Publications by authors named "Raymond Ripp"

29Publications

Circular code motifs in the ribosome: a missing link in the evolution of translation?

RNA 2019 12 10;25(12):1714-1730. Epub 2019 Sep 10.

Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France.

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http://dx.doi.org/10.1261/rna.072074.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859856PMC
December 2019

OrthoInspector 3.0: open portal for comparative genomics.

Nucleic Acids Res 2019 01;47(D1):D411-D418

Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323921PMC
January 2019

Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes.

Biosystems 2019 Jan 24;175:57-74. Epub 2018 Oct 24.

CSTB, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400, Illkirch, France. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03032647183031
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http://dx.doi.org/10.1016/j.biosystems.2018.10.014DOI Listing
January 2019

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

Life (Basel) 2017 Dec 3;7(4). Epub 2017 Dec 3.

Complex Systems and Translational Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.

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http://dx.doi.org/10.3390/life7040052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745565PMC
December 2017

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers.

J Med Internet Res 2017 06 16;19(6):e212. Epub 2017 Jun 16.

ICUBE UMR 7357, Complex Systems and Translational Bioinformatics, Université de Strasbourg - CNRS - FMTS, Strasbourg, France.

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http://dx.doi.org/10.2196/jmir.6676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493784PMC
June 2017

MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases.

Hum Mutat 2017 10 27;38(10):1316-1324. Epub 2017 Jun 27.

Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France.

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http://dx.doi.org/10.1002/humu.23277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638098PMC
October 2017

Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling.

Mol Biol Evol 2017 08;34(8):2016-2034

Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, Fédération de Médecine Translationnelle, Strasbourg, France.

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http://dx.doi.org/10.1093/molbev/msx146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850483PMC
August 2017

Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse.

PLoS One 2015 23;10(2):e0118024. Epub 2015 Feb 23.

LBGI Bioinformatique et Génomique Intégratives, ICube Laboratory and Strasbourg Federation of Translational Medecine (FMTS), University of Strasbourg and CNRS, Strasbourg, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118024PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338146PMC
January 2016

OrthoInspector 2.0: Software and database updates.

Bioinformatics 2015 Feb 1;31(3):447-8. Epub 2014 Oct 1.

LBGI, Computer Science Department, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de médecine translationnelle, 4 rue Kirschleger 67085 Strasbourg, France and Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD.

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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu642DOI Listing
February 2015

PARSEC: PAtteRn SEarch and Contextualization.

Bioinformatics 2013 Oct 7;29(20):2643-4. Epub 2013 Aug 7.

Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) CNRS/INSERM/UDS, 67404, Illkirch, France.

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http://dx.doi.org/10.1093/bioinformatics/btt455DOI Listing
October 2013

Seven new loci associated with age-related macular degeneration.

Authors:
Lars G Fritsche Wei Chen Matthew Schu Brian L Yaspan Yi Yu Gudmar Thorleifsson Donald J Zack Satoshi Arakawa Valentina Cipriani Stephan Ripke Robert P Igo Gabriëlle H S Buitendijk Xueling Sim Daniel E Weeks Robyn H Guymer Joanna E Merriam Peter J Francis Gregory Hannum Anita Agarwal Ana Maria Armbrecht Isabelle Audo Tin Aung Gaetano R Barile Mustapha Benchaboune Alan C Bird Paul N Bishop Kari E Branham Matthew Brooks Alexander J Brucker William H Cade Melinda S Cain Peter A Campochiaro Chi-Chao Chan Ching-Yu Cheng Emily Y Chew Kimberly A Chin Itay Chowers David G Clayton Radu Cojocaru Yvette P Conley Belinda K Cornes Mark J Daly Baljean Dhillon Albert O Edwards Evangelos Evangelou Jesen Fagerness Henry A Ferreyra James S Friedman Asbjorg Geirsdottir Ronnie J George Christian Gieger Neel Gupta Stephanie A Hagstrom Simon P Harding Christos Haritoglou John R Heckenlively Frank G Holz Guy Hughes John P A Ioannidis Tatsuro Ishibashi Peronne Joseph Gyungah Jun Yoichiro Kamatani Nicholas Katsanis Claudia N Keilhauer Jane C Khan Ivana K Kim Yutaka Kiyohara Barbara E K Klein Ronald Klein Jaclyn L Kovach Igor Kozak Clara J Lee Kristine E Lee Peter Lichtner Andrew J Lotery Thomas Meitinger Paul Mitchell Saddek Mohand-Saïd Anthony T Moore Denise J Morgan Margaux A Morrison Chelsea E Myers Adam C Naj Yusuke Nakamura Yukinori Okada Anton Orlin M Carolina Ortube Mohammad I Othman Chris Pappas Kyu Hyung Park Gayle J T Pauer Neal S Peachey Olivier Poch Rinki Ratna Priya Robyn Reynolds Andrea J Richardson Raymond Ripp Guenther Rudolph Euijung Ryu José-Alain Sahel Debra A Schaumberg Hendrik P N Scholl Stephen G Schwartz William K Scott Humma Shahid Haraldur Sigurdsson Giuliana Silvestri Theru A Sivakumaran R Theodore Smith Lucia Sobrin Eric H Souied Dwight E Stambolian Hreinn Stefansson Gwen M Sturgill-Short Atsushi Takahashi Nirubol Tosakulwong Barbara J Truitt Evangelia E Tsironi André G Uitterlinden Cornelia M van Duijn Lingam Vijaya Johannes R Vingerling Eranga N Vithana Andrew R Webster H-Erich Wichmann Thomas W Winkler Tien Y Wong Alan F Wright Diana Zelenika Ming Zhang Ling Zhao Kang Zhang Michael L Klein Gregory S Hageman G Mark Lathrop Kari Stefansson Rando Allikmets Paul N Baird Michael B Gorin Jie Jin Wang Caroline C W Klaver Johanna M Seddon Margaret A Pericak-Vance Sudha K Iyengar John R W Yates Anand Swaroop Bernhard H F Weber Michiaki Kubo Margaret M Deangelis Thierry Léveillard Unnur Thorsteinsdottir Jonathan L Haines Lindsay A Farrer Iris M Heid Gonçalo R Abecasis

