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Items: 1 to 50 of 188

1.

Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation.

Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y.

PLoS Genet. 2019 Aug 22;15(8):e1008013. doi: 10.1371/journal.pgen.1008013. [Epub ahead of print]

2.

Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle.

Lewandowska-Sabat AM, Kirsanova E, Klopp C, Solberg TR, Heringstad B, Østerås O, Boysen P, Olsaker I.

Front Genet. 2019 Jul 26;10:689. doi: 10.3389/fgene.2019.00689. eCollection 2019.

3.

Marangoni Flow in Freely Suspended Liquid Films.

Trittel T, Harth K, Klopp C, Stannarius R.

Phys Rev Lett. 2019 Jun 14;122(23):234501. doi: 10.1103/PhysRevLett.122.234501.

PMID:
31298879
4.

Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation.

Striberny A, Jørgensen EH, Klopp C, Magnanou E.

BMC Genomics. 2019 Jun 27;20(1):529. doi: 10.1186/s12864-019-5874-z.

5.

Transcriptome variation in response to gastrointestinal nematode infection in goats.

Aboshady HM, Mandonnet N, Stear MJ, Arquet R, Bederina M, Sarry J, Tosser-Klopp G, Klopp C, Johansson AM, Jonas E, Bambou JC.

PLoS One. 2019 Jun 20;14(6):e0218719. doi: 10.1371/journal.pone.0218719. eCollection 2019.

6.

The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system.

Du K, Wuertz S, Adolfi M, Kneitz S, Stöck M, Oliveira M, Nóbrega R, Ormanns J, Kloas W, Feron R, Klopp C, Parrinello H, Journot L, He S, Postlethwait J, Meyer A, Guiguen Y, Schartl M.

Sci Rep. 2019 Mar 28;9(1):5293. doi: 10.1038/s41598-019-41457-x.

7.

RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed.

Hérault F, Houée-Bigot M, Baéza E, Bouchez O, Esquerré D, Klopp C, Diot C.

BMC Genomics. 2019 Jan 7;20(1):13. doi: 10.1186/s12864-018-5415-1.

8.

Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents.

Segura A, Bertoni M, Auffret P, Klopp C, Bouchez O, Genthon C, Durand A, Bertin Y, Forano E.

BMC Genomics. 2018 Oct 23;19(1):766. doi: 10.1186/s12864-018-5167-y.

9.

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.

Illikoud N, Klopp C, Roulet A, Bouchez O, Marsaud N, Jaffrès E, Zagorec M.

Stand Genomic Sci. 2018 Oct 10;13:22. doi: 10.1186/s40793-018-0333-z. eCollection 2018.

10.

Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea.

Bertucci A, Pierron F, Gourves PY, Klopp C, Lagarde G, Pereto C, Dufour V, Gonzalez P, Coynel A, Budzinski H, Baudrimont M.

Ecotoxicol Environ Saf. 2018 Dec 15;165:96-106. doi: 10.1016/j.ecoenv.2018.08.090. Epub 2018 Sep 4.

PMID:
30193169
11.

Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing.

Croville G, Le Loc'h G, Zanchetta C, Manno M, Camus-Bouclainville C, Klopp C, Delverdier M, Lucas MN, Donnadieu C, Delpont M, Guérin JL.

J Virol Methods. 2018 Nov;261:34-39. doi: 10.1016/j.jviromet.2018.08.003. Epub 2018 Aug 4.

PMID:
30086381
12.

De novo transcriptome analysis to search for sex-differentiation genes in the Siberian sturgeon.

Vizziano-Cantonnet D, Lasalle A, Di Landro S, Klopp C, Genthon C.

Gen Comp Endocrinol. 2018 Nov 1;268:96-109. doi: 10.1016/j.ygcen.2018.08.007. Epub 2018 Aug 3.

PMID:
30081002
13.

Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout.

