P. Hingamp

发表

Microarray Data Standards: An Open Letter

C. Ball, J. Matese, M. Ringwald, 2004, Environmental Health Perspectives.

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

Jason E. Stewart, Irene F. Kim, F. Holstege, 2001, Nature Genetics.

Submission of Microarray Data to Public Repositories

C. Ball, J. Matese, M. Ringwald, 2004, PLoS biology.

Structure and function of the global ocean microbiome

Luis Pedro Coelho, Jens Roat Kultima, Francisco M. Cornejo-Castillo, 2015, Science.

Eukaryotic plankton diversity in the sunlit ocean

P. Bork, S. Sunagawa, J. Raes, 2015, Science.

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

Francisco M. Cornejo-Castillo, P. Bork, S. Sunagawa, 2014, Environmental microbiology.

A Holistic Approach to Marine Eco-Systems Biology

P. Bork, J. Raes, J. Weissenbach, 2011, PLoS biology.

A global ocean atlas of eukaryotic genes

P. Bork, S. Sunagawa, E. Pelletier, 2018, Nature Communications.

Patterns and ecological drivers of ocean viral communities

P. Bork, S. Sunagawa, P. Wincker, 2015, Science.

Plankton networks driving carbon export in the oligotrophic ocean

Luis Pedro Coelho, P. Bork, S. Sunagawa, 2015, Nature.

Metabolic Architecture of the Deep Ocean Microbiome

Francisco M. Cornejo-Castillo, P. Bork, S. Sunagawa, 2019, bioRxiv.

Microbial abundance, activity and population genomic profiling with mOTUs2

Peer Bork, Shinichi Sunagawa, Pascal Hingamp, 2019, Nature Communications.

Global Trends in Marine Plankton Diversity across Kingdoms of Life

Luis Pedro Coelho, G. Cochrane, P. Bork, 2019, Cell.

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Peer Bork, Bas E. Dutilh, Shinichi Sunagawa, 2016, bioRxiv.

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

P. Hingamp, L. Dixon, R. Mayer, 1995, Journal of virology.

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Natalia N. Ivanova, Evelien M. Adriaenssens, G. Cochrane, 2018, Nature Biotechnology.

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

Susumu Goto, Pascal Hingamp, Hiroyuki Ogata, 2017, mSphere.

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

Luis Pedro Coelho, G. Cochrane, P. Bork, 2019, Cell.

Feature extraction and signal processing for nylon DNA microarrays

F. Bertucci, B. Loriod, S. Granjeaud, 2004, BMC Genomics.

Diversity and evolution of bacterial bioluminescence genes in the global ocean

P. Hingamp, Y. Timsit, Thomas Vannier, 2020, NAR genomics and bioinformatics.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

G. Cochrane, P. Bork, S. Sunagawa, 2019, Cell.

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luis Pedro Coelho, P. Bork, S. Sunagawa, 2019, Global Biogeochemical Cycles.

A ubiquitin conjugating enzyme encoded by African swine fever virus.

P. Hingamp, L. Dixon, R. Mayer, 1992, The EMBO journal.

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

H. Ogata, S. Goto, P. Hingamp, 2018, Microbes and environments.

Standards for microarray data: an open letter.

Paul T. Spellman, John Quackenbush, Yoshio Tateno, 2004, Environmental health perspectives.

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

S. Granjeaud, R. Tagett, J. Rougemont, 2006, BMC Genomics.

The underlying principles of scientific publication.

Duccio Cavalieri, John Quackenbush, Terry Gaasterland, 2002, Bioinformatics.

The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

Tom O. Delmont, G. Cochrane, P. Bork, 2022, Nucleic Acids Res..

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

P. Bork, S. Sunagawa, J. Poulain, 2018, Nature Communications.

An open letter to the scientific journals

Catherine Brooksbank, Duccio Cavalieri, Paul T. Spellman, 2002, Bioinform..

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

Jean-Michel Claverie, Hervé Moreau, Peer Bork, 2013, The ISME Journal.

Open science resources for the discovery and analysis of Tara Oceans data

Peer Bork, Shinichi Sunagawa, Daniele Iudicone, 2015, Scientific Data.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

G. Cochrane, P. Bork, S. Sunagawa, 2019, Cell.

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

P. Hingamp, S. Wing, L. Combaret, 2000, Molecular and Cellular Biology.

Macroscale patterns of oceanic zooplankton composition and size structure

G. Cochrane, P. Bork, S. Sunagawa, 2021, Scientific Reports.

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

Paul Bachelerie, Magali Lescot, Shinichi Sunagawa, 2018, bioRxiv.

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

P. Hingamp, S. Wing, J. Trasler, 2005, Molecular and Cellular Biology.

Microbial abundance, activity and population genomic profiling with mOTUs2

Luis Pedro Coelho, P. Bork, S. Sunagawa, 2019, Nature Communications.

