Genotoul-bioinfo

Adress
24 Chemin de Borde Rouge 31326 Castanet Tolosan
Structure(s)
Not documented
Unit:
MIAT 0875
[field_pole_regional_de_rattachem]
Scientific leader(s)
Technical leader(s)
Technical leader
Not documented
Certificat(s)
  • CATI / CTAI
  • CNOC (INRA)
  • France-Génomique
  • ISO 9001
  • Label IBiSA
  • NF X50-900
  • PF stratégique nationale INRA
Infrastructure
Propriétaire
Effective storage
3 200.00 To
Cluster: cores number
2 984 cores
CPU/hours a year
20 000 000 H / an
Bioinformatic tools number
650
Users number (last year)
850
Servers description

● Stockage scratch HPC
→ 900 Tera Octets utiles
→ 25 Giga bits / seconde

● Stockage NAS

→ 3 baies ISILON (au total 1.8 Peta Octets utiles)
→ 2 baies COMPELLENT/FLUIDFS (au total 450 Tera Octets utiles)
→ Au total 3.2 Peta Octets utiles

The platform has about twenty physical servers complemented by seventy-five virtual servers that provide the login services, development, inputs / outputs, relational databases, genomic databases, administration, supervision, web, virtualization, backup, project hosting, bioinformatics software. The primary server, serving as access to users is called "genologin."
Some examples (not exhaustive) web services hosted by the platform: NG6, galaxy, rnaspace, peroxibase, phyleasprog, Multalin, framed, MetExplore, Iccare, blast, emboss, BioMAJ ...
Additionally we host (formalization by convention) data, web sites or information systems or other platforms other research teams in the region: get-Plage, biochip, Anexplo, TOXALIM, hsern, sigenae: gbf , LRSV, genphyse
Some details:
● Cluster computing

  • 64 nodes IVYBRIDGE (20c) = 1280 cores (2560 threads), 16 Tera Octets RAM
  • 48 nodes BROADWELL (32c) = 1536 cores (3072 threads), 12 Tera Octets RAM
  • 1 node SMP1 = 120 coeurs, 3 Tera Octets RAM
  • 1 node SMP2 = 48 coeurs, 1.5 Tera Octets RAM
  • Interconnection Infiniband (QDR) QDR (40Gbs) / FDR (56 Gbs)

● HPC Storage
→ 900 Tera Octets useful
→ 25 Giga bits / seconde
● NAS Storage
→ 3 bays ISILON (au total 1.8 Peta Octets useful)
→ 2 bays COMPELLENT/FLUIDFS (total of 450 Tera Octets useful)
→ total of  3.2 Peta Octets useful
● Server Virtualization
→ farm Vmware 3 servers
→ Bay DELL-MD discs (SAN mode) 40TB
→ 75 hosted virtual machines 


Access conditions

Free access for academic, paying for private companies.
Quotas (saved, not saved) set up for storage and the number of hours of calculation for academic (250GB respectively; 1TB and 100000h) and the private (the calculation - 500 hours - to test the infrastructure).
For storage, ability to "rent" disk space from 1TB for academic people.

Annual visits:
11 561 an
Unique visits:
8 952 an
Quotes:
14
Downloads:
Not documented

Dgenies

Description

D-GENIES is a standalone and WEB application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference , zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy to install open source software package (GPL) developed in Python and JavaScript.

Access conditions

D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is freely available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
14
Downloads:
Not documented

mixkernel

Description

Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package.

Access conditions

mixKernel is freely available on CRAN. It is fully compatible with the mixOmics package and a tutorial describing the approach can be found on mixOmics web site.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
1 124

Jvenn

Description

A javascript plugin for venn diagrams.

A demo is available here: http://bioinfo.genotoul.fr/jvenn/example.html

Access conditions

The software package is available under the GNU General Public License (GPL) and can be downloaded from the gitlab forgemia : https://forgemia.inra.fr/genotoul-bioinfo/jvenn.

