Genotoul-bioinfo
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
24 Chemin de Borde Rouge 31326 Castanet Tolosan
Structure(s)
Not documented
Unit:
MIAT 0875
Website
http://bioinfo.genotoul.fr/Scientific leader(s)
Technical leader(s)
Certificat(s)
- CATI / CTAI
- CNOC (INRA)
- France-Génomique
- ISO 9001
- Label IBiSA
- NF X50-900
- PF stratégique nationale INRA
Infrastructure
Propriétaire
Effective storage
4 247.00 To
Cluster: cores number
3 040 cores
CPU/hours a year
50 000 000 H / an
Bioinformatic tools number
758
Users number (last year)
950
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 "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
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), 16 Tera Octets RAM
- 1 node SMP1 = 48c /96 threads, 1.5 Tera Octets RAM
- 1 node SMP2 = 96c / 192 threads, 3 Tera Octets RAM
- Interconnection Infiniband (QDR) QDR (40Gbs) / FDR (56 Gbs)
● HPC Storage
→ 5 Peta Octets utiles (Spectrum Scale)
● NAS Storage
→ 3 bays ISILON (au total 1.8 Peta Octets useful)
→ 1 bay COMPELLENT/FLUIDFS (total of 300 Tera Octets useful)
● Server Virtualization
→ farm Vmware V6.7 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: 27 508 an
Unique visits: 16 856 an
Quotes: 42
Downloads: Not documented
DgeniesDescriptionD-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 conditionsD-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: 13
Downloads: Not documented
mixkernelDescriptionKernel-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 conditionsmixKernel 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: 37 976 an
Unique visits: 69 155 an
Quotes: 223
Downloads: Not documented
JvennDescriptionA javascript plugin for venn diagrams. A demo is available here: http://bioinfo.genotoul.fr/jvenn/example.html Access conditionsThe 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: Not documented
Unique visits: Not documented
Quotes: 15
Downloads: Not documented
RNAbrowse nouvelle versionDescription35 instances including 10 Sigenae. Access conditionsThe 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. |
Annual visits: 11 183 an
Unique visits: 7 544 an
Quotes: 31
Downloads: Not documented
RNAspaceDescriptionRNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. Access conditionsRNAspace 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: 28 559 an
Unique visits: 14 823 an
Quotes: 26
Downloads: Not documented
NG6DescriptionThe 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. Access conditionsThe 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. |
Annual visits: 2 085 an
Unique visits: 286 an
Quotes: 48
Downloads: Not documented
Galaxy (piloté par Sigenae)DescriptionGalaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are:
Access conditionsAvailable on a web site with login and password. |
Annual visits: 765 an
Unique visits: 689 an
Quotes: Not documented
Downloads: Not documented
Interface web blastDescriptionWeb blast interface Access conditionsAvailable on the web site. |
Annual visits: 662 an
Unique visits: 468 an
Quotes: Not documented
Downloads: Not documented
Interface web EmbossDescriptionemboss tools interface. Access conditionsSite web |
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, epigenetic.
- Bioinformatics analysis of ncRNA: annotation, prediction, search targets, in archaea, bacteria, plants and animals.
