3820DOI Listing
April 2017

How should we measure proportionality on relative gene expression data?

Theory Biosci 2016 Jun 13;135(1-2):21-36. Epub 2016 Jan 13.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1007/s12064-015-0220-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870310PMC
June 2016

Transcript profiling of jasmonate-elicited Taxus cells reveals a β-phenylalanine-CoA ligase.

Plant Biotechnol J 2016 Jan 21;14(1):85-96. Epub 2015 Apr 21.

Secció de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1111/pbi.12359DOI Listing
January 2016

Principal Component Analysis of the Effects of Environmental Enrichment and (-)-epigallocatechin-3-gallate on Age-Associated Learning Deficits in a Mouse Model of Down Syndrome.

Front Behav Neurosci 2015 11;9:330. Epub 2015 Dec 11.

Systems Biology Program, Cellular and Systems Neurobiology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology Barcelona, Spain ; Centre for Genomic Regulation, Universitat Pompeu Fabra Barcelona, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras Barcelona, Spain.

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http://dx.doi.org/10.3389/fnbeh.2015.00330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675859PMC
December 2015

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift.

Genome Biol Evol 2015 Oct 1;7(10):2843-58. Epub 2015 Oct 1.

Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evv183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684695PMC
October 2015

The impact of Docker containers on the performance of genomic pipelines.

PeerJ 2015 24;3:e1273. Epub 2015 Sep 24.

Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain.

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https://peerj.com/preprints/1171v1.pdf
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https://peerj.com/articles/1273
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http://dx.doi.org/10.7717/peerj.1273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586803PMC
September 2015

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Nucleic Acids Res 2015 Jul 8;43(W1):W3-6. Epub 2015 Apr 8.

Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkv310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489230PMC
July 2015

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

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.

PLoS One 2013 11;8(10):e75542. Epub 2013 Oct 11.

Comparative Bioinformatics, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona, Spain ; Universitat Pompeu Fabra (UPF), Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075542PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795737PMC
July 2014

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.

Nucleic Acids Res 2014 Jul 27;42(Web Server issue):W356-60. Epub 2014 Jun 27.

Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gku459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086076PMC
July 2014

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

Mol Biol Evol 2014 Jun 1;31(6):1625-37. Epub 2014 Apr 1.

Comparative Bioinformatics, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, Spain

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http://dx.doi.org/10.1093/molbev/msu117DOI Listing
June 2014

T-Coffee: Tree-based consistency objective function for alignment evaluation.

Methods Mol Biol 2014 ;1079:117-29

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

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http://dx.doi.org/10.1007/978-1-62703-646-7_7DOI Listing
May 2014

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance.

New Phytol 2013 Jul 29;199(1):212-27. Epub 2013 Apr 29.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain.

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http://dx.doi.org/10.1111/nph.12292DOI Listing
July 2013

T-RMSD: a web server for automated fine-grained protein structural classification.

Nucleic Acids Res 2013 Jul 28;41(Web Server issue):W358-62. Epub 2013 May 28.

Bioinformatics and Genomics Programme, Centre For Genomic Regulation, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkt383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692075PMC
July 2013

Detecting and comparing non-coding RNAs in the high-throughput era.

Int J Mol Sci 2013 Jul 24;14(8):15423-58. Epub 2013 Jul 24.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.3390/ijms140815423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759867PMC
July 2013

Epistasis as the primary factor in molecular evolution.

Nature 2012 Oct 14;490(7421):535-8. Epub 2012 Oct 14.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.

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http://dx.doi.org/10.1038/nature11510DOI Listing
October 2012

An improved understanding of TNFL/TNFR interactions using structure-based classifications.

Trends Biochem Sci 2012 Sep 11;37(9):353-63. Epub 2012 Jul 11.

Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain.

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http://dx.doi.org/10.1016/j.tibs.2012.06.002DOI Listing
September 2012

Use of ChIP-Seq data for the design of a multiple promoter-alignment method.

Nucleic Acids Res 2012 Apr 9;40(7):e52. Epub 2012 Jan 9.

Bioinformatics and Genomics program, Centre for Genomic Regulation and UPF, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkr1292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326335PMC
April 2012

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.

BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S1. Epub 2012 Mar 28.

Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Spain.

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http://dx.doi.org/10.1186/1471-2105-13-S4-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303701PMC
March 2012

AMPA: an automated web server for prediction of protein antimicrobial regions.

Bioinformatics 2012 Jan 3;28(1):130-1. Epub 2011 Nov 3.

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btr604DOI Listing
January 2012

STRIKE: evaluation of protein MSAs using a single 3D structure.

Bioinformatics 2011 Dec 28;27(24):3385-91. Epub 2011 Oct 28.

Bioinformatics and Genomics Program, Centre for Genomic Regulation and UPF, Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btr587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232373PMC
December 2011

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.

Nat Protoc 2011 Nov;6(11):1669-82

Comparative Bioinformatics Group, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.

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http://dx.doi.org/10.1038/nprot.2011.393DOI Listing
November 2011

The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.

Mol Biol Evol 2011 Nov;28(11):3213-23

Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD UMR6236-198, Université de la Méditerranée, Faculté de Médecine, Marseille, France.

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http://dx.doi.org/10.1093/molbev/msr239DOI Listing
November 2011

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.

BMC Genomics 2011 Nov 8;12:552. Epub 2011 Nov 8.

Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-12-552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221674PMC
November 2011

BlastR--fast and accurate database searches for non-coding RNAs.

Nucleic Acids Res 2011 Sep 30;39(16):6886-95. Epub 2011 May 30.

Bioinformatics and Genomics program, Center for Genomic Regulation (CRG) and UPF, Barcelona, C/ D. Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkr335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167602PMC
September 2011

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

Nucleic Acids Res 2011 Jul 9;39(Web Server issue):W13-7. Epub 2011 May 9.