Annual visits:
4 720 an
Unique visits:
2 250 an
Quotes:
17
Downloads:
1 982

RNAbrowse nouvelle version

Description

35 instances including 10 Sigenae.
Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quiet diverse. RNAbrowse is an user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data.

Access conditions

The software package is available under the GNU General Public License (GPL) and can be downloaded from the gitlab formia : https://forgemia.inra.fr/genotoul-bioinfo/ngspipelines.
Available on web sites for users.

Annual visits:
17 558 an
Unique visits:
14 318 an
Quotes:
27
Downloads:
Not documented

RNAspace

Description

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.
RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs. RNAspace also allows to export putative RNAs in various formats.

Access conditions

RNAspace is an open source project. It is developed in Python. It is copyrighted with the GNU General Public License, and is free (in the GNU sense) for all to use, and is in constant development. RNAspace is hosted at Sourceforge. It is also available as a web server at rnaspace.org

Annual visits:
33 094 an
Unique visits:
18 359 an
Quotes:
40
Downloads:
1 543

NG6

Description

The platform works in tight collaboration with the GeT sequencing platform for the management and the analysis of data produced by their Roche 454 and Illumina HiSeq sequencers.
NG6 is an extensible sequencing provider oriented LIMS. It includes read quality control and first level analysis processes which ease the data validation made jointly by the sequencing facility staff ant the end-users. It provides a secured user-friendly interface to visualize and download the raw sequences files and the analysis results.

Access conditions

The NG6 code is freely available on the gitlab formia : https://forgemia.inra.fr/genotoul-bioinfo/ng6. To ease the installation, the package and all its dependencies are also available as a virtual machine. Installing and maintaining the system would require expertise in Linux system administration.
Available by the web site for users

Annual visits:
9 963 an
Unique visits:
4 112 an
Quotes:
6
Downloads:
Not documented

Galaxy (piloté par Sigenae)

Description

Galaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are:

  • Make bioinfo Linux tools accessible to biogists.
  • Hide the complexity of the infrastructure.
  • Allow creation, execution and sharing of workflows.
Access conditions

Available on a web site with login and password.

Annual visits:
325 an
Unique visits:
194 an
Quotes:
Not documented
Downloads:
Not documented

Interface web blast

Description
Access conditions

Available on the web site.

Annual visits:
14 274 an
Unique visits:
10 059 an
Quotes:
Not documented
Downloads:
Not documented

Interface web Emboss

Description

emboss tools interface.

Access conditions

Site web

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
2
Downloads:
1 357

JFlow

Description

Workflow management system in JS using Makeflow/Weaver

JFlow-toolshed provides components and workflows for the jflow workflow engine: https://mulcyber.toulouse.inra.fr/projects/jflow-toolshed/

Access conditions

The software package is available under the GNU General Public License (GPL) and can be downloaded from the mulcyber forge.

Domains of activity
  • Biomedical
  • Agri-food
  • Environment
  • Biotechnology
  • Biology
Description of expertise domains

The areas of expertise of GenoToul bioinfo platform are:
- The processing of data from the high-throughput sequencing: assembly, annotation, analysis of expression (RNAseq, de novo RNAseq, sRNAseq), metagenomics analysis of variants, méthylSeq.
- Bioinformatics analysis of ncRNA: annotation, prediction, search targets, in archaea, bacteria, plants and animals.