Verrier ER, Genet C, Laloë D, Jaffrezic F, Rau A, Esquerre D, Dechamp N, Ciobotaru C, Hervet C, Krieg F, Jouneau L, Klopp C, Quillet E, Boudinot P.

BMC Genomics. 2018 Jun 19;19(1):482. doi: 10.1186/s12864-018-4860-1.

14.

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.

15.

D-GENIES: dot plot large genomes in an interactive, efficient and simple way.

Cabanettes F, Klopp C.

PeerJ. 2018 Jun 4;6:e4958. doi: 10.7717/peerj.4958. eCollection 2018.

16.

Highly Promiscuous Oxidases Discovered in the Bovine Rumen Microbiome.

Ufarté L, Potocki-Veronese G, Cecchini D, Tauzin AS, Rizzo A, Morgavi DP, Cathala B, Moreau C, Cleret M, Robe P, Klopp C, Laville E.

Front Microbiol. 2018 May 4;9:861. doi: 10.3389/fmicb.2018.00861. eCollection 2018.

17.

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle.

Mondet F, Rau A, Klopp C, Rohmer M, Severac D, Le Conte Y, Alaux C.

BMC Genomics. 2018 May 4;19(1):328. doi: 10.1186/s12864-018-4668-z.

18.

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential.

Choque E, Klopp C, Valiere S, Raynal J, Mathieu F.

BMC Genomics. 2018 Mar 15;19(1):200. doi: 10.1186/s12864-018-4574-4.

19.

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation.

Gaulin E, Pel MJC, Camborde L, San-Clemente H, Courbier S, Dupouy MA, Lengellé J, Veyssiere M, Le Ru A, Grandjean F, Cordaux R, Moumen B, Gilbert C, Cano LM, Aury JM, Guy J, Wincker P, Bouchez O, Klopp C, Dumas B.

BMC Biol. 2018 Apr 18;16(1):43. doi: 10.1186/s12915-018-0508-5.

20.

Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling.

Mat AM, Klopp C, Payton L, Jeziorski C, Chalopin M, Amzil Z, Tran D, Wikfors GH, Hégaret H, Soudant P, Huvet A, Fabioux C.

Aquat Toxicol. 2018 Jun;199:127-137. doi: 10.1016/j.aquatox.2018.03.030. Epub 2018 Mar 27.

PMID:
29621672
21.

Ten steps to get started in Genome Assembly and Annotation.

Dominguez Del Angel V, Hjerde E, Sterck L, Capella-Gutierrez S, Notredame C, Vinnere Pettersson O, Amselem J, Bouri L, Bocs S, Klopp C, Gibrat JF, Vlasova A, Leskosek BL, Soler L, Binzer-Panchal M, Lantz H.

F1000Res. 2018 Feb 5;7. pii: ELIXIR-148. doi: 10.12688/f1000research.13598.1. eCollection 2018.

22.

Discovery of carbamate degrading enzymes by functional metagenomics.

Ufarté L, Laville E, Duquesne S, Morgavi D, Robe P, Klopp C, Rizzo A, Pizzut-Serin S, Potocki-Veronese G.

PLoS One. 2017 Dec 14;12(12):e0189201. doi: 10.1371/journal.pone.0189201. eCollection 2017.

23.

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing.

Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, Esquerré D, Barbieri J, Klopp C, Philippe R, Blanquet V, Boichard D, Rocha D, Boussaha M.

Genet Sel Evol. 2017 Oct 24;49(1):77. doi: 10.1186/s12711-017-0352-z.

24.

Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract.

Segura A, Auffret P, Klopp C, Bertin Y, Forano E.

Stand Genomic Sci. 2017 Oct 10;12:61. doi: 10.1186/s40793-017-0272-0. eCollection 2017.

25.

Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France.

Auffret P, Segura A, Bertin Y, Klopp C, Bouchez O, Kérourédan M, Bibbal D, Brugère H, Forano E.

Genome Announc. 2017 Oct 5;5(40). pii: e01097-17. doi: 10.1128/genomeA.01097-17.

