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Items: 38

1.

POsitive Multistate Protein design.

Vucinic J, Simoncini D, Ruffini M, Barbe S, Schiex T.

Bioinformatics. 2019 Jun 14. pii: btz497. doi: 10.1093/bioinformatics/btz497. [Epub ahead of print]

PMID:
31199465
2.

EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes.

Sallet E, Gouzy J, Schiex T.

Methods Mol Biol. 2019;1962:97-120. doi: 10.1007/978-1-4939-9173-0_6.

PMID:
31020556
3.

Computational design of symmetrical eight-bladed β-propeller proteins.

Noguchi H, Addy C, Simoncini D, Wouters S, Mylemans B, Van Meervelt L, Schiex T, Zhang KYJ, Tame JRH, Voet ARD.

IUCrJ. 2019 Jan 1;6(Pt 1):46-55. doi: 10.1107/S205225251801480X. eCollection 2019 Jan 1.

4.

A structural homology approach for computational protein design with flexible backbone.

Simoncini D, Zhang KYJ, Schiex T, Barbe S.

Bioinformatics. 2019 Jul 15;35(14):2418-2426. doi: 10.1093/bioinformatics/bty975.

PMID:
30496341
5.

Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems.

Charpentier A, Mignon D, Barbe S, Cortes J, Schiex T, Simonson T, Allouche D.

J Chem Inf Model. 2019 Jan 28;59(1):127-136. doi: 10.1021/acs.jcim.8b00510. Epub 2018 Nov 14.

PMID:
30380857
6.

Cost function network-based design of protein-protein interactions: predicting changes in binding affinity.

Viricel C, de Givry S, Schiex T, Barbe S.

Bioinformatics. 2018 Aug 1;34(15):2581-2589. doi: 10.1093/bioinformatics/bty092.

PMID:
29474517
7.

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

Blanc-Mathieu R, Perfus-Barbeoch L, Aury JM, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Bailly-Bechet M, Castagnone-Sereno P, Flot JF, Kozlowski DK, Cazareth J, Couloux A, Da Silva C, Guy J, Kim-Jo YJ, Rancurel C, Schiex T, Abad P, Wincker P, Danchin EGJ.

PLoS Genet. 2017 Jun 8;13(6):e1006777. doi: 10.1371/journal.pgen.1006777. eCollection 2017 Jun.

8.

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.

Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage G, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB.

Nature. 2017 Jun 1;546(7656):148-152. doi: 10.1038/nature22380. Epub 2017 May 22.

PMID:
28538728
9.

Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction.

Simoncini D, Schiex T, Zhang KY.

Proteins. 2017 May;85(5):852-858. doi: 10.1002/prot.25244. Epub 2017 Mar 3.

PMID:
28066917
10.

Deterministic Search Methods for Computational Protein Design.

Traoré S, Allouche D, André I, Schiex T, Barbe S.

Methods Mol Biol. 2017;1529:107-123.

PMID:
27914047
11.

Fast search algorithms for computational protein design.

Traoré S, Roberts KE, Allouche D, Donald BR, André I, Schiex T, Barbe S.

J Comput Chem. 2016 May 5;37(12):1048-58. doi: 10.1002/jcc.24290. Epub 2016 Feb 2.

12.

Guaranteed Discrete Energy Optimization on Large Protein Design Problems.

Simoncini D, Allouche D, de Givry S, Delmas C, Barbe S, Schiex T.

J Chem Theory Comput. 2015 Dec 8;11(12):5980-9. doi: 10.1021/acs.jctc.5b00594. Epub 2015 Nov 25.

PMID:
26610100
13.

EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes.

Sallet E, Gouzy J, Schiex T.

Bioinformatics. 2014 Sep 15;30(18):2659-61. doi: 10.1093/bioinformatics/btu366. Epub 2014 May 30.

PMID:
24880686
14.

A new framework for computational protein design through cost function network optimization.

Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Schiex T, Barbe S.

Bioinformatics. 2013 Sep 1;29(17):2129-36. doi: 10.1093/bioinformatics/btt374. Epub 2013 Jul 10.

PMID:
23842814
15.

Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.

Sallet E, Roux B, Sauviac L, Jardinaud MF, Carrère S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D, Bruand C, Schiex T.

DNA Res. 2013 Aug;20(4):339-54. doi: 10.1093/dnares/dst014. Epub 2013 Apr 18.

16.

Detecting long tandem duplications in genomic sequences.

Audemard E, Schiex T, Faraut T.