- Biostatistic : integration of heterogeneous data
Keywords:
- NGS data analysis
- Methodology
- Genome and transcriptome assembly
- Read mapping
- 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
- Data integration
- 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/UnixDescriptionThis 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 conditionsYou 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
ClusterDescriptionThis 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 conditionsYou 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 callingDescriptionThis 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 conditionsYou 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 statisticsDescriptionThis 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 conditionsYou 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
sRNASeqDescriptionThis 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 conditionsYou 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 assemblyDescriptionThis 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 conditionsYou 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 phylogenyDescriptionThis training session is organized by the bios4Biol CATI and the genotoul bioinfo platform and aims at initiating participants to molecular phylogenetics studies. Access conditionsYou 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 constructionDescriptionThis training session is organized by the bios4Biol CATI and aims at training participants to construct and interpret phylogenetic trees. Access conditionsYou 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 pressureDescriptionThis training session is organized by the bios4Biol CATI. Access conditionsYou 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 stepDescriptionGalaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are: Organized jointly by the Sigenae and the Bioinfo Genotoul platform. Access conditionsYou 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 callingDescriptionAs the command line training but with Galaxy. Organized jointly by the Sigenae and bioinfo genotoul platforms. Access conditionsYou 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 assembliesDescriptionAs the command line training but with Galaxy. Organized jointly by the Sigenae and the Bioinfo Genotoul platforms. Access conditionsYou 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 : sRNAseqDescriptionAs the command line training but with Galaxy. Organized jointly by the Sigenae and Bioinfo Genotoul platforms. Access conditionsYou 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 dataDescriptionThis 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 conditionsSubscribe 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 assembliesDescriptionThis 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 conditionsYou 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 documentedTrainees: 12 trainees / year
Training time: 6 day(s) / year
No upcoming session scheduled
Master Bioinfo ToulouseDescriptionOrganized by Sigenae and Bioinfo Genotoul platforms. Access conditionsNot documented |
Internal publications
Nous ne mentionnons 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 : Publications (sigenae.org)
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.
Nagnan-Le Meillour P, Descamps A, Le Danvic C, Grandmougin M, Saliou JM, Klopp C, Milhes M, Bompard C, Chesneau D, Poissenot K, Keller M. Identification of potential chemosignals in the European water vole Arvicola terrestris. Sci Rep. 2019 Dec 5;9(1):18378. doi: 10.1038/s41598-019-54935-z. PubMed PMID: 31804568.
Dalmon A, Gayral P, Decante D, Klopp C, Bigot D, Thomasson M, Herniou EA, Alaux C, Le Conte Y. Viruses in the Invasive Hornet Vespa velutina. Viruses. 2019 Nov 8;11(11). pii: E1041. doi: 10.3390/v11111041. PubMed PMID: 31717432.