26.

The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles.

Belhabich-Baumas K, Joret C, Jády BE, Plisson-Chastang C, Shayan R, Klopp C, Henras AK, Henry Y, Mougin A.

Nucleic Acids Res. 2017 Oct 13;45(18):10824-10836. doi: 10.1093/nar/gkx734.

27.

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France.

Bertucci A, Pierron F, Thébault J, Klopp C, Bellec J, Gonzalez P, Baudrimont M.

Environ Sci Pollut Res Int. 2017 Dec;24(35):27145-27159. doi: 10.1007/s11356-017-0294-6. Epub 2017 Sep 30.

PMID:
28963680
28.

Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome.

Pasquier J, Braasch I, Batzel P, Cabau C, Montfort J, Nguyen T, Jouanno E, Berthelot C, Klopp C, Journot L, Postlethwait JH, Guiguen Y, Bobe J.

J Exp Zool B Mol Dev Evol. 2017 Nov;328(7):709-721. doi: 10.1002/jez.b.22770. Epub 2017 Sep 25.

29.

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype.

Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert PF, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V.

J Exp Bot. 2017 Jul 10;68(15):4339-4355. doi: 10.1093/jxb/erx224.

30.

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species.

Bourneuf E, Otz P, Pausch H, Jagannathan V, Michot P, Grohs C, Piton G, Ammermüller S, Deloche MC, Fritz S, Leclerc H, Péchoux C, Boukadiri A, Hozé C, Saintilan R, Créchet F, Mosca M, Segelke D, Guillaume F, Bouet S, Baur A, Vasilescu A, Genestout L, Thomas A, Allais-Bonnet A, Rocha D, Colle MA, Klopp C, Esquerré D, Wurmser C, Flisikowski K, Schwarzenbacher H, Burgstaller J, Brügmann M, Dietschi E, Rudolph N, Freick M, Barbey S, Fayolle G, Danchin-Burge C, Schibler L, Bed'Hom B, Hayes BJ, Daetwyler HD, Fries R, Boichard D, Pin D, Drögemüller C, Capitan A.

Sci Rep. 2017 Sep 13;7(1):11466. doi: 10.1038/s41598-017-11523-3.

31.

Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936.

Durrens P, Klopp C, Biteau N, Fitton-Ouhabi V, Dementhon K, Accoceberry I, Sherman DJ, Noël T.

Genome Announc. 2017 Aug 3;5(31). pii: e00724-17. doi: 10.1128/genomeA.00724-17.

32.

Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description.

Auer L, Mariadassou M, O'Donohue M, Klopp C, Hernandez-Raquet G.

Mol Ecol Resour. 2017 Nov;17(6):e122-e132. doi: 10.1111/1755-0998.12700. Epub 2017 Aug 3.

PMID:
28695665
33.

About Ganoderma boninense in oil palm plantations of Sumatra and peninsular Malaysia: Ancient population expansion, extensive gene flow and large scale dispersion ability.

Mercière M, Boulord R, Carasco-Lacombe C, Klopp C, Lee YP, Tan JS, Syed Alwee SSR, Zaremski A, De Franqueville H, Breton F, Camus-Kulandaivelu L.

Fungal Biol. 2017 Jun - Jul;121(6-7):529-540. doi: 10.1016/j.funbio.2017.01.001. Epub 2017 Feb 1.

PMID:
28606348
34.

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila.

Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G.

Nat Genet. 2017 Jun;49(6):876-886. doi: 10.1038/ng.3848. Epub 2017 Apr 24.

35.

The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis.

Nouwen N, Arrighi JF, Cartieaux F, Chaintreuil C, Gully D, Klopp C, Giraud E.

Sci Rep. 2017 Mar 27;7(1):448. doi: 10.1038/s41598-017-00559-0.

36.

Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle.

Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D.

DNA Res. 2017 Jun 1;24(3):221-233. doi: 10.1093/dnares/dsx004.