BMC Bioinformatics. 2012 May 8;13:83. doi: 10.1186/1471-2105-13-83.

17.

Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis.

Vignes M, Vandel J, Allouche D, Ramadan-Alban N, Cierco-Ayrolles C, Schiex T, Mangin B, de Givry S.

PLoS One. 2011;6(12):e29165. doi: 10.1371/journal.pone.0029165. Epub 2011 Dec 27.

18.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

19.

The genome of Theobroma cacao.

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C.

Nat Genet. 2011 Feb;43(2):101-8. doi: 10.1038/ng.736. Epub 2010 Dec 26.

PMID:
21186351
20.

Contribution of radiation hybrids to genome mapping in domestic animals.

Faraut T, de Givry S, Hitte C, Lahbib-Mansais Y, Morisson M, Milan D, Schiex T, Servin B, Vignal A, Galibert F, Yerle M.

Cytogenet Genome Res. 2009;126(1-2):21-33. doi: 10.1159/000245904. Epub 2009 Dec 9.

PMID:
20016154
21.

FrameDP: sensitive peptide detection on noisy matured sequences.

Gouzy J, Carrere S, Schiex T.

Bioinformatics. 2009 Mar 1;25(5):670-1. doi: 10.1093/bioinformatics/btp024. Epub 2009 Jan 19.

22.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P.

Nat Biotechnol. 2008 Aug;26(8):909-15. doi: 10.1038/nbt.1482. Epub 2008 Jul 27.

PMID:
18660804
23.

LeARN: a platform for detecting, clustering and annotating non-coding RNAs.

Noirot C, Gaspin C, Schiex T, Gouzy J.

BMC Bioinformatics. 2008 Jan 14;9:21. doi: 10.1186/1471-2105-9-21.

24.

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.

Aubourg S, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Lecharny A, Renou JP.

BMC Genomics. 2007 Nov 2;8:401.

25.

High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.

Prasad A, Schiex T, McKay S, Murdoch B, Wang Z, Womack JE, Stothard P, Moore SS.

BMC Genomics. 2007 Sep 4;8:310.

26.

A comparative genome approach to marker ordering.

Faraut T, de Givry S, Chabrier P, Derrien T, Galibert F, Hitte C, Schiex T.

Bioinformatics. 2007 Jan 15;23(2):e50-6.

PMID:
17237105
27.

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes.

Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND.

Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14959-64. Epub 2006 Sep 26. Erratum in: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):18026. Scheix, Thomas [corrected to Schiex, Thomas].

28.

Searching RNA motifs and their intermolecular contacts with constraint networks.

Thébault P, de Givry S, Schiex T, Gaspin C.

Bioinformatics. 2006 Sep 1;22(17):2074-80. Epub 2006 Jul 4.

PMID:
16820426
29.

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.

30.

CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.

de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T.

Bioinformatics. 2005 Apr 15;21(8):1703-4. Epub 2004 Dec 14.

PMID:
15598829
31.

EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences.

Foissac S, Bardou P, Moisan A, Cros MJ, Schiex T.

Nucleic Acids Res. 2003 Jul 1;31(13):3742-5.

32.
33.

Rearranged gene order between pig and human in a QTL region on SSC 7.

Demeure O, Renard C, Yerle M, Faraut T, Riquet J, Robic A, Schiex T, Rink A, Milan D.

Mamm Genome. 2003 Jan;14(1):71-80.

PMID:
12532270
34.

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.

Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer MJ, Niebel A, Schiex T, Jaillon O, Chatagnier O, Godiard L, Micheli F, Kahn D, Gianinazzi-Pearson V, Gamas P.

Nucleic Acids Res. 2002 Dec 15;30(24):5579-92. Erratum in: Nucleic Acids Res. 2003 Mar 15;31(6):1803.

35.

Current methods of gene prediction, their strengths and weaknesses.

Mathé C, Sagot MF, Schiex T, Rouzé P.

Nucleic Acids Res. 2002 Oct 1;30(19):4103-17. Review.

36.

Genome sequence of the plant pathogen Ralstonia solanacearum.

Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA.

Nature. 2002 Jan 31;415(6871):497-502.

PMID:
11823852
37.

A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.

Laurent V, Wajnberg E, Mangin B, Schiex T, Gaspin C, Vanlerberghe-Masutti F.

Genetics. 1998 Sep;150(1):275-82.

38.

CARTHAGENE: constructing and joining maximum likelihood genetic maps.

Schiex T, Gaspin C.

Proc Int Conf Intell Syst Mol Biol. 1997;5:258-67.

PMID:
9322047

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