Kottler VA, Feron R, Nanda I, Klopp C, Du K, Kneitz S, Helmprobst F, Lamatsch DK, Lopez-Roques C, Lluch J, Journot L, Parrinello H, Guiguen Y, Schartl M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics. 2019 Nov 8. pii: genetics.302698.2019. doi:10.1534/genetics.119.302698. [Epub ahead of print] PubMed PMID: 31704715
Goñi-Urriza M, Klopp C, Ranchou-Peyruse M, Ranchou-Peyruse A, Monperrus M, Khalfaoui-Hassani B, Guyoneaud R. Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains. Res Microbiol. 2019 Oct 23. pii: S0923-2508(19)30121-4. doi: 10.1016/j.resmic.2019.10.003. [Epub ahead of print] PubMed PMID: 31655199
Péden R, Poupin P, Sohm B, Flayac J, Giambérini L, Klopp C, Louis F, Pain-Devin S, Potet M, Serre RF, Devin S. Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. Sci Data. 2019 Oct 25;6(1):234. doi: 10.1038/s41597-019-0252-x. PubMed PMID: 31653851; PubMed Central PMCID: PMC6814772
Striberny A, Jørgensen EH, Klopp C, Magnanou E. Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation. BMC Genomics. 2019 Jun 27;20(1):529. doi: 10.1186/s12864-019-5874-z. PubMed PMID: 31248377; PubMed Central PMCID: PMC6598377
Ipoutcha T, Tsarmpopoulos I, Talenton V, Gaspin C, Moisan A, Walker CA, Brownlie J, Blanchard A, Thebault P, Sirand-Pugnet P. Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes). Front Microbiol. 2019 Nov 21;10:2701. doi: 10.3389/fmicb.2019.02701. eCollection 2019. PubMed PMID: 31824468; PubMed Central PMCID: PMC6882279
Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E, Ferrandon D. Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster. Microbiol Resour Announc. 2019 Aug 1;8(31). pii: e00077-19. doi:10.1128/MRA.00077-19. PubMed PMID: 31371528; PubMed Central PMCID: PMC6675976
Jehl, F.; Muret, K.; Bernard, M.; Boutin, M.; Lagoutte, L.; Désert, C.; Dehais, P.; Esquerré, D.; Acloque, H.; Giuffra, E.; Djebali, S.; Foissac, S.; Derrien, T.; Pitel, F.; Zerjal, T.; Klopp, C.; Lagarrigue, S. An Integrative Atlas of Chicken Long Non-Coding Genes and Their Annotations across 25 Tissues. Sci Rep 2020, 10 (1), 20457. https://doi.org/10.1038/s41598-020-77586-x
Mat, A. M.; Sarrazin, J.; Markov, G. V.; Apremont, V.; Dubreuil, C.; Eché, C.; Fabioux, C.; Klopp, C.; Sarradin, P.-M.; Tanguy, A.; Huvet, A.; Matabos, M. Biological Rhythms in the Deep-Sea Hydrothermal Mussel Bathymodiolus Azoricus. Nat Commun 2020, 11 (1), 3454. https://doi.org/10.1038/s41467-020-17284-4
Feron, R.; Zahm, M.; Cabau, C.; Klopp, C.; Roques, C.; Bouchez, O.; Eché, C.; Valière, S.; Donnadieu, C.; Haffray, P.; Bestin, A.; Morvezen, R.; Acloque, H.; Euclide, P. T.; Wen, M.; Jouano, E.; Schartl, M.; Postlethwait, J. H.; Schraidt, C.; Christie, M. R.; Larson, W. A.; Herpin, A.; Guiguen, Y. Characterization of a Y‐specific Duplication/Insertion of the Anti‐Mullerian Hormone Type II Receptor Gene Based on a Chromosome‐scale Genome Assembly of Yellow Perch, Perca Flavescens. Mol Ecol Resour 2020, 20 (2), 531–543. https://doi.org/10.1111/1755-0998.13133
Miyauchi, S.; Hage, H.; Drula, E.; Lesage-Meessen, L.; Berrin, J.-G.; Navarro, D.; Favel, A.; Chaduli, D.; Grisel, S.; Haon, M.; Piumi, F.; Levasseur, A.; Lomascolo, A.; Ahrendt, S.; Barry, K.; LaButti, K. M.; Chevret, D.; Daum, C.; Mariette, J.; Klopp, C.; Cullen, D.; de Vries, R. P.; Gathman, A. C.; Hainaut, M.; Henrissat, B.; Hildén, K. S.; Kües, U.; Lilly, W.; Lipzen, A.; Mäkelä, M. R.; Martinez, A. T.; Morel-Rouhier, M.; Morin, E.; Pangilinan, J.; Ram, A. F. J.; Wösten, H. A. B.; Ruiz-Dueñas, F. J.; Riley, R.; Record, E.; Grigoriev, I. V.; Rosso, M.-N. Conserved White-Rot Enzymatic Mechanism for Wood Decay in the Basidiomycota Genus Pycnoporus. DNA Research 2020, 27 (2), dsaa011. https://doi.org/10.1093/dnares/dsaa011