Nat Genet 2013 Apr 3;45(4):433-9, 439e1-2. Epub 2013 Mar 3.

Institute of Human Genetics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1038/ng.2578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739472PMC
April 2013

Functional insights into the core-TFIIH from a comparative survey.

Genomics 2013 Mar 10;101(3):178-86. Epub 2012 Nov 10.

Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, UDS), BP163, 67404 Illkirch Cedex, France.

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http://dx.doi.org/10.1016/j.ygeno.2012.11.003DOI Listing
March 2013

Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism.

BMC Genomics 2012 Jul 2;13:297. Epub 2012 Jul 2.

Department of Molecular and Cellular Genetics, UMR7156 CNRS/Université de Strasbourg, 21 rue Descartes, 67084, Strasbourg, France.

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http://dx.doi.org/10.1186/1471-2164-13-297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473312PMC
July 2012

KD4v: Comprehensible Knowledge Discovery System for Missense Variant.

Nucleic Acids Res 2012 Jul 27;40(Web Server issue):W71-5. Epub 2012 May 27.

Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.

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http://dx.doi.org/10.1093/nar/gks474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394327PMC
July 2012

MSV3d: database of human MisSense Variants mapped to 3D protein structure.

Database (Oxford) 2012 3;2012:bas018. Epub 2012 Apr 3.

Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (UMR7104), 67404 Illkirch.

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http://dx.doi.org/10.1093/database/bas018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317913PMC
June 2012

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels.

BMC Genomics 2011 Oct 28;12:530. Epub 2011 Oct 28.

CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29682 Roscoff, France.

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http://dx.doi.org/10.1186/1471-2164-12-530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218092PMC
October 2011

The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina.

Hum Mol Genet 2010 Jan 20;19(2):250-61. Epub 2009 Oct 20.

Department of Genetics, Institut de la Vision, INSERM Université Pierre et Marie Curie-Paris 6, UMR-S 968, Paris, France.

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http://dx.doi.org/10.1093/hmg/ddp484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796890PMC
January 2010

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina.

BMC Genomics 2008 May 5;9:208. Epub 2008 May 5.

Laboratoire de Bioiformatique et de Genomique Integratives, Institut de Génétique et de Biologie Moléculaire et Céllulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.

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http://dx.doi.org/10.1186/1471-2164-9-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386825PMC
May 2008

Blast sampling for structural and functional analyses.

BMC Bioinformatics 2007 Feb 23;8:62. Epub 2007 Feb 23.

Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.

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http://dx.doi.org/10.1186/1471-2105-8-62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1819393PMC
February 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

The evolutionary origin of peroxisomes: an ER-peroxisome connection.

Mol Biol Evol 2006 Apr 1;23(4):838-45. Epub 2006 Feb 1.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Sante et de la Recherche Medicale/Université Louis Pasteur/Collège de France, Illkirch, France.

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http://dx.doi.org/10.1093/molbev/msj103DOI Listing
April 2006

ICDS database: interrupted CoDing sequences in prokaryotic genomes.

Nucleic Acids Res 2006 Jan;34(Database issue):D338-43

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France.

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http://dx.doi.org/10.1093/nar/gkj060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347423PMC
January 2006

Structural genomics of eukaryotic targets at a laboratory scale.

J Struct Funct Genomics 2005 ;6(2-3):81-8

Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM/Université Louis Pasteur, Parc d'Innovation, 1 rue Laurent Fries, BP10142, 67404, Illkirch, cedex, France.

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http://dx.doi.org/10.1007/s10969-005-1909-6DOI Listing
June 2006

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.

Proteins 2005 Oct;61(1):127-36

Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Molculaire et Cellulaire, (CNRS/INSERM/ULP), Illkirch Cedex, France.

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http://doi.wiley.com/10.1002/prot.20527
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http://dx.doi.org/10.1002/prot.20527DOI Listing
October 2005

PipeAlign: A new toolkit for protein family analysis.

Nucleic Acids Res 2003 Jul;31(13):3829-32

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168925PMC
http://dx.doi.org/10.1093/nar/gkg518DOI Listing
July 2003

Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.

Nucleic Acids Res 2002 Dec;30(24):5382-90

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, ULP), BP163, 67404 Illkirch Cedex, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140077PMC
http://dx.doi.org/10.1093/nar/gkf693DOI Listing
December 2002