Genotoul-bioinfo

Adress
24 Chemin de Borde Rouge 31326 Castanet Tolosan
Structure(s)
Not documented
Unit:
MIAT 0875
Regional Center
IFB South West
Scientific leader
Gaspin Christine
Technical leader
Not documented
Certificat(s)
  • CATI / CTAI
  • CNOC (INRA)
  • France-Génomique
  • ISO 9001
  • Label IBiSA
  • NF X50-900
  • PF stratégique nationale INRA
Infrastructure
Hébergée
Effective storage
2 290.00 To
Cluster: cores number
3 176 cores
CPU/hours a year
20 000 000 H / an
Bioinformatic tools number
717
Users number (last year)
1 012
Servers description

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 "Genotoul."
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
→ 3000 hearts
→ 20 million of annual calculation time
→ 34 Tera Bytes of RAM
→ Interconnection Infiniband (QDR)
● HPC Storage
→ Spectrum-Scale-4.2 (GPFS)
→ 800TB useful disk space (fast and capacitive disks), Data Placement and Migration Policy
→ 12GB / s of bandwidth
● NAS Storage
→ 2 Isilon clusters (512 To and replicates 512 To)
→ 2 COMPELLENT clusters (160To and replicates 360To)
● Server Virtualization
→ farm Vmware 4 servers
→ Bay DELL-MD discs (SAN mode) 60TB
→ 96 hosted virtual machines (late 2016)


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:
4 720 an
Unique visits:
2 250 an
Quotes:
11
Downloads:
1 982

RNAbrowse nouvelle version

Description

55 instances including 18 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 mulcyber forge.
Available on web sites for users.

Annual visits:
12 170 an
Unique visits:
6 888 an
Quotes:
18
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:
31
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 mulcyber forge. 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:
6 851 an
Unique visits:
1 704 an
Quotes:
Not documented
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:
Not documented
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.

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 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 :
06-03-2017

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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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 :
07-03-2017

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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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
Upcoming session :
08-03-2017

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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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 : 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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

An account on the platform Bioinfo Genotoul is necessary (request a form on the website), 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 :
03-07-2017

Galaxy: metagenomic: sequence analysis of amplicons from MiSeq and 454 sequencing with FROGS with Galaxy first step and statistics

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.

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
(9)

2 active and 7 in the maintenance

Collaborations
National projets
(6)

5 ended in 2016. One INCA project. 1 LABEX project accepted. 1 ANR project accepted in 2016 (not in the previous count).

International and European projects
(1)

Salhostrop accepted in 2016

Projets with industry
(1)

1 PIA and 4 CPU use charged

Collaboration projects not founded through an external organism
(35)
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

External publications
Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, Bento P, Da Silva C, Labadie K, Albertii A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet A, Guyomard R, galiana D, Bobe J, Volff JN, gene C, Wincker P, Jaillon O, Roest Crollius H, Guigen Y. The rainbow trout genome provides novel insights into evolution after whole-genome duplication invertebrates. NATURE COMMUNICATIONS, 5:3657, DOI: 10.103.

Etienne Liais, Guillaume Croville, Jérôme Mariette, Maxence Delverdier, Marie-Noelle Lucas, Christophe Klopp, Jérôme Lluch, Cécile Donnadieu, James S. Guy, Léni Corrand, Mariette F. Ducatez, and Jean-Luc Guérin. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France. Emerg Infect Dis.

Canales J, Bautista R, Label P, Gómez-Maldonado J, Lesur I, Fernández-Pozo N, Rueda-López M, Guerrero-Fernández D, Castro-Rodríguez V, Benzekri H, Cañas RA, Guevara MA, Rodrigues A, Seoane P, Teyssier C, Morel A, Ehrenmann F, Le Provost G, Lalanne C, Noirot C, Klopp C, Reymond I, García-Gutiérrez A, Trontin JF, Lelu-Walter MA, Miguel C, Cervera MT, Cantón FR, Plomion C, Harvengt L, Avila C, Gonzalo Claros M, Cánovas FM.De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnol J. 2013 Nov 21. doi: 10.1111/pbi.12136

Bastien G, Arnal G, Bozonnet S, Laguerre S, Ferreira F, Fauré R, henrissat B, Lefèvre F, Robe P, Bouchez O, Noirot C, Dumon C, O'Donohue M. Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnology for Biofuels. 2013, 6:78. doi: 10.1186/1754-6834-6-78.