37.

Reconstructing the genome of the most recent common ancestor of flowering plants.

Murat F, Armero A, Pont C, Klopp C, Salse J.

Nat Genet. 2017 Apr;49(4):490-496. doi: 10.1038/ng.3813. Epub 2017 Mar 13.

PMID:
28288112
38.

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.

Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C.

PeerJ. 2017 Feb 16;5:e2988. doi: 10.7717/peerj.2988. eCollection 2017.

39.

Variant discovery in the sheep milk transcriptome using RNA sequencing.

Suárez-Vega A, Gutiérrez-Gil B, Klopp C, Tosser-Klopp G, Arranz JJ.

BMC Genomics. 2017 Feb 15;18(1):170. doi: 10.1186/s12864-017-3581-1.

40.

Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain.

Goñi Urriza M, Gassie C, Bouchez O, Klopp C, Guyoneaud R.

Genome Announc. 2017 Jan 19;5(3). pii: e01483-16. doi: 10.1128/genomeA.01483-16.

41.

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.

Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C.

Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248.

42.

Long noncoding RNA repertoire in chicken liver and adipose tissue.

Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S.

Genet Sel Evol. 2017 Jan 10;49(1):6. doi: 10.1186/s12711-016-0275-0.

43.

De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam.

Mazzitelli JY, Bonnafe E, Klopp C, Escudier F, Geret F.

Ecotoxicology. 2017 Jan;26(1):127-140. doi: 10.1007/s10646-016-1748-1. Epub 2016 Dec 15.

PMID:
27981403
44.

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

Boussaha M, Michot P, Letaief R, Hozé C, Fritz S, Grohs C, Esquerré D, Duchesne A, Philippe R, Blanquet V, Phocas F, Floriot S, Rocha D, Klopp C, Capitan A, Boichard D.

Genet Sel Evol. 2016 Nov 15;48(1):87.

45.

Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections.

Hammoumi S, Vallaeys T, Santika A, Leleux P, Borzym E, Klopp C, Avarre JC.

PeerJ. 2016 Sep 27;4:e2516. eCollection 2016.

46.

Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.

Guellerin M, Passerini D, Fontagné-Faucher C, Robert H, Gabriel V, Loux V, Klopp C, Le Loir Y, Coddeville M, Daveran-Mingot ML, Ritzenthaler P, Le Bourgeois P.

Genome Announc. 2016 Sep 15;4(5). pii: e00692-16. doi: 10.1128/genomeA.00692-16.

47.

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats.

Aubé J, Senin P, Pringault O, Bonin P, Deflandre B, Bouchez O, Bru N, Biritxinaga-Etchart E, Klopp C, Guyoneaud R, Goñi-Urriza M.

Mar Pollut Bull. 2016 Oct 15;111(1-2):115-125. doi: 10.1016/j.marpolbul.2016.07.023. Epub 2016 Jul 20.

PMID:
27449831
48.

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome.

Suárez-Vega A, Gutiérrez-Gil B, Klopp C, Tosser-Klopp G, Arranz JJ.

Sci Data. 2016 Jul 5;3:160051. doi: 10.1038/sdata.2016.51.

49.

A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes.

Chaintreuil C, Rivallan R, Bertioli DJ, Klopp C, Gouzy J, Courtois B, Leleux P, Martin G, Rami JF, Gully D, Parrinello H, Séverac D, Patrel D, Fardoux J, Ribière W, Boursot M, Cartieaux F, Czernic P, Ratet P, Mournet P, Giraud E, Arrighi JF.

DNA Res. 2016 Aug;23(4):365-76. doi: 10.1093/dnares/dsw020. Epub 2016 Jun 13.

50.

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I, Journot L, Pontarotti P, Klopp C, Postlethwait JH, Guiguen Y, Bobe J.

BMC Genomics. 2016 May 18;17:368. doi: 10.1186/s12864-016-2709-z.

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