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1

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

Logares, Ramiro, Sunagawa, Shinichi, Salazar, Guillem, Cornejo-Castillo, Francisco M., Ferrera, Isabel, Sarmento, Hugo, Hingamp, Pascal, Ogata, Hiroyuki, de Vargas, Colomban, Lima-Mendez, Gipsi, Raes,

Journal:

Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

2

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, Emese, Pech, Nicolas, Gilles, André, Dubut, Vincent, Hingamp, Pascal, Trilles, Aurélie, Grenier, Rémi, Martin, Jean-François

Journal:

Molecular Ecology Resources

Year:

2014

Language:

english

File:

PDF, 218 KB

english, 2014

3

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, J. M.

Journal:

Genome Research

Year:

2010

Language:

english

File:

PDF, 1.71 MB

english, 2010

4

Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean

Mihara, Tomoko, Koyano, Hitoshi, Hingamp, Pascal, Grimsley, Nigel, Goto, Susumu, Ogata, Hiroyuki

Journal:

Microbes and Environments

Year:

2018

Language:

english

File:

PDF, 3.71 MB

english, 2018

5

Linking Virus Genomes with Host Taxonomy

Mihara, Tomoko, Nishimura, Yosuke, Shimizu, Yugo, Nishiyama, Hiroki, Yoshikawa, Genki, Uehara, Hideya, Hingamp, Pascal, Goto, Susumu, Ogata, Hiroyuki

Journal:

Year:

2016

Language:

english

File:

PDF, 2.09 MB

english, 2016

6

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

Li, Yanze, Hingamp, Pascal, Watai, Hiroyasu, Endo, Hisashi, Yoshida, Takashi, Ogata, Hiroyuki

Journal:

Year:

2018

Language:

english

File:

PDF, 3.11 MB

english, 2018

7

Breast cancer revisited using DNA array-based gene expression profiling

François Bertucci, Patrice Viens, Pascal Hingamp, Valery Nasser, Rémi Houlgatte, Daniel Birnbaum

Journal:

International Journal of Cancer

Year:

2003

Language:

english

File:

PDF, 441 KB

english, 2003

8

Prognosis of Breast Cancer and Gene Expression Profiling Using DNA Arrays

FRANÇOIS BERTUCCI, RÉMI HOULGATTE, SAMUEL GRANJEAUD, VALÉRY NASSER, BÉATRICE LORIOD, EMMANUEL BEAUDOING, PASCAL HINGAMP, JOCELYNE JACQUEMIER, PATRICE VIENS, DANIEL BIRNBAUM, CATHERINE NGUYEN

Journal:

Annals of the New York Academy of Sciences

Year:

2002

Language:

english

File:

PDF, 5.75 MB

english, 2002

9

10.1038/ng1201-365

Brazma, Alvis, Hingamp, Pascal, Quackenbush, John, Sherlock, Gavin, Spellman, Paul, Stoeckert, Chris, Aach, John, Ansorge, Wilhelm, Ball, Catherine A., Causton, Helen C., Gaasterland, Terry, Glenisson

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 527 KB

english, 2001

10

The EMBL nucleotide sequence database

Pascal Hingamp, Alexandra E. van den Broek, Guenter Stoesser, Wendy Baker

Journal:

Molecular Biotechnology

Year:

1999

Language:

english

File:

PDF, 769 KB

english, 1999

11

DNA microarray data and contextual analysis of correlation graphs

Jacques Rougemont, Pascal Hingamp

Journal:

BMC Bioinformatics

Year:

2003

Language:

english

File:

PDF, 1.43 MB

english, 2003

12

Feature extraction and signal processing for nylon DNA microarrays

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

Journal:

Year:

2004

Language:

english

File:

PDF, 2.44 MB

english, 2004

13

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

Paul Honoré, Samuel Granjeaud, Rebecca Tagett, Stéphane Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono, Pascal Hingamp

Journal:

Year:

2006

Language:

english

File:

PDF, 744 KB

english, 2006

14

A guide to microarray experiments-an open letter to the scientific journals

Catherine A Ball, Gavin Sherlock, Helen Parkinson, Philippe Rocca-Sera, Catherine Brooksbank, Helen C Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Pau

Journal:

Year:

2002

Language:

english

File:

PDF, 47 KB

english, 2002

15

Toxicogenomics || Microarray Data Standards: An Open Letter

Catherine Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock, Pau

Journal:

Environmental Health Perspectives

Year:

2004

Language:

english

File:

PDF, 1.11 MB

english, 2004

16

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.

Journal:

Applied and Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

17

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

Hingamp, Pascal, Grimsley, Nigel, Acinas, Silvia G, Clerissi, Camille, Subirana, Lucie, Poulain, Julie, Ferrera, Isabel, Sarmento, Hugo, Villar, Emilie, Lima-Mendez, Gipsi, Faust, Karoline, Sunagawa,

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 1.34 MB

english, 2013

18

Divergent N-Terminal Sequences Target an Inducible Testis Deubiquitinating Enzyme to Distinct Subcellular Structures

Lin, H., Keriel, A., Morales, C. R., Bedard, N., Zhao, Q., Hingamp, P., Lefrancois, S., Combaret, L., Wing, S. S.

Journal:

Molecular and Cellular Biology

Year:

2000

Language:

english

File:

PDF, 2.26 MB

english, 2000

19

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, S. S.