Keywords:
  • NGS data analysis
  • Genomics (DNA-seq)
  • Genome analysis
  • Structural and functional genome annotation
  • Transcriptomics (RNA-seq)
  • Differential gene expression analysis
  • Transcripts and transcript variants analysis
  • Variant calling
  • Exomes
  • Whole genomes
  • Small and long non-coding RNAs
  • Methylation profiles
  • Metagenomics, metatranscriptomics
  • Sequence analysis
  • (multiple) Sequence Alignment
  • Sequence annotation
  • Sequence motif discovery
  • Homology/Orthology prediction
  • Biostatistics
  • Descriptive statistics
  • Statistical tests
  • Regression
  • Multivariate analysis
  • Interoperability
  • Interfaces, web portals
  • Workflows developments
  • Cluster
  • Evolution and phylogeny
  • Molecular evolution
  • Phylogenomics
  • Selection detection
  • Comparative genomics
  • Genome comparison

Formation professionnelle

Trainees:
10 trainees / year
Training time:
1 day(s) / year
Upcoming session :
14-10-2019

Linux/Unix

Description

This training presents the following points: how to access the platform, how to use a Unix environment, how to create and manipulate and transfer files with command line from your computer toward our cluster and vice versa. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private

Trainees:
12 trainees / year
Training time:
1 day(s) / year
Upcoming session :
15-10-2019

Cluster

Description

This training session is designed to help you deal with the platform compute cluster and data banks. You will launch your first processing batch on the cluster and will learn how to track and manage them. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
10 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Read alignment and SNP calling

Description

This training session, organized jointly with the Sigenae platform, is designed to help you deal with NGS data, in particular Roche 454 and Illumina Solexa technologies. You will discover the new sequence formats, the new assembly formats and the known biases of these technologies. You will use mapping on reference genome software, polymorphisms detection (with the GATK pipeline), polymorphisms annotation and alignment visualization software. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
10 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

RNASeq alignment and transcripts assemblies with statistics

Description

This training session is designed to help you deal with sequences from the SGS (Second Generation Sequencing) particularly Illumina platforms (GAIIx, HiSeq). You will discover the new sequence file formats, learn about the usual biases of this data type and run different kind of analysis such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of the genes and transcripts. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

sRNASeq

Description

This training session is designed to help you to deal with small RNA sequences produced from the SGS (Second Generation Sequencing) technology particularly Illumina platforms (HiSeq). You will discover sequence file formats, learn about expression profiles of miRNA and other small non coding RNA and run different kind of analysis such as reads cleaning, alignment on a reference genome, detection and annotation of new and known miRNA, and expression quantification. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

RNAseq de novo assembly

Description

This training session has been designed to give you an overview of the methods and tools used to de novo assemble transcriptomic short reads. You will learn how to pre-process your raw data (fastq files), how an assembler works and how to use it. Finally you will learn how to assess the quality of your assemblies in order to choose the best one. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

Sequences alignment and phylogeny

Description

This training session is organized by the bios4Biol CATI and the genotoul bioinfo platform and aims at initiating participants to molecular phylogenetics studies.
You will discover how to build a sequence dataset, to align sequences, to edit and refine the resulting alignment.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

Methods for phylogenetics trees construction

Description

This training session is organized by the bios4Biol CATI and aims at training participants to construct and interpret phylogenetic trees.
You will discover how to choose an evolutionary model and a phylogenetic inference method (among distance, parsimony, maximum likelihood and Bayesian methods) and how to evaluate the robustness of a tree using bootstrap.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

Phylogenomy and selection pressure

Description

This training session is organized by the bios4Biol CATI.
Morning : phylogenomics
The morning course will provide insigths about sampling problems in phylogenomics studies (genes, species) and methodological aspects of phylogenomics studies with two major focus on super-matrix and super-tree methods.
Afternoon : selection pressure
The afternoon course will be dedicated to the use of the PAML4 package in order to study selection pressures in a sequence alignment.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
20 trainees / year
Training time:
2 day(s) / year
No upcoming session scheduled

Galaxy : first step

Description

Galaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are:
    First, making bioinfo Linux tools accessible to biologists.
    Then, it is possible to add Linux tools by developpers into Galaxy workbench.
    Then, Galaxy is used to hide the complexity of the infrastructure and to allow creation, execution and sharing of workflows.
You will acquire the following competencies required for the other Galaxy trainning:
    Login to Galaxy: Galaxy Workbench (To access to Galaxy, you need to have an LDAP Genotoul login and password).
    Begin to use some tools provided (BWA, SAM tools, FastQC).
    Work on files.