Centre For Genomic Regulation (Pompeu Fabra University), Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkr245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125728PMC
July 2011

A user-friendly web portal for T-Coffee on supercomputers.

BMC Bioinformatics 2011 May 12;12:150. Epub 2011 May 12.

Department of Computer Science and Industrial Engineering, University of Lleida, C/Jaume II 69, E-25001 Lleida, Spain.

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http://dx.doi.org/10.1186/1471-2105-12-150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112243PMC
May 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Predicting phenotypic traits of prokaryotes from protein domain frequencies.

BMC Bioinformatics 2010 Sep 24;11:481. Epub 2010 Sep 24.

Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955703PMC
September 2010

T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

J Mol Biol 2010 Jul 13;400(3):605-17. Epub 2010 May 13.

EMBL/CRG Systems Biology Research Unit Center for Genomic Regulation, UPF, Barcelona, Catalunya, 08003, Spain.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836100049
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http://dx.doi.org/10.1016/j.jmb.2010.05.012DOI Listing
July 2010

Computing multiple sequence/structure alignments with the T-coffee package.

Authors:
Cedric Notredame

Curr Protoc Bioinformatics 2010 Mar;Chapter 3:Unit 3.8.1-25

Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1002/0471250953.bi0308s29DOI Listing
March 2010

Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

Bioinformatics 2009 Oct 30;25(19):2455-65. Epub 2009 Jul 30.

Centre For Genomic Regulation, Pompeus Fabre University, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752613PMC
October 2009

Segment-based multiple sequence alignment.

Bioinformatics 2008 Aug;24(16):i187-92

International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr 63-73, 14195 Berlin, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn281DOI Listing
August 2008

R-Coffee: a web server for accurately aligning noncoding RNA sequences.

Nucleic Acids Res 2008 Jul 15;36(Web Server issue):W10-3. Epub 2008 May 15.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gkn278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447777PMC
July 2008

R-Coffee: a method for multiple alignment of non-coding RNA.

Nucleic Acids Res 2008 May 17;36(9):e52. Epub 2008 Apr 17.

The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland.

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http://dx.doi.org/10.1093/nar/gkn174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396437PMC
May 2008

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.

BMC Genomics 2007 Oct 31;8:398. Epub 2007 Oct 31.

Computational Cancer Genomics Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-8-398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211324PMC
October 2007

Recent evolutions of multiple sequence alignment algorithms.

PLoS Comput Biol 2007 Aug;3(8):e123

Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, Marseille, France.

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http://dx.doi.org/10.1371/journal.pcbi.0030123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963500PMC
August 2007

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

Nucleic Acids Res 2007 Jul 25;35(Web Server issue):W645-8. Epub 2007 May 25.

Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne.

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http://dx.doi.org/10.1093/nar/gkm333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933118PMC
July 2007

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Bioinformatics 2006 Oct;22(19):2439-40

CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR-13288, Marseille cedex 09, France.

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http://dx.doi.org/10.1093/bioinformatics/btl404DOI Listing
October 2006

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W600-3

Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR 13288, Marseille cedex 09, France.

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http://dx.doi.org/10.1093/nar/gkl170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538918PMC
July 2006

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W604-8

Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France.

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http://dx.doi.org/10.1093/nar/gkl092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538866PMC
July 2006

The iRMSD: a local measure of sequence alignment accuracy using structural information.

Bioinformatics 2006 Jul;22(14):e35-9

Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl218DOI Listing
July 2006

M-Coffee: combining multiple sequence alignment methods with T-Coffee.

Nucleic Acids Res 2006 23;34(6):1692-9. Epub 2006 Mar 23.

The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland.

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http://dx.doi.org/10.1093/nar/gkl091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1410914PMC
April 2006

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

Bioinformatics 2003 ;19 Suppl 1:i215-21

Department of Biochemistry, University College, Cork, Ireland.

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http://dx.doi.org/10.1093/bioinformatics/btg1029DOI Listing
October 2004

3DCoffee: combining protein sequences and structures within multiple sequence alignments.

J Mol Biol 2004 Jul;340(2):385-95

Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360400521
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http://dx.doi.org/10.1016/j.jmb.2004.04.058DOI Listing
July 2004

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W37-40

Information Génomique et Structurale UPR2589-CNRS, CNRS, 31, Chemin Joseph Aiguier, 13 402 Marseille Cedex 20, France.

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http://dx.doi.org/10.1093/nar/gkh382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441520PMC
July 2004

CaspR: a web server for automated molecular replacement using homology modelling.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W606-9

Information Génomique & Structurale (UPR CNRS 2589), Institut de Biologie Structurale et Microbiologie, 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

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http://dx.doi.org/10.1093/nar/gkh400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441538PMC
July 2004

Computing multiple sequence/structure alignments with the T-coffee package.

Curr Protoc Bioinformatics 2004 Feb;Chapter 3:Unit3.8

Swiss Institute of Bioinformatics, Epalinges, Switzerland.

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http://dx.doi.org/10.1002/0471250953.bi0308s04DOI Listing
February 2004

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

Nucleic Acids Res 2003 Jul;31(13):3503-6

Information Genomique et Structurale, CNRS, 31 Chemin Joseph Aiguier, 13 402 Marseille Cedex 20, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168929PMC
http://dx.doi.org/10.1093/nar/gkg522DOI Listing
July 2003

Recent progress in multiple sequence alignment: a survey.

Pharmacogenomics 2002 Jan;3(1):131-44

Information Génétique et Structurale, UMR 1889, 31 Chemin Joseph Aiguier, 13 006 Marseille, France.

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http://dx.doi.org/10.1517/14622416.3.1.131DOI Listing
January 2002