Journal:

Molecular and Cellular Biology

Year:

2005

Language:

english

File:

PDF, 491 KB

english, 2005

20

An open letter to the scientific journals

Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C. J., Stewa

Journal:

Year:

2002

Language:

english

File:

PDF, 36 KB

english, 2002

21

A Novel Rat Homolog of the Saccharomyces cerevisiae Ubiquitin-Conjugating Enzymes UBC4 and UBC5 with Distinct Biochemical Features Is Induced during Spermatogenesis

Wing, S. S., Bedard, N., Morales, C., Hingamp, P., Trasler, J.

Journal:

Molecular and Cellular Biology

Year:

2005

File:

PDF, 17 KB

2005

22

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

Lombard, V., Camon, E. B., Parkinson, H. E., Hingamp, P., Stoesser, G., Redaschi, N.

Journal:

Year:

2002

Language:

english

File:

PDF, 174 KB

english, 2002

23

Patterns and ecological drivers of ocean viral communities

Brum, J. R., Ignacio-Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., Gorsky, G., Gregory, A. C., Guidi, L., Hingamp, P., Iud

Journal:

Year:

2015

Language:

english

File:

PDF, 3.11 MB

english, 2015

24

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

Lescot, Magali, Hingamp, Pascal, Kojima, Kenji K, Villar, Emilie, Romac, Sarah, Veluchamy, Alaguraj, Boccara, Martine, Jaillon, Olivier, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Claverie, J

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 1.22 MB

english, 2015

25

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

Clerissi, Camille, Desdevises, Yves, Romac, Sarah, Audic, Stéphane, de Vargas, Colomban, Acinas, Silvia G, Casotti, Raffaella, Poulain, Julie, Wincker, Patrick, Hingamp, Pascal, Ogata, Hiroyuki, Grims

Journal:

Environmental Microbiology Reports

Year:

2015

Language:

english

File:

PDF, 716 KB

english, 2015

26

A novel rat homolog of the Saccharomyces cerevisiae ubiquitin-conjugating enzymes UBC4 and UBC5 with distinct biochemical features is induced during spermatogenesis.

Wing, S S, Bédard, N, Morales, C, Hingamp, P, Trasler, J

Journal:

Molecular and Cellular Biology

Year:

1996

Language:

english

File:

PDF, 713 KB

english, 1996

27

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

Cornejo-Castillo, Francisco M., Cabello, Ana M., Salazar, Guillem, Sánchez-Baracaldo, Patricia, Lima-Mendez, Gipsi, Hingamp, Pascal, Alberti, Adriana, Sunagawa, Shinichi, Bork, Peer, de Vargas, Colomb

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.09 MB

english, 2016

28

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

Nishimura, Yosuke, Watai, Hiroyasu, Honda, Takashi, Mihara, Tomoko, Omae, Kimiho, Roux, Simon, Blanc-Mathieu, Romain, Yamamoto, Keigo, Hingamp, Pascal, Sako, Yoshihiko, Sullivan, Matthew B., Goto, Sus

Journal:

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

29

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

Yoshida, Takashi, Nishimura, Yosuke, Watai, Hiroyasu, Haruki, Nana, Morimoto, Daichi, Kaneko, Hiroto, Honda, Takashi, Yamamoto, Keigo, Hingamp, Pascal, Sako, Yoshihiko, Goto, Susumu, Ogata, Hiroyuki

Journal:

The ISME Journal

Year:

2018

Language:

english

File:

PDF, 1.46 MB

english, 2018

30

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

Villar, Emilie, Vannier, Thomas, Vernette, Caroline, Lescot, Magali, Cuenca, Miguelangel, Alexandre, Aurélien, Bachelerie, Paul, Rosnet, Thomas, Pelletier, Eric, Sunagawa, Shinichi, Hingamp, Pascal

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 2.46 MB

english, 2018

31

Submission of Microarray Data to Public Repositories

Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, Matese, John C, Parkinson, Helen, Quackenbush, John, Ringwald, Martin, Sansone, Susanna-Assunta, Sherloc

Journal:

Year:

2004

Language:

english

File:

PDF, 65 KB

english, 2004

32

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, Takashi, Nishimura, Yosuke, Watai, Hiroyasu, Haruki, Nana, Morimoto, Daichi, Kaneko, Hiroto, Honda, Takashi, Yamamoto, Keigo, Hingamp, Pascal, Sako, Yoshihiko, Goto, Susumu, Ogata, Hiroyuki

Journal:

The ISME Journal

Year:

2018

Language:

english

File:

PDF, 230 KB

english, 2018

33

A ubiquitin conjugating enzyme encoded by African swine fever virus.

Hingamp, P.M., Arnold, J.E., Mayer, R.J., Dixon, L.K.

Journal:

The EMBO Journal

Year:

1992

Language:

english

File:

PDF, 1.13 MB

english, 1992

34

Microarray Data Standards: An Open Letter

Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, Matese, John C., Parkinson, Helen, Quackenbush, John, Ringwald, Martin, Sansone, Susanna-Assunta, Sherlock

Journal:

Environmental Health Perspectives

Year:

2004

Language:

english

File:

PDF, 336 KB

english, 2004

35

Microbial abundance, activity and population genomic profiling with mOTUs2

Milanese, Alessio, Mende, Daniel R, Paoli, Lucas, Salazar, Guillem, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Hingamp, Pascal, Alves, Renato, Costea, Paul I, Coelho, Luis Pedro, Schmidt, Thomas S

Journal:

Nature Communications

Year:

2019

File:

PDF, 1.11 MB

2019

36

Diversity and evolution of bacterial bioluminescence genes in the global ocean

Vannier, Thomas, Hingamp, Pascal, Turrel, Floriane, Tanet, Lisa, Lescot, Magali, Timsit, Youri

Journal:

NAR Genomics and Bioinformatics

Year:

2020

File:

PDF, 3.13 MB

2020

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