The Eukaryote Genome Annotation Platform at Genoscope (2009)
Betina M. Porcel, Franck Aniere, Sylvain Bonneval, Benjamin Noel, Jean-Marc Aury, Corinne Da Silva, ...
The Genoscope annotation workflow for eukaryote genomes relies on evidence from ab initio gene models predictions combined with homology searches, using collections of expressed sequences - full...
Annotating genomes with massive-scale RNA sequencing (2008)
Denoeud, France, Aury, Jean-Marc, Da Silva, Corinne, Noel, Benjamin, Rogier, Odile, Delledonne, Massimo, ...
Abstract Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been...
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita (2008)
Abad, Pierre, Gouzy, Jerome, Aury, Jean-Marc, Castagnone-Sereno, Philippe, Danchin, Etienne G. J., Deleury, Emeline, ...
© 2008 Nature Publishing Group. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike license. The definitive version was published in Nature...
The genome sequence of the model ascomycete fungus Podospora anserina (2008)
Espagne, Eric, Lespinet, Olivier, Malagnac, Fabienne, Da Silva, Corinne, Jaillon, Olivier, Porcel, Betina M, ...
Abstract Background The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development....
2008 Espagne et Volume al. 9, Issue 5, Article R77 Open Access (2008)
Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne Da, Olivier Jaillon, Betina M Porcel, ...
The genome sequence of the model ascomycete fungus Podospora anserina
Duret, Laurent, Cohen, Jean, Jubin, Claire, Dessen, Philippe, Goût, Jean-François, Mousset, Sylvain, ...
Ciliates are the only unicellular eukaryotes known to separate germinal and somatic functions. Diploid but silent micronuclei transmit the genetic information to the next sexual generation. Polyploid...
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia (2006)
Plattner, Helmut, Auryl, Jean-Marc, Jaillon, Olivier, Duret, Laurent, Noel, Benjamin, Jubin, Claire, ...
The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly...
Gene Loss and Evolutionary Rates Following Whole Genome Duplication in Teleost Fishes (2006)
Brunet, Frédéric G., Crollius, Hugues Roest, Paris, Mathilde, Aury, Jean-Marc, Gibert, Patricia, Jaillon, Olivier, ...
Teleost fishes provide the first unambiguous support for ancient whole genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be...
Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes (2006)
Brunet, Frédéric G., Crollius, Hugues Roest, Paris, Mathilde, Aury, Jean-Marc, Gibert, Patricia, Jaillon, Olivier, ...
Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be...
Castelli, Vanina, Aury, Jean-Marc, Jaillon, Olivier, Wincker, Patrick, Clepet, Christian, Menard, Manuella, ...
To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides...
Lutfalla, Georges, Crollius, Hugues, Stange-thomann, Nicole, Jaillon, Olivier, Mogensen, Knud, Monneron, Danièle
Abstract Background The high degree of sequence conservation between coding regions in fish and mammals can be exploited to identify genes in mammalian genomes by comparison with the sequence of...
Jaillon, Olivier, Dossat, Carole, Eckenberg, Ralph, Eiglmeier, Karin, Segurens, Béatrice, Aury, Jean-Marc, ...
We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily...
Bouneau, Laurence, Fischer, Cécile, Ozouf-Costaz, Catherine, Froschauer, Alexander, Jaillon, Olivier, Coutanceau, Jean-Pierre, ...
The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR...
Bouneau, Laurence, Fischer, Cécile, Ozouf-Costaz, Catherine, Froschauer, Alexander, Jaillon, Olivier, Coutanceau, Jean-Pierre, ...
The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR...
Grützner,Frank, Roest Crollius,Hugues, Lütjens,Götz, Jaillon,Olivier, Weissenbach,Jean, Ropers,Hans Hilger, ...
The freshwater pufferfish Tetraodon nigroviridis (TNI) has become highly attractive as a compact reference vertebrate genome for gene finding and validation. We have mapped genes, which are more or...
Grützner, Frank, Roest Crollius, Hugues, Lütjens, Götz, Jaillon, Olivier, Weissenbach, Jean, Ropers, Hans Hilger, ...
The freshwater pufferfish Tetraodon nigroviridis (TNI) has become highly attractive as a compact reference vertebrate genome for gene finding and validation. We have mapped genes, which are more or...
Grützner, Frank, Crollius, Hugues Roest, Lütjens, Götz, Jaillon, Olivier, Weissenbach, Jean, Ropers, Hans-Hilger, ...
Grützner, Frank, Crollius, Hugues Roest, Lütjens, Götz, Jaillon, Olivier, Weissenbach, Jean, Ropers, Hans-Hilger, ...
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis (2002)
Journet, Etienne-Pascal, Van Tuinen, Diederik, Gouzy, Jérome, Crespeau, Hervé, Carreau, Véronique, Farmer, Mary-Jo, ...
We report on a large‐scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula...
Bolotin, Alexander, Wincker, Patrick, Mauger, Stéphane, Jaillon, Olivier, Malarme, Karine, Weissenbach, Jean, ...
Bolotin, Alexander, Wincker, Patrick, Mauger, Stéphane, Jaillon, Olivier, Malarme, Karine, Weissenbach, Jean, ...
Charlier, Carole, Segers, Karin, Wagenaar, Danny, Karim, Latifa, Berghmans, Stéphane, Jaillon, Olivier, ...