V Bourret, G Croville, J Mariette, C Klopp, O Bouchez, L Tiley, JL Guérin. Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells. Infection, Genetics and Evolution. 2013 May.

Chancerel E, Lamy JB, Lesur I, Noirot C, Klopp C, Ehrenmann F, Boury C, Le Provost G, Label P, Lalanne C, Léger V, Salin F, Gion JM, Plomion C. High- density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biol. 2013 Apr 18;11(1):50.

Bouzid W, Klopp C, Verdenaud M, Ducancel F, Vétillard A. Profiling the venom gland transcriptome of Tetramorium bicarinatum (Hymenoptera: Formicidae): The first transcriptome analysis of an ant species. Toxicon. 2013 Apr 11. doi:pii: S0041-0101(13)00105-0. 10.1016/j.toxicon.2013.03.010.

Ueno S, Klopp C, Leplé JC, Derory J, Noirot C, Léger V, Prince E, Kremer A, Plomion C, Le Provost G. Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics. 2013 Apr 10;14:236. doi: 10.1186/1471-2164-14-236.

Hinaux H, Poulain J, Da Silva C, Noirot C, Jeffery WR, Casane D, Rétaux S. De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes. PLoS One. 2013;8(1):e53553. doi: 10.1371/journal.pone.0053553. Epub 2013 Jan 9.

Quelen C, Eloit Y, Noirot C, Bousquet M, Brousset P. RNA editing in acute myeloid leukaemia with normal karyotype. Br J Haematol. 2015 Aug 7. doi:10.1111/bjh.13631. [Epub ahead of print] PubMed PMID: 26251186


Esquerré T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign-Bousquet M, Girbal L. Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics. 2015 Apr 9;16:275. doi: 10.1186/s12864-015-1482-8. PubMed PMID: 25887031


Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF. Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics. 2015 May 29;16:179. doi: 10.1186/s12859-015-0594-0. PubMed PMID: 26022464


Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour. 2015 May 6. doi: 10.1111/1755-0998.12425


Pratlong M, Haguenauer A, Chabrol O, Klopp C, Pontarotti P and Aurelle D. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies. 2015


Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K Hastings, Richard D Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Céline Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W Teague, Abu Z Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acid Research. 2015


Mazzitelli J-Y, Bonnafe E, Klopp C, Escudier F, Geret F. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology. 2016; 1–14. doi:10.1007/s10646-016-1748-1


Hammoumi S, Vallaeys T, Santika A, Leleux P, Borzym E, Klopp C, et al. Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ. 2016;4: e2516. doi:10.7717/peerj.2516


Guellerin M, Passerini D, Fontagné-Faucher C, Robert H, Gabriel V, Loux V, Klopp C, et al. Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough. Genome Announc. 2016;4: e00692-16. doi:10.1128/genomeA.00692-16


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


André Pornon, Nathalie Escaravage, Monique Burrus, Hélène Holota, Aurélie Khimoun, Jérôme Mariette, Charlène Pellizzari, Amaia Iribar, Roselyne Etienne, Pierre Taberlet, Marie Vidal, Peter Winterton, Lucie Zinger & Christophe Andalo. 2016. Using metabarcoding to reveal and quantify plant-pollinator interactions. Scientific Reports 6, Article number: 27282. doi:10.1038/srep27282.


Juanchich A. Bardou P., Rué O., Gabillard JC, Gaspin C., Bobe J., Guigen Y., Chacacterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics. 2016 Mar 1;17:164


Feugeas JP, Tourret J, Launay A, Bouvet O, Hoede C, Denamur E, and Tenaillon O. Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies. Mol Biol Evol first published online June 28, 2016 doi:10.1093/molbev/msw105.


Clémence Chaintreuil, Ronan Rivallan, David J. Bertioli, Christophe Klopp, Jérôme Gouzy, Brigitte Courtois, Philippe Leleux, Guillaume Martin, Jean-François Rami, Djamel Gully, Hugues Parrinello, Dany Séverac, Delphine Patrel, Joël Fardoux, William Ribière, Marc Boursot, Fabienne Cartieaux, Pierre Czernic, Pascal Ratet, Pierre Mournet, Eric Giraud, and Jean-François Arrighi. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Res (2016) 23 (4): 365-376. doi:10.1093/dnares/dsw020.


Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C. (2016) Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ Preprints 4:e2284v1 https://doi.org/10.7287/peerj.preprints.2284v1.