Organized jointly by the Sigenae and the Bioinfo Genotoul platform.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Trainees:
20 trainees / year
Training time:
2 day(s) / year
Upcoming session :
08-10-2018

Galaxy : Reads alignment and SNP calling

Description

As the command line training but with Galaxy. Organized jointly by the Sigenae and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private

Trainees:
10 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Galaxy : RNASeq alignment and transcripts assemblies

Description

As the command line training but with Galaxy. Organized jointly by the Sigenae and the Bioinfo Genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private

Trainees:
0 trainees / year
Training time:
0 day(s) / year
No upcoming session scheduled

Galaxy : sRNAseq

Description

As the command line training but with Galaxy. Organized jointly by the Sigenae and Bioinfo Genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private

Trainees:
30 trainees / year
Training time:
12 day(s) / year
Upcoming session :
01-07-2019

FROGS formation : tools for bioinformatics and statistics analyses with amplicon metagenomics data

Description

This training session, organized by Bioinfo Genotoul, Sigenae, NED (GenPhySE) and TWB, is designed to help you to deal with NGS data of 16S, 18S ... DNA produced with MiSeq from Illumina and Roche 454 technologies in the Galaxy workbench.

You will discover how to use our Galaxy instance, clean reads, clusterize them, do the taxonomic affiliation and perform statistics to interpret your results.

Prerequisites: knowledge of R or in another programming language

Access conditions

Subscribe by the web page : http://bioinfo.genotoul.fr/index.php/training-2/galaxy-training/.

Prices : 165 euros per day for academic people, 550 per day otherwise.

Trainees:
10 trainees / year
Training time:
1 day(s) / year
Upcoming session :
17-10-2019

RNASeq alignment and transcripts assemblies

Description

This training session is designed to help you deal with sequences from the SGS (Second Generation Sequencing) particularly Illumina platforms (GAIIx, HiSeq). You will discover the new sequence file formats, learn about the usual biases of this data type and run different kind of analysis such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of the genes and transcripts. Organized jointly by the MIAT unit and bioinfo genotoul platforms.

Access conditions

You need to register (via the website) and pay 165 euros a day for academic and 550 euros a day for a private.

Formation universitaire

No website documented
Trainees:
12 trainees / year
Training time:
6 day(s) / year
No upcoming session scheduled

Master Bioinfo Toulouse

Description

Organized by Sigenae and Bioinfo Genotoul platforms.

Access conditions
Not documented
Users distribution
International
1 %
National
52 %
Regional
10 %
Local
37%
Explanation about this distribution:
Not documented
Platform's own projects
(10)

1 active and 9 in the maintenance

Collaborations
National projets
(4)

Currently 4 ANR projects, 1 LABEX, 1 FEDE4R / Région Occitanie.

International and European projects
(1)

Salhostrop accepted in 2016

Projects with industry

Quelques locations de CPU et de stockage

Collaboration projects not founded through an external organism
(36)
Not documented
Provision of services not founded through an external organism
(0)
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

- Regional Day bioinfo / biostat (1 / year since 2009 except in 2013)
⁃ JOBIM '13 (Participation of the whole team in the organization of this event)
⁃ Workshop "Bioinformatics of ncRNA"

Internal publications
Nous  ne  mentionnons  ici  que  les  publications  en  lien  direct  avec  la  PF.  Voir  par exemple   aussi   les   publications   de   l’équipe   Sigenae,   qui   s’appuie   sur   les équipements  de  la  PF  pour  l’hébergement  de  son  SI  et  la  réalisation  de  ses traitements : http://www.sigenae.org/index.php?id=156

Mariette J, Noirot C, Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C, Klopp C. (2014) RNAbrowse: RNA-Seq De Novo Assembly Results Browser. PLoS ONE 9(5): e96821. doi: 10.1371/journal.pone.0096821.

Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293.

Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Ibouniyamine Nabihoudine, Céline Noirot, Marie-Stéphane Trotard, Christine Gaspin and Christophe Klopp. Jflow: a workflow management system for web applications. Bioinformatics. 2015. doi 10.1093/bioinformatics/btv589


Jérôme Mariette, Madalina Olteanu, Nathalie Villa-Vialaneix. 2016. Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing. doi:10.1016/j.neucom.2016.11.014.


Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics. 2018 Apr 15;34(8):1287-1294. doi: 10.1093/bioinformatics/btx791. PubMed PMID: 29228191


Mariette J, Villa-Vialaneix N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2018 Mar 15;34(6):1009-1015. doi: 10.1093/bioinformatics/btx682. PubMed PMID: 29077792.


Mariette, J. and Villa-Vialaneix, N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2017. btx682. doi: 10.1093/bioinformatics/btx682


Mariette, J., Olteanu, M. and Villa-Vialaneix, N., Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing, 225, pp.31-48., 2017; doi:10.1016/j.neucom.2016.11.014.

External publications

Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res. 2017 Jun 1;24(3):251-260

 

Urriza MG, Gassie C, Bouchez O, Klopp C, Guyoneaud R. Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain. Genome Announc. 2017;5: e01483-16. doi:10.1128/genomeA.01483-16

Panicz R, Klopp C, Igielski R, Hofsoe P, Sadowski J, Coller Jr JA. Tench (Tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles. Aquaculture. 2017;479: 200–207. doi:10.1016/j.aquaculture.2017.05.047

 

Nouwen N, Arrighi J-F, Cartieaux F, Chaintreuil C, Gully D, Klopp C, et al. The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene /photosynthetic Bradyrhizobium symbiosis. Scientific Reports. 2017;7: 448. doi:10.1038/s41598-017-00559-0

 

Murat F, Armero A, Pont C, Klopp C, Salse J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet. 2017;49: 490–496. doi:10.1038/ng.3813

Mercière M, Boulord R, Carasco-Lacombe C, Klopp C, Lee Y-P, Tan JS, et al. About Ganoderma boninense in oil palm plantations of Sumatra and peninsular Malaysia: Ancient population expansion, extensive gene flow and large scale dispersion ability. Fungal Biology. 2017; doi:10.1016/j.funbio.2017.01.001

 

Jean-Yves Mazzitelli, Elsa Bonnafe, Christophe Klopp, Frédéric Escudier and Florence Geret. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology. 2017;26: 127–140. doi:10.1007/s10646-016-1748-1

Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ. 2017;5: e2988. doi:10.7717/peerj.2988

 

Jadwiga Rzeznik-Orignac, Dimitri Kalenitchenko, Jérôme Mariette, Jean-Yves Bodiou, Nadine Le Bris, Evelyne Derelle. Comparison of meiofaunal diversity by combined morphological and molecular approaches in a shallow Mediterranean sediment. Marine Biology. 2017; 164:40. doi:10.1007/s00227-017-3074-4

 

Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart. Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. mSystems Mar 2017, 2 (2) e00186-16; DOI: 10.1128/mSystems.00186-16.


Laura Payton, Mickael Perrigault, Claire Hoede, Jean-Charles Massabuau, Mohamedou Sow, Arnaud Huvet, Floriane Boullot, Caroline Fabioux, Hélène Hegaret & Damien Tran; Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum; Scientific Reports | 7: 3480 | 2017; DOI:10.1038/s41598-017-03797;


Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre-François Bert, Mindy Stephania Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat; Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. J Exp Bot; 2017; doi: 10.1093/jxb/erx224


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. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biol. 2018 Apr 18;16(1):43. doi: 10.1186/s12915-018-0508-5. PubMed PMID: 29669603; PubMed Central PMCID: PMC5907361