Bolotin, Alexander, Wincker, Patrick, Mauger, Stéphane, Jaillon, Olivier, Malarme, Karine, Weissenbach, Jean, ...
Dasilva, Corinne, Hadji, Hajer, Ozouf-Costaz, Catherine, Nicaud, Sophie, Jaillon, Olivier, Weissenbach, Jean, ...
Tetraodon nigroviridis is among the smallest known vertebrate genomes and as such represents an interesting model for studying genome architecture and evolution. Previous studies have shown that...
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
Journet, Etienne-Pascal, Van Tuinen, Diederik, Gouzy, Jérome, Crespeau, Hervé, Carreau, Véronique, Farmer, Mary-Jo, ...
We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during...
Lutfalla, Georges, Crollius, Hugues Roest, Stange-thomann, Nicole, Jaillon, Olivier, Mogensen, Knud, Monneron, Danièle
Grützner, Frank, Crollius, Hugues Roest, Lütjens, Götz, Jaillon, Olivier, Weissenbach, Jean, Ropers, Hans-Hilger, ...
The freshwater pufferfish Tetraodon nigroviridis (TNI) has become highly attractive as a compact reference vertebrate genome for gene finding and validation. We have mapped genes, which are more or...
Charlier, Carole, Segers, Karin, Wagenaar, Danny, Karim, Latifa, Berghmans, Stéphane, Jaillon, Olivier, ...
Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of the MULGE5-OY3 marker interval known to contain the clpg locus, were completely...
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
Bolotin, Alexander, Wincker, Patrick, Mauger, Stéphane, Jaillon, Olivier, Malarme, Karine, Weissenbach, Jean, ...
Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic...
Castelli, Vanina, Aury, Jean-Marc, Jaillon, Olivier, Wincker, Patrick, Clepet, Christian, Menard, Manuella, ...
To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides...
Jaillon, Olivier, Dossat, Carole, Eckenberg, Ralph, Eiglmeier, Karin, Segurens, Béatrice, Aury, Jean-Marc, ...
We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily...
Bouneau, Laurence, Fischer, Cécile, Ozouf-Costaz, Catherine, Froschauer, Alexander, Jaillon, Olivier, Coutanceau, Jean-Pierre, ...
The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR...
Dasilva, Corinne, Hadji, Hajer, Ozouf-Costaz, Catherine, Nicaud, Sophie, Jaillon, Olivier, Weissenbach, Jean, ...
Tetraodon nigroviridis is among the smallest known vertebrate genomes and as such represents an interesting model for studying genome architecture and evolution. Previous studies have shown that...
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
Journet, Etienne-Pascal, Van Tuinen, Diederik, Gouzy, Jérome, Crespeau, Hervé, Carreau, Véronique, Farmer, Mary-Jo, ...
We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during...
Lutfalla, Georges, Crollius, Hugues Roest, Stange-thomann, Nicole, Jaillon, Olivier, Mogensen, Knud, Monneron, Danièle
Grützner, Frank, Crollius, Hugues Roest, Lütjens, Götz, Jaillon, Olivier, Weissenbach, Jean, Ropers, Hans-Hilger, ...
The freshwater pufferfish Tetraodon nigroviridis (TNI) has become highly attractive as a compact reference vertebrate genome for gene finding and validation. We have mapped genes, which are more or...
Charlier, Carole, Segers, Karin, Wagenaar, Danny, Karim, Latifa, Berghmans, Stéphane, Jaillon, Olivier, ...
Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of the MULGE5-OY3 marker interval known to contain the clpg locus, were completely...
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
Bolotin, Alexander, Wincker, Patrick, Mauger, Stéphane, Jaillon, Olivier, Malarme, Karine, Weissenbach, Jean, ...
Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic...
Castelli, Vanina, Aury, Jean-Marc, Jaillon, Olivier, Wincker, Patrick, Clepet, Christian, Menard, Manuella, ...
To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides...
Jaillon, Olivier, Dossat, Carole, Eckenberg, Ralph, Eiglmeier, Karin, Segurens, Béatrice, Aury, Jean-Marc, ...
We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily...
Bouneau, Laurence, Fischer, Cécile, Ozouf-Costaz, Catherine, Froschauer, Alexander, Jaillon, Olivier, Coutanceau, Jean-Pierre, ...
The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR...
The genome sequence of the model ascomycete fungus Podospora anserina
Espagne, Eric, Lespinet, Olivier, Malagnac, Fabienne, Da Silva, Corinne, Jaillon, Olivier, Porcel, Betina M, ...
A 10X draft sequence of Podospora anserina genome shows highly dynamic evolution since its divergence from Neurospora crassa.
Duret, Laurent, Cohen, Jean, Jubin, Claire, Dessen, Philippe, Goût, Jean-François, Mousset, Sylvain, ...
Ciliates are the only unicellular eukaryotes known to separate germinal and somatic functions. Diploid but silent micronuclei transmit the genetic information to the next sexual generation. Polyploid...
Annotating genomes with massive-scale RNA sequencing
Denoeud, France, Aury, Jean-Marc, Da Silva, Corinne, Noel, Benjamin, Rogier, Odile, Delledonne, Massimo, ...
A method for de novo genome annotation using high-throughput cDNA sequencing data.