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Items: 17

1.

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.

2.

A comparative transcriptomic approach to understanding the formation of cork.

Boher P, Soler M, Sánchez A, Hoede C, Noirot C, Paiva JAP, Serra O, Figueras M.

Plant Mol Biol. 2018 Jan;96(1-2):103-118. doi: 10.1007/s11103-017-0682-9. Epub 2017 Nov 15.

PMID:
29143299
3.

Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum.

Payton L, Perrigault M, Hoede C, Massabuau JC, Sow M, Huvet A, Boullot F, Fabioux C, Hegaret H, Tran D.

Sci Rep. 2017 Jun 14;7(1):3480. doi: 10.1038/s41598-017-03797-4.

4.

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.

5.

Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress.

Bétous R, Renoud ML, Hoede C, Gonzalez I, Jones N, Longy M, Sensebé L, Cazaux C, Hoffmann JS.

Stem Cells Transl Med. 2017 Jan;6(1):68-76. doi: 10.5966/sctm.2015-0401. Epub 2016 Aug 2.

6.

Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies.

Feugeas JP, Tourret J, Launay A, Bouvet O, Hoede C, Denamur E, Tenaillon O.

Mol Biol Evol. 2016 Oct;33(10):2515-29. doi: 10.1093/molbev/msw105. Epub 2016 Jun 28.

PMID:
27352853
7.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

8.

RNAbrowse: RNA-Seq de novo assembly results browser.

Mariette J, Noirot C, Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C, Klopp C.

PLoS One. 2014 May 13;9(5):e96821. doi: 10.1371/journal.pone.0096821. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e106187.

9.

PASTEC: an automatic transposable element classification tool.

Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H.

PLoS One. 2014 May 2;9(5):e91929. doi: 10.1371/journal.pone.0091929. eCollection 2014.

10.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GH, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ.

Nat Commun. 2011 Feb 15;2:202. doi: 10.1038/ncomms1189.

11.

Animal and human pathogenic Escherichia coli strains share common genetic backgrounds.

Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, Keroudean M, Glodt J, Picard B, Oswald E, Denamur E.

Infect Genet Evol. 2011 Apr;11(3):654-62. doi: 10.1016/j.meegid.2011.02.005. Epub 2011 Feb 13.

PMID:
21324381
12.

Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.

Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, Ver Loren van Themaat E, Brown JK, Butcher SA, Gurr SJ, Lebrun MH, Ridout CJ, Schulze-Lefert P, Talbot NJ, Ahmadinejad N, Ametz C, Barton GR, Benjdia M, Bidzinski P, Bindschedler LV, Both M, Brewer MT, Cadle-Davidson L, Cadle-Davidson MM, Collemare J, Cramer R, Frenkel O, Godfrey D, Harriman J, Hoede C, King BC, Klages S, Kleemann J, Knoll D, Koti PS, Kreplak J, López-Ruiz FJ, Lu X, Maekawa T, Mahanil S, Micali C, Milgroom MG, Montana G, Noir S, O'Connell RJ, Oberhaensli S, Parlange F, Pedersen C, Quesneville H, Reinhardt R, Rott M, Sacristán S, Schmidt SM, Schön M, Skamnioti P, Sommer H, Stephens A, Takahara H, Thordal-Christensen H, Vigouroux M, Wessling R, Wicker T, Panstruga R.

Science. 2010 Dec 10;330(6010):1543-6. doi: 10.1126/science.1194573.

13.

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species.

Lescat M, Hoede C, Clermont O, Garry L, Darlu P, Tuffery P, Denamur E, Picard B.

BMC Microbiol. 2009 Dec 29;9:273. doi: 10.1186/1471-2180-9-273.

14.

A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A.

Lescat M, Calteau A, Hoede C, Barbe V, Touchon M, Rocha E, Tenaillon O, Médigue C, Johnson JR, Denamur E.

Antimicrob Agents Chemother. 2009 Jun;53(6):2283-8. doi: 10.1128/AAC.00123-09. Epub 2009 Apr 13.

15.

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E.

PLoS Genet. 2009 Jan;5(1):e1000344. doi: 10.1371/journal.pgen.1000344. Epub 2009 Jan 23.

16.

Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment.

Nora T, Charpentier C, Tenaillon O, Hoede C, Clavel F, Hance AJ.

J Virol. 2007 Jul;81(14):7620-8. Epub 2007 May 9.

17.

Selection acts on DNA secondary structures to decrease transcriptional mutagenesis.

Hoede C, Denamur E, Tenaillon O.

PLoS Genet. 2006 Nov 3;2(11):e176. Epub 2006 Sep 1.

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