Roberto Sierra, Silvia J. Cañas-Duarte, Fabien Burki, Arne Schwelm, Johan Fogelqvist, Christina Dixelius, Laura N. González-García, Gillian H. Gile, Claudio H. Slamovits, Christophe Klopp, Silvia Restrepo, Isabelle Arzul, and Jan Pawlowski. Evolutionary Origins of Rhizarian Parasites. Mol Biol Evol (2016) 33 (4): 980-983. doi:10.1093/molbev/msv340.


Bétous R, Renoud ML, Hoede C, Gonzalez I, Jones N, Longy M, Sensebé L, Cazaux C, Hoffmann JS. Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress. Stem Cells Transl Med. 2016 Aug 24. DOI:10.5966/sctm.2015-0401

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

Acknowledgement
Puchalska, P., Concepción García, M., & Luisa Marina, M. Identification of native angiotensin-I converting enzyme inhibitory peptides in commercial soybean based infant formulas using HPLC-Q-ToF-MS. Food chemistry, 157, 62-69.

 

Malé, P. J. G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., ... & Chave, J. (2014). Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular ecology resources.

 

David Allouche, Jessica Davies, Simon de Givry, George Katsirelos, Thomas Schiex, Seydou Traoré, Isabelle André, Sophie Barbe, Steve Prestwich, Barry O'Sullivan. Computational protein design as an optimization problem.

 

Laure Fresard, Sophie Leroux, Bertrand Servin, David Gourichon, Patrice Dehais, Magali San Cristobal, Nathalie Marsaud, Florence Vignoles, Bertrand Bedhom, Jean-Luc Coville, Farhad Hormozdiari, Catherine Beaumont, Tatiana Zerjal, Alain Vignal, Mireille Morisson, Sandrine Lagarrigue and Frederique Pitel. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Research, 2014, 1–15. doi:10.1093/nar/gkt1390.

 

Gschloessl B, Vogel H, Burban C, Heckel D, Streiff R, Kerdelhué C. 2014. Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing. Insect Biochem Mol Biol. ;46:31-42.

 

Vignaud, T. M., Maynard, J. A., Leblois, R., Meekan, M. G., Vázquez?Juárez, R., Ramírez?Macías, D., ... & Planes, S. (2014). Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Molecular Ecology.

 

Elsen JM, de Givry S, Katsirelos G, and Shumbusho F. Optimizing the reference population in a genomic selection design. In CP-13 workshop on Constraint Based Methods for Bioinformatics, pages 37-46, Uppsala, Sweden, 2013.

 

de Givry S, Prestwich S, and O'Sullivan B. Dead-End Elimination for Weighted CSP. In Proc. of CP-13, pages 263-272, Uppsala, Sweden, 2013

 

Thepot S, Ben Abdelali R, Chevret S, Renneville A, Beyne Rauzy O, Prebet T, Park S, Stamatoullas A, Guerci-Bresler A, Cheze S, Tertian G, Choufi B, Legros L, Bastie JN, Delaunay J, Wattel E, Dreyfus, Vey N, Preudhomme C, Fenaux P, and Gardin C. Prognostic Factors Of Response and Survival To Azacitidine (AZA) ± EPO In RBC Transfusion Dependent (TD) IPSS Low and Int-1 (LR) MDS Resistant To EPO, With Particular Emphasis Of Genetic Lesions: A Study By The GFM. ASH (American Society of Hematology), 2013.

 

Girardot M, Hirasawa R, Kacem S, Fritsch L, Pontis J, Kota SK, Filipponi D, Fabbrizio E, Sardet C, Lohmann F, Kadam S, Ait-Si-Ali S, Feil R. PRMT5- mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome. Nucleic Acids Res. 2013 Oct 3. doi: 10.1093/nar/gkt884.

 

Robic A, Faraut T, Prunier A. Pathway and genes involved in steroid hormone metabolism in male pigs: a review and update. Journal of steroid biochemistry and molecular biology. Available online 12 November 2013. doi:10.1016/j.jsbmb. 2013.11.001.

 

Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Schiex T, Barbe S. A new framework for computational protein design through cost function network optimization. Bioinformatics. 2013 Sep 1;29(17):2129-36. doi: 10.1093/ bioinformatics/btt374. Epub 2013 Jul 10.

 

Blanc-Mathieu R, Sanchez-Ferandin S, Eyre-Walker A, Piganeau G. Organellar Inheritance in the Green Lineage: Insights from Ostreococcus tauri. Genome Biol Evol. 2013 Jan;5(8):1503-11. doi: 10.1093/gbe/evt106.
 