Mice Lacking the UBC4-testis Gene Have a Delay in Postnatal Testis Development but Normal Spermatogenesis and Fertility

P. Hingamp, D. Cyr, S. Wing, 2005, Molecular and Cellular Biology.

Breast cancer revisited using DNA array‐based gene expression profiling

Daniel Birnbaum, Pascal Hingamp, Rémi Houlgatte, 2003, International journal of cancer.

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

Vincent Lombard, Helen E. Parkinson, Nicole Redaschi, 2002, Bioinform..

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Corinne Da Silva, Tom O. Delmont, G. Cochrane, 2022, Cell genomics.

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

H. Ogata, P. Hingamp, Takashi Yoshida, 2018, Viruses.

Tara Oceans: towards global ocean ecosystems biology

G. Cochrane, P. Bork, S. Sunagawa, 2020, Nature Reviews Microbiology.

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

G. Cochrane, P. Bork, S. Sunagawa, 2022, Science.

The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms

P. Hingamp, C. de Vargas, N. Henry, 2021, Molecular ecology resources.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Francisco M. Cornejo-Castillo, G. Cochrane, P. Bork, 2017, Scientific Data.

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

Francisco M. Cornejo-Castillo, P. Bork, S. Sunagawa, 2016, Nature Communications.

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

J. Claverie, O. Jaillon, P. Wincker, 2015, The ISME Journal.

Environmental characteristics of Agulhas rings affect interocean plankton transport

Peer Bork, Shinichi Sunagawa, Stéphane Audic, 2015, Science.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Francisco M. Cornejo-Castillo, P. Bork, S. Sunagawa, 2021, Communications biology.

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

J. Poulain, P. Wincker, H. Ogata, 2015, Environmental microbiology reports.

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

J. Poulain, H. Ogata, P. Hingamp, 2014, Applied and Environmental Microbiology.

Linking Virus Genomes with Host Taxonomy

Susumu Goto, Genki Yoshikawa, Pascal Hingamp, 2016, Viruses.

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

H. Ogata, S. Goto, P. Hingamp, 2018, The ISME Journal.

An open letter on microarray data from the MGED Society.

John Quackenbush, Yoshio Tateno, Helen Parkinson, 2004, Microbiology.

Standards for Microarray Data

Duccio Cavalieri, John Quackenbush, Terry Gaasterland, 2002, Science.

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

J. Poulain, J. Claverie, P. Hingamp, 2010, Genome research.

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

H. Ogata, S. Goto, P. Hingamp, 2018, The ISME Journal.

Prognosis of Breast Cancer and Gene Expression Profiling Using DNA Arrays

Samuel Granjeaud, Daniel Birnbaum, Pascal Hingamp, 2002, Annals of the New York Academy of Sciences.

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

P. Hingamp, S. Wing, J. Trasler, 1996, Molecular and cellular biology.

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

Pascal Hingamp, Emese Meglécz, André Gilles, 2014, Molecular ecology resources.

DNA microarray data and contextual analysis of correlation graphs

Jacques Rougemont, Pascal Hingamp, J. Rougemont, 2003, BMC Bioinformatics.

African swine fever virus genome content and variability.

P. Hingamp, L. Dixon, S. Twigg, 1993, Archives of virology. Supplementum.

Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure

G. Cochrane, P. Bork, S. Sunagawa, 2021, Scientific Reports.

Metagenome Annotation Using a Distributed Grid of Undergraduate Students

Daniel Gautheret, Pascal Hingamp, Céline Brochier, 2008, PLoS biology.

The EMBL Nucleotide Sequence Database

Vincent Lombard, Rolf Apweiler, Peter Stoehr, 2004, Nucleic Acids Res..

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Tom O. Delmont, G. Cochrane, P. Bork, 2020, bioRxiv.

Repository of the Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association

Luis Pedro Coelho, Corinne Da Silva, S. Sunagawa, 2023 .

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

P. Bork, S. Sunagawa, J. Poulain, 2018, Nature Communications.

Descriptor : Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

P. Bork, S. Sunagawa, J. Raes, 2017 .

Minimum Information about an Uncultivated Virus Genome ( MIUViG ) : a community consensus on standards and best practices for describing genome sequences from uncultivated viruses

Natalia N. Ivanova, Frederik, G. Cochrane, 2018 .

Eukaryotic plankton diversity in the sunlit ocean

P. Bork, S. Sunagawa, J. Raes, 2015, Science.

The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms

P. Hingamp, C. de Vargas, N. Henry, 2020, Molecular ecology resources.

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

J. Poulain, P. Wincker, H. Ogata, 2015, Environmental microbiology reports.

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus

S. Sunagawa, J. Poulain, O. Jaillon, 2016, The ISME Journal.