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Items: 39

1.

Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster.

Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E, Ferrandon D.

Microbiol Resour Announc. 2019 Aug 1;8(31). pii: e00077-19. doi: 10.1128/MRA.00077-19.

2.

Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay.

Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L.

Methods Enzymol. 2018;612:47-66. doi: 10.1016/bs.mie.2018.07.003. Epub 2018 Aug 29.

PMID:
30502954
3.

Oak genome reveals facets of long lifespan.

Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J.

Nat Plants. 2018 Jul;4(7):440-452. doi: 10.1038/s41477-018-0172-3. Epub 2018 Jun 18.

4.

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria.

Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H.

BMC Genomics. 2017 Nov 16;18(1):882. doi: 10.1186/s12864-017-4242-0.

5.

Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001.

Caldelari I, Chane-Woon-Ming B, Noirot C, Moreau K, Romby P, Gaspin C, Marzi S.

Genome Announc. 2017 Aug 10;5(32). pii: e00783-17. doi: 10.1128/genomeA.00783-17.

6.

Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes.

Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E.

DNA Res. 2017 Jun 1;24(3):251-260. doi: 10.1093/dnares/dsx002.

7.

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria.

Bécavin C, Koutero M, Tchitchek N, Cerutti F, Lechat P, Maillet N, Hoede C, Chiapello H, Gaspin C, Cossart P.

mSystems. 2017 Mar 14;2(2). pii: e00186-16. doi: 10.1128/mSystems.00186-16. eCollection 2017 Mar-Apr.

8.

Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing.

Juanchich A, Bardou P, Rué O, Gabillard JC, Gaspin C, Bobe J, Guiguen Y.

BMC Genomics. 2016 Mar 1;17:164. doi: 10.1186/s12864-016-2505-9.

9.

Jflow: a workflow management system for web applications.

Mariette J, Escudié F, Bardou P, Nabihoudine I, Noirot C, Trotard MS, Gaspin C, Klopp C.

Bioinformatics. 2016 Feb 1;32(3):456-8. doi: 10.1093/bioinformatics/btv589. Epub 2015 Oct 10.

10.

The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes.

Belkorchia A, Gasc C, Polonais V, Parisot N, Gallois N, Ribière C, Lerat E, Gaspin C, Pombert JF, Peyret P, Peyretaillade E.

PLoS One. 2015 Sep 30;10(9):e0139075. doi: 10.1371/journal.pone.0139075. eCollection 2015.

11.

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data.

Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF.

BMC Bioinformatics. 2015 May 29;16:179. doi: 10.1186/s12859-015-0594-0.

12.

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A.

Mol Ecol Resour. 2016 Jan;16(1):254-65. doi: 10.1111/1755-0998.12425. Epub 2015 May 29.

PMID:
25944057
13.

Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates.

Esquerré T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign-Bousquet M, Girbal L.

BMC Genomics. 2015 Apr 9;16:275. doi: 10.1186/s12864-015-1482-8.

14.

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks.

Thébault P, Bourqui R, Benchimol W, Gaspin C, Sirand-Pugnet P, Uricaru R, Dutour I.

Brief Bioinform. 2015 Sep;16(5):795-805. doi: 10.1093/bib/bbu045. Epub 2014 Dec 3.

15.

Structural and functional partitioning of bread wheat chromosome 3B.

Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C.

Science. 2014 Jul 18;345(6194):1249721. doi: 10.1126/science.1249721.

16.

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noël B, Bento P, Da Silva C, Labadie K, Alberti A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet E, Guyomard R, Galiana D, Bobe J, Volff JN, Genêt C, Wincker P, Jaillon O, Roest Crollius H, Guiguen Y.

Nat Commun. 2014 Apr 22;5:3657. doi: 10.1038/ncomms4657.

17.

Diversity of CRISPR systems in the euryarchaeal Pyrococcales.

Norais C, Moisan A, Gaspin C, Clouet-d'Orval B.

RNA Biol. 2013 May;10(5):659-70. doi: 10.4161/rna.23927. Epub 2013 Feb 19. Review.

18.

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C.

RNA. 2011 Nov;17(11):1947-56. doi: 10.1261/rna.2844911. Epub 2011 Sep 23.

19.

Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi.

Phok K, Moisan A, Rinaldi D, Brucato N, Carpousis AJ, Gaspin C, Clouet-d'Orval B.

BMC Genomics. 2011 Jun 13;12:312. doi: 10.1186/1471-2164-12-312.

20.

Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function.

Gaspin C, Rami JF, Lescure B.

BMC Plant Biol. 2010 Dec 20;10:283. doi: 10.1186/1471-2229-10-283.

21.

Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions.

Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P.

PLoS One. 2010 May 20;5(5):e10725. doi: 10.1371/journal.pone.0010725.

22.

A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.

Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P.

Nucleic Acids Res. 2009 Nov;37(21):7239-57. doi: 10.1093/nar/gkp668.

23.

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.

Grosjean H, Gaspin C, Marck C, Decatur WA, de Crécy-Lagard V.

BMC Genomics. 2008 Oct 9;9:470. doi: 10.1186/1471-2164-9-470.

24.

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.

25.

Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.

Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P.

Genes Dev. 2007 Jun 1;21(11):1353-66.

26.

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
27.

Two different mechanisms for tRNA ribose methylation in Archaea: a short survey.

Clouet-d'Orval B, Gaspin C, Mougin A.

Biochimie. 2005 Sep-Oct;87(9-10):889-95. Epub 2005 Mar 7.

PMID:
16164996
28.

The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.

Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A.

RNA. 2005 Jul;11(7):1051-63.

29.

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.

Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, Couloux A, Déhais P, Deléage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlné G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Rivière S, Rombauts S, Rouzé P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M, Lecharny A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6.

30.

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
31.
33.

Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes.

Gaspin C, Cavaillé J, Erauso G, Bachellerie JP.

J Mol Biol. 2000 Apr 7;297(4):895-906. Erratum in: J Mol Biol 2000 Jul 21;300(4):1017-8.

PMID:
10736225
34.

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.

35.

ESSA: an integrated and interactive computer tool for analysing RNA secondary structure.

Chetouani F, Monestié P, Thébault P, Gaspin C, Michot B.

Nucleic Acids Res. 1997 Sep 1;25(17):3514-22.

36.

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
37.
38.

DRAWNA: a program for drawing schematic views of nucleic acids.

Massire C, Gaspin C, Westhof E.

J Mol Graph. 1994 Sep;12(3):201-6, 196.

PMID:
7529557
39.

Automatic display of RNA secondary structures.

Muller G, Gaspin C, Etienne A, Westhof E.

Comput Appl Biosci. 1993 Oct;9(5):551-61.

PMID:
7507400

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