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Items: 47

1.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.

Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J; Tara Oceans Coordinators, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S.

Cell. 2019 Nov 14;179(5):1068-1083.e21. doi: 10.1016/j.cell.2019.10.014.

PMID:
31730850
2.

Microbial abundance, activity and population genomic profiling with mOTUs2.

Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S.

Nat Commun. 2019 Mar 4;10(1):1014. doi: 10.1038/s41467-019-08844-4.

3.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

PMID:
30556814
4.

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.

Li Y, Hingamp P, Watai H, Endo H, Yoshida T, Ogata H.

Viruses. 2018 Sep 13;10(9). pii: E496. doi: 10.3390/v10090496.

5.

Correction: Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.

Yoshida T, Nishimura Y, Watai H, Haruki N, Morimoto D, Kaneko H, Honda T, Yamamoto K, Hingamp P, Sako Y, Goto S, Ogata H.

ISME J. 2018 Dec;12(12):3046. doi: 10.1038/s41396-018-0247-1.

6.

Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean.

Mihara T, Koyano H, Hingamp P, Grimsley N, Goto S, Ogata H.

Microbes Environ. 2018 Jul 4;33(2):162-171. doi: 10.1264/jsme2.ME17203. Epub 2018 May 25.

7.

The Ocean Gene Atlas: exploring the biogeography of plankton genes online.

Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S, Hingamp P.

Nucleic Acids Res. 2018 Jul 2;46(W1):W289-W295. doi: 10.1093/nar/gky376.

8.

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.

Yoshida T, Nishimura Y, Watai H, Haruki N, Morimoto D, Kaneko H, Honda T, Yamamoto K, Hingamp P, Sako Y, Goto S, Ogata H.

ISME J. 2018 May;12(5):1287-1295. doi: 10.1038/s41396-018-0052-x. Epub 2018 Jan 30. Erratum in: ISME J. 2018 Dec;12(12):3046.

9.

A global ocean atlas of eukaryotic genes.

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P.

Nat Commun. 2018 Jan 25;9(1):373. doi: 10.1038/s41467-017-02342-1.

10.

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P.

Nat Commun. 2018 Jan 22;9(1):310. doi: 10.1038/s41467-017-02235-3.

11.

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean.

Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, Blanc-Mathieu R, Yamamoto K, Hingamp P, Sako Y, Sullivan MB, Goto S, Ogata H, Yoshida T.

mSphere. 2017 Mar 1;2(2). pii: e00359-16. doi: 10.1128/mSphere.00359-16. eCollection 2017 Mar-Apr.

12.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG.

Nat Commun. 2016 Mar 22;7:11071. doi: 10.1038/ncomms11071.

13.

Linking Virus Genomes with Host Taxonomy.

Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H.

Viruses. 2016 Mar 1;8(3):66. doi: 10.3390/v8030066.

14.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.

Nature. 2016 Apr 28;532(7600):465-470. doi: 10.1038/nature16942. Epub 2016 Feb 10.

15.

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.

Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H.

ISME J. 2016 May;10(5):1134-46. doi: 10.1038/ismej.2015.192. Epub 2015 Nov 27.

16.

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes.

Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H, Grimsley N.

Environ Microbiol Rep. 2015 Dec;7(6):979-89. doi: 10.1111/1758-2229.12345.

PMID:
26472079
17.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E.

Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.

18.

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB.

Science. 2015 May 22;348(6237):1261498. doi: 10.1126/science.1261498. Erratum in: Science. 2016 Aug 12;353(6300). pii: aah6502. doi: 10.1126/science.aah6502.

19.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D.

Science. 2015 May 22;348(6237):1261447. doi: 10.1126/science.1261447.

20.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P.

Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

21.

QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate.

Meglécz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R, Martin JF.

Mol Ecol Resour. 2014 Nov;14(6):1302-13. doi: 10.1111/1755-0998.12271. Epub 2014 May 26.

PMID:
24785154
22.

Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes.

Clerissi C, Grimsley N, Ogata H, Hingamp P, Poulain J, Desdevises Y.

Appl Environ Microbiol. 2014 May;80(10):3150-60. doi: 10.1128/AEM.00123-14. Epub 2014 Mar 14.

23.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG.

Environ Microbiol. 2014 Sep;16(9):2659-71. doi: 10.1111/1462-2920.12250. Epub 2013 Sep 18.

PMID:
24102695
24.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H.

ISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11.

25.

A holistic approach to marine eco-systems biology.

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P; Tara Oceans Consortium.

PLoS Biol. 2011 Oct;9(10):e1001177. doi: 10.1371/journal.pbio.1001177. Epub 2011 Oct 18.

26.

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus.

Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM.

Genome Res. 2010 May;20(5):664-74. doi: 10.1101/gr.102582.109. Epub 2010 Apr 1.

