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Items: 1 to 50 of 179

1.

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 Sep 4;165:96-106. doi: 10.1016/j.ecoenv.2018.08.090. [Epub ahead of print]

PMID:
30193169
2.

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
3.

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 Aug 3. pii: S0016-6480(18)30131-X. doi: 10.1016/j.ygcen.2018.08.007. [Epub ahead of print]

PMID:
30081002
4.

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.

5.

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.

PMID:
29915331
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

PMID:
28944589
20.

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.

21.

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.

22.

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.

23.

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
24.

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
25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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
35.

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.

36.

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.

37.

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.

38.

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
39.

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.

40.

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.

41.

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.

42.

Correction: Design and Characterization of a 52K SNP Chip for Goats.

Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieu-Tonon C, Eggen A, Heuven HC, Jamli S, Jiken AJ, Klopp C, Lawley CT, McEwan J, Martin P, Moreno CR, Mulsant P, Nabihoudine I, Pailhoux E, Palhière I, Rupp R, Sarry J, Sayre BL, Tircazes A, Wang J, Wang W, Zhang W; International Goat Genome Consortium.

PLoS One. 2016 Mar 24;11(3):e0152632. doi: 10.1371/journal.pone.0152632. eCollection 2016. No abstract available.

43.

Evolutionary Origins of Rhizarian Parasites.

Sierra R, Cañas-Duarte SJ, Burki F, Schwelm A, Fogelqvist J, Dixelius C, González-García LN, Gile GH, Slamovits CH, Klopp C, Restrepo S, Arzul I, Pawlowski J.

Mol Biol Evol. 2016 Apr;33(4):980-3. doi: 10.1093/molbev/msv340. Epub 2015 Dec 16.

PMID:
26681153
44.

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing.

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

Sci Rep. 2015 Dec 18;5:18399. doi: 10.1038/srep18399.

45.

The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3.

Roux PF, Frésard L, Boutin M, Leroux S, Klopp C, Djari A, Esquerré D, Martin PG, Zerjal T, Gourichon D, Pitel F, Lagarrigue S.

G3 (Bethesda). 2015 Dec 4;6(2):321-35. doi: 10.1534/g3.115.022251.

46.

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

Riviere G, Klopp C, Ibouniyamine N, Huvet A, Boudry P, Favrel P.

BMC Bioinformatics. 2015 Dec 2;16:401. doi: 10.1186/s12859-015-0833-4.

47.

RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies.

Hamidou Soumana I, Klopp C, Ravel S, Nabihoudine I, Tchicaya B, Parrinello H, Abate L, Rialle S, Geiger A.

Front Microbiol. 2015 Nov 13;6:1259. doi: 10.3389/fmicb.2015.01259. eCollection 2015.

48.

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.

49.

Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds.

Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D.

PLoS One. 2015 Aug 28;10(8):e0135931. doi: 10.1371/journal.pone.0135931. eCollection 2015.

50.

A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife.

Razzauti M, Galan M, Bernard M, Maman S, Klopp C, Charbonnel N, Vayssier-Taussat M, Eloit M, Cosson JF.

PLoS Negl Trop Dis. 2015 Aug 18;9(8):e0003929. doi: 10.1371/journal.pntd.0003929. eCollection 2015.

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