Carré C, Gamboa F, Cros D, Hickey JM, Gorjanc G, Manfredi E. Genetic prediction of complex traits: integrating infinitesimal and marked genetic effects. Genetica. 2013 Jun;141(4-6):239-46. doi: 10.1007/s10709-013-9722-9. Epub 2013 May 30.

 

Ben C, Debellé F, Berges H, Bellec A, Jardinaud MF, Anson P, Huguet T, Gentzbittel L, Vailleau F. MtQRRS1, an R-locus required for Medicago truncatula quantitative resistance to Ralstonia solanacearum. New Phytol. 2013 Aug;199(3): 758-72. doi: 10.1111/nph.12299. Epub 2013 May 2.

 

Nizar Fawal, Qiang Li, Bruno Savelli, Marie Brette, Gisele Passaia, Maxime Fabre, Catherine Mathé and Christophe Dunand. PeroxiBase: a database for large- scale evolutionary analysis of peroxidases. Nucleic Acids Res. 2013 Jan 1;41(D1):D441-4. doi: 10.1093/nar/gks1083. Epub 2012 Nov 24.

 

Colombani C, Legarra A, Fritz S, Guillaume F, Croiseau P, Ducrocq V, Robert- Granié C. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesC? methods for genomic selection in French Holstein and Montbéliarde breeds. J Dairy Sci. 2013 Jan;96(1):575-91. doi: 10.3168/jds. 2011-5225. Epub 2012 No.

 

Luis Alberto Garcia-Cortes, Andres Legarra, Claude Chevalet, Miguel Angel Toro. Variance and Covariance of Actual Relationships between Relatives at One Locus.PLoS One. 2013;8(2):e57003. doi: 10.1371/journal.pone.0057003. Epub 2013 Feb 22.

 

Gschloessl B, Beyne E, Audiot P, Bourguet D, Striff R. De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis. BMC Research Notes. 2013;6:73. doi:10.1186/1756-0500-6-73. Epub 2013 Feb 28.

 

Baloche G, Legarra A, Sallé G, Larroque H, Astruc JM, Robert-Granié C, Barillet F. Assessment of accuracy of genomic prediction for French Lacaune dairysheep. J Dairy Sci. 2014 Feb;97(2):1107-16. doi: 10.3168/jds.2013-7135.

 

Vitezica ZG, Varona L, Legarra A. On the additive and dominant variance and covariance of individuals within the genomic selection scope. Genetics. 2013 Dec;195(4):1223-30.

 

Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi JM, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Nayel ML, Young ND, Jacquet C. High-density genome- wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches. New Phytol. 2013 Nov 28.

 

Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics. 2013 Mar;193(3):929-41.

 

Auclair S, Rossetti R, Meslin C, Monestier O, Di Pasquale E, Pascal G, Persani L, Fabre S. Positive selection in bone morphogenetic protein 15 targets a natural mutation associated with primary ovarian insufficiency in human. PLoS One. 2013 Oct 16;8(10):e78199. doi: 10.1371/journal.pone.0078199. eCollection 2013.

 

Forneris NS, Legarra A, Vitezica ZG, Tsuruta S, Aguilar I, Misztal I, Cantet RJ. Quality control of genotypes using heritability estimates of gene content at the marker. Genetics. 2015 Mar;199(3):675-81

 

Legarra A, Christensen OF, Vitezica ZG, Aguilar I, Misztal I. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics. 2015 Jun;200(2):455-68. doi: 10.1534/genetics.115.177014.

 

Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, Fritz S, Moreno CR, Ricard A, Elsen JM. A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genet Sel Evol. 2015 Feb 12;47:6. doi: 10.1186/s12711-015-0087-7.

 

Legarra A. Comparing estimates of genetic variance across different relationship models. Theor Popul Biol. 2015 Sep 2. pii: S0040-5809(15)00083-0. doi: 10.1016/j.tpb.2015.08.005.

 

Legarra A, Vitezica ZG. Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP. Genet Sel Evol. 2015 Nov 17;47(1):89.doi: 10.1186/s12711-015-0165-x.

 

Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biological Journal of the Linnean Society. 2015. doi:10.1111/bij.12509.

 

Hinaux H, Blin M, Fumey J, Legendre L, Heuzé A, Casane D, Rétaux S. Lens defects in Astyanax mexicanus Cavefish: Evolution of crystallins and a role for alphaA-crystallin. Developmental Neurobiology. 2015. Vol 75, issue 5, page 505-521. doi:10.1002/dneu.22239.