27.

Metagenome annotation using a distributed grid of undergraduate students.

Hingamp P, Brochier C, Talla E, Gautheret D, Thieffry D, Herrmann C.

PLoS Biol. 2008 Nov 25;6(11):e296. doi: 10.1371/journal.pbio.0060296. No abstract available.

28.

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies.

Honoré P, Granjeaud S, Tagett R, Deraco S, Beaudoing E, Rougemont J, Debono S, Hingamp P.

BMC Genomics. 2006 Sep 20;7:240.

29.

Mice lacking the UBC4-testis gene have a delay in postnatal testis development but normal spermatogenesis and fertility.

Bedard N, Hingamp P, Pang Z, Karaplis A, Morales C, Trasler J, Cyr D, Gagnon C, Wing SS.

Mol Cell Biol. 2005 Aug;25(15):6346-54.

30.

An open letter on microarray data from the MGED Society.

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N; Microarray Gene Expression Data (MGED) Society.

Microbiology. 2004 Nov;150(Pt 11):3522-4. No abstract available.

PMID:
15528642
31.

Standards for microarray data: an open letter.

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N; MGED Society.

Environ Health Perspect. 2004 Aug;112(12):A666-7. No abstract available.

32.

Submission of microarray data to public repositories.

Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.

PLoS Biol. 2004 Sep;2(9):E317. Epub 2004 Aug 31. No abstract available.

33.

Feature extraction and signal processing for nylon DNA microarrays.

Lopez F, Rougemont J, Loriod B, Bourgeois A, Loï L, Bertucci F, Hingamp P, Houlgatte R, Granjeaud S.

BMC Genomics. 2004 Jun 29;5(1):38.

34.

DNA microarray data and contextual analysis of correlation graphs.

Rougemont J, Hingamp P.

BMC Bioinformatics. 2003 Apr 29;4:15. Epub 2003 Apr 29.

35.

Prognosis of breast cancer and gene expression profiling using DNA arrays.

Bertucci F, Houlgatte R, Granjeaud S, Nasser V, Loriod B, Beaudoing E, Hingamp P, Jacquemier J, Viens P, Birnbaum D, Nguyen C.

Ann N Y Acad Sci. 2002 Dec;975:217-31.

PMID:
12538167
36.

Breast cancer revisited using DNA array-based gene expression profiling.

Bertucci F, Viens P, Hingamp P, Nasser V, Houlgatte R, Birnbaum D.

Int J Cancer. 2003 Feb 20;103(5):565-71. Review.

37.

The underlying principles of scientific publication.

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J; Microarray Gene Expression Data.

Bioinformatics. 2002 Nov;18(11):1409. Review. No abstract available.

PMID:
12424109
38.

Standards for microarray data.

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J; Microarray Gene Expression Data (MGED) Society.

Science. 2002 Oct 18;298(5593):539. No abstract available.

PMID:
12387284
39.

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.

Lombard V, Camon EB, Parkinson HE, Hingamp P, Stoesser G, Redaschi N.

Bioinformatics. 2002 May;18(5):763-4.

PMID:
12050074
40.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.

Nat Genet. 2001 Dec;29(4):365-71.

PMID:
11726920
41.

Divergent N-terminal sequences target an inducible testis deubiquitinating enzyme to distinct subcellular structures.

Lin H, Keriel A, Morales CR, Bedard N, Zhao Q, Hingamp P, Lefrançois S, Combaret L, Wing SS.

Mol Cell Biol. 2000 Sep;20(17):6568-78.

42.

The EMBL Nucleotide Sequence Database. Contributing and accessing data.

Hingamp P, van den Broek AE, Stoesser G, Baker W.

Mol Biotechnol. 1999 Oct;12(3):255-67. Review.

PMID:
10631682
43.

The EMBL nucleotide sequence database.

Baker W, van den Broek A, Camon E, Hingamp P, Sterk P, Stoesser G, Tuli MA.

Nucleic Acids Res. 2000 Jan 1;28(1):19-23.

45.

Characterization of a ubiquitinated protein which is externally located in African swine fever virions.

Hingamp PM, Leyland ML, Webb J, Twigger S, Mayer RJ, Dixon LK.

J Virol. 1995 Mar;69(3):1785-93.

46.

African swine fever virus genome content and variability.

Dixon LK, Baylis SA, Vydelingum S, Twigg SR, Hammond JM, Hingamp PM, Bristow C, Wilkinson PJ, Smith GL.

Arch Virol Suppl. 1993;7:185-99.

PMID:
8219803
47.

A ubiquitin conjugating enzyme encoded by African swine fever virus.

Hingamp PM, Arnold JE, Mayer RJ, Dixon LK.

EMBO J. 1992 Jan;11(1):361-6.

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