Choque E, Klopp C, Valiere S, Raynal J, Mathieu F. Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential. BMC Genomics. 2018 Mar 15;19(1):200. doi: 10.1186/s12864-018-4574-4. PubMed PMID:29703136


Fumey J, Hinaux H, Noirot C, Thermes C, Rétaux S, Casane D. Evidence for late Pleistocene origin of Astyanax mexicanus cavefish. BMC Evol Biol. 2018 Apr 18;18(1):43. doi: 10.1186/s12862-018-1156-7. PubMed PMID: 29665771; PubMed Central PMCID: PMC5905186


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. Oak genome reveals facets of long lifespan. Nat Plants. 2018 Jun 18. doi: 10.1038/s41477-018-0172-3. PubMed PMID: 29915331.


Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C,Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay. Methods Enzymol. 2018;612:47-66. doi: 10.1016/bs.mie.2018.07.003. Epub 2018 Aug 29. PubMed PMID:30502954.


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. Ten steps to get started in Genome Assembly and Annotation. F1000Res. 2018 Feb 5;7. pii: ELIXIR-148. doi: 10.12688/f1000research.13598.1. eCollection 2018. PubMed PMID: 29568489; PubMed Central PMCID: PMC5850084.


Mat AM, Klopp C, Payton L, Jeziorski C, Chalopin M, Amzil Z, Tran D, Wikfors GH, Hégaret H, Soudant P, Huvet A, Fabioux C. Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling. Aquat Toxicol. 2018 Jun;199:127-137. doi: 10.1016/j.aquatox.2018.03.030. Epub 2018 Mar 27. PubMed PMID: 29621672.


Mondet F, Rau A, Klopp C, Rohmer M, Severac D, Le Conte Y, Alaux C. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics. 2018 May 4;19(1):328. doi: 10.1186/s12864-018-4668-z. PubMed PMID: 29728057; PubMed Central PMCID: PMC5936029.


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. Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing. J Virol Methods. 2018 Nov;261:34-39. doi: 10.1016/j.jviromet.2018.08.003. Epub 2018 Aug PubMed PMID: 30086381.


Bertucci A, Pierron F, Gourves PY, Klopp C, Lagarde G, Pereto C, Dufour V, Gonzalez P, Coynel A, Budzinski H, Baudrimont M. Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea. Ecotoxicol Environ Saf. 2018 Dec 15;165:96-106. doi: 10.1016/j.ecoenv.2018.08.090. Epub 2018 Sep 4. PubMed PMID: 30193169.


Illikoud N, Klopp C, Roulet A, Bouchez O, Marsaud N, Jaffrès E, Zagorec M. One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. Stand Genomic Sci. 2018 Oct 10;13:22. doi: 10.1186/s40793-018-0333-z. eCollection 2018. PubMed PMID:30338025; PubMed Central PMCID: PMC6180393.


de Lima E Silva C, Mariette J, Verweij RA, van Gestel CAM. Assessing the toxicity of thiamethoxam, in natural LUFA 2.2 soil, through three generations of Folsomia candida. Ecotoxicology. 2018 Sep;27(7):764-771. doi:10.1007/s10646-018-1922-8. Epub 2018 Apr 3. PubMed PMID: 29616379; PubMed Central PMCID: PMC6132986.

Publications with the hosting laboratory

J Mariette, N Villa-Vialaneix. 2016. Aggregating Self-Organizing Maps with topology preservation. Advances in Self-Organizing Maps and Learning Vector Quantization, 27-37


Mariette, J., Olteanu, M. and Villa-Vialaneix, N., Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing, 225, pp.31-48.; 2017; doi:10.1016/j.neucom.2016.11.014.


Mariette, J. and Villa-Vialaneix, N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2017. btx682. doi: 10.1093/bioinformatics/btx682


Mariette J, Villa-Vialaneix N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2018 Mar 15;34(6):1009-1015. doi: 10.1093/bioinformatics/btx682. PubMed PMID: 29077792.

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