 

San Clemente H and Jamet E. WallProtDB, a database resource for plant cell wall proteomics. PlantMethods. 2015. 11:2. doi:10.1186/s13007-015-0045-y.

 

Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro A.B, Nys Y, Gautron J. Data set for the proteomic inventory and quantitative analysis of chicken eggshell matrix proteins during the primary events of eggshell mineralization and the active growth phase of calcification. Data in Brief, Available online 7 July 2015, ISSN 2352-3409, doi:10.1016/j.dib.2015.06.019.

 

Kocher A, Guilbert E, Lhuillier E, Murienne J. Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. Comptes Rendus Biologies, Volume 338, Issue 3, March 2015, Pages 149-160, ISSN 1631-0691, doi:10.1016/j.crvi.2014.12.004.

 

Duhoux A, Carrère S, Gouzy J, Bonin L, Délye C. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. Plant Mol Biol. 2015 Jan 31. doi:10.1007/s11103-015-0292-3.

 

San Clemente H, Jamet E, WallProtDB, a database resource for plant cell wall proteomic, Plant methods 2015, 11:2, doi:10.1186/s13007-015-0045-y

 

Lauressergues D, Couzigou JM, San Clemente H, Martinez Y, Dunand C, Bécard G, Combier JP, Primary transcripts of microRNAs encode regulatory peptide, Nature 520, 90–93 (02 April 2015), doi:10.1038/nature14346.

 

Bonhomme M, Boitard S, San Clemente H, Dumas B, Young N and Jacquet C, Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganism, Molecular Biology and Evolution, avril 2015, doi: 10.1093/molbev/msv092.

 

David Simoncini, David Allouche, Simon de Givry, Céline Delmas, Sophie Barbe, and Thomas Schiex, J. Chem. Theory Comput., Just Accepted Manuscript, DOI: 10.1021/acs.jctc.5b00594, Publication Date (Web): November 11, 2015.

Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C, Kremer A. 2016. Extensive recent secondary contacts between four European white oak species. New Phytologist.

Hurley, B., O’Sullivan, B., Allouche, D., Katsirelos, G., Schiex, T., Zytnicki, M., de Givry, S.: Multi-Language Evaluation of Exact Solvers in Graphical Model Discrete Optimization. In: Proc. of CP-AI-OR’2016. Ban ff, Canada (2016)

Lalis A., R. Leblois, S. Liefried, A. Ouarour, C. Reddy Beeravolu, J. Michaux, A. Hamani, C. Denys, V. Nicolas. 2016. New molecular data favor an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa. Journal of Zoological Systematics and Evolutionary Research 54 : 1-12. Doi : 10.1111/jzs.12111.

Zenboudji S., M. Cheylan, V. Arnal, A. Bertolero, R. Leblois, G. Astruc, G. Bertorelle, J. L. Pretus, M. Lo Valvo, G. Sotgiu, C. Montgelard. 2016. High genetic structure and contrasting demographic history in the endangered Mediterranean tortoise Testudo hermanni hermanni. Biological Conservation 195 : 279–291; doi:10.1016/j.biocon.2016.01.007

Lalis A., R. Leblois, E. Stoetzel, T. Benazzou, K. Souttou, C. Denys, V. Nicolas. 2016. Integrating phylogeographic patterns of mtDNA and nDNA divergence to infer the evolutionary history of Meriones shawii (Rodentia: Muridae): a comparison of genetic and fossil data. Biological Journal of the Linean Society, In Press.

Vitezica, Z. G., Varona, L., Elsen, J. M., Misztal, I., Herring, W., & Legarra, A. (2016). Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs. Genetics Selection Evolution, 48(1), 1

Richard, F.D., Alves, R., Kajava, A.V., 2016. Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics btw118. doi:10.1093/bioinformatics/btw11

Boitard, S., Boussaha, M., Capitan, A., Rocha, D., Servin, B. (2016). Uncovering Adaptation from Sequence Data : Lessons from Genome Resequencing of Four Cattle Breeds. Genetics, 203 (1), 433-450.

Boitard, S., Rodriguez, W., Jay, F., Mona, S., Austerlitz, F. (2016). Inferring population size history from large samples of genome-wide molecular data – an approximate bayesian computation approach. PLOS Genetics, 12 (3), 1-36

Merle C, Leblois R, Rousset F, Pudlo P. Resampling: An improvement of importance sampling in varying population size models. Theor Popul Biol. 2016 Oct 3. doi: 10.1016/j.tpb.2016.09.002;

 

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