Policarpo, M.; Fumey, J.; Lafargeas, P.; Naquin, D.; Thermes, C.; Naville, M.; Dechaud, C.; Volff, J.-N.; Cabau, C.; Klopp, C.; Møller, P. R.; Bernatchez, L.; García-Machado, E.; Rétaux, S.; Casane, D. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals. Molecular Biology and Evolution 2020, msaa249. https://doi.org/10.1093/molbev/msaa249
Payton, L.; Noirot, C.; Hoede, C.; Hüppe, L.; Last, K.; Wilcockson, D.; Ershova, E. A.; Valière, S.; Meyer, B. Daily Transcriptomes of the Copepod Calanus Finmarchicus during the Summer Solstice at High Arctic Latitudes. Scientific Data 2020, 7 (1), 415. https://doi.org/10.1038/s41597-020-00751-4
Żarski, D.; Le Cam, A.; Nynca, J.; Klopp, C.; Ciesielski, S.; Sarosiek, B.; Montfort, J.; Król, J.; Fontaine, P.; Ciereszko, A.; Bobe, J. Domestication Modulates the Expression of Genes Involved in Neurogenesis in High‐quality Eggs of Sander Lucioperca. Mol Reprod Dev 2020, 87 (9), 934–951. https://doi.org/10.1002/mrd.23414
Baksay, S.; Pornon, A.; Burrus, M.; Mariette, J.; Andalo, C.; Escaravage, N. Experimental Quantification of Pollen with DNA Metabarcoding Using ITS1 and TrnL. Scientific Reports 2020, 10 (1), 4202. https://doi.org/10.1038/s41598-020-61198-6
Goñi-Urriza, M.; Klopp, C.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Monperrus, M.; Khalfaoui-Hassani, B.; Guyoneaud, R. Genome Insights of Mercury Methylation among Desulfovibrio and Pseudodesulfovibrio Strains. Research in Microbiology 2020, 171 (1), 3–12. https://doi.org/10.1016/j.resmic.2019.10.003
Takehana, Y.; Zahm, M.; Cabau, C.; Klopp, C.; Roques, C.; Bouchez, O.; Donnadieu, C.; Barrachina, C.; Journot, L.; Kawaguchi, M.; Yasumasu, S.; Ansai, S.; Naruse, K.; Inoue, K.; Shinzato, C.; Schartl, M.; Guiguen, Y.; Herpin, A. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias Javanicus : A Small Aquarium Fish Model for Studies on Adaptation to Salinity. G3 2020, 10 (3), 907–915. https://doi.org/10.1534/g3.119.400725
Kottler, V. A.; Feron, R.; Nanda, I.; Klopp, C.; Du, K.; Kneitz, S.; Helmprobst, F.; Lamatsch, D. K.; Lopez-Roques, C.; Lluch, J.; Journot, L.; Parrinello, H.; Guiguen, Y.; Schartl, M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics 2020, 214 (1), 193–209. https://doi.org/10.1534/genetics.119.302698
Aubé, J.; Senin, P.; Bonin, P.; Pringault, O.; Jeziorski, C.; Bouchez, O.; Klopp, C.; Guyoneaud, R.; Goñi-Urriza, M. Meta-Omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. Microbial Ecology 2020, 80 (2), 286–295. https://doi.org/10.1007/s00248-020-01493-x
Bazile, J.; Jaffrezic, F.; Dehais, P.; Reichstadt, M.; Klopp, C.; Laloe, D.; Bonnet, M. Molecular Signatures of Muscle Growth and Composition Deciphered by the Meta-Analysis of Age-Related Public Transcriptomics Data. Physiological Genomics 2020, 52 (8), 322–332. https://doi.org/10.1152/physiolgenomics.00020.2020
Genevière, A.-M.; Derelle, E.; Escande, M.-L.; Grimsley, N.; Klopp, C.; Ménager, C.; Michel, A.; Moreau, H. Responses to Iron Oxide and Zinc Oxide Nanoparticles in Echinoderm Embryos and Microalgae: Uptake, Growth, Morphology, and Transcriptomic Analysis. Nanotoxicology 2020, 1–20. https://doi.org/10.1080/17435390.2020.1827074
Wen, M.; Feron, R.; Pan, Q.; Guguin, J.; Jouanno, E.; Herpin, A.; Klopp, C.; Cabau, C.; Zahm, M.; Parrinello, H.; Journot, L.; Burgess, S. M.; Omori, Y.; Postlethwait, J. H.; Schartl, M.; Guiguen, Y. Sex Chromosome and Sex Locus Characterization in Goldfish, Carassius Auratus (Linnaeus, 1758). BMC Genomics 2020, 21 (1), 552. https://doi.org/10.1186/s12864-020-06959-3
Du, K.; Stöck, M.; Kneitz, S.; Klopp, C.; Woltering, J. M.; Adolfi, M. C.; Feron, R.; Prokopov, D.; Makunin, A.; Kichigin, I.; Schmidt, C.; Fischer, P.; Kuhl, H.; Wuertz, S.; Gessner, J.; Kloas, W.; Cabau, C.; Iampietro, C.; Parrinello, H.; Tomlinson, C.; Journot, L.; Postlethwait, J. H.; Braasch, I.; Trifonov, V.; Warren, W. C.; Meyer, A.; Guiguen, Y.; Schartl, M. The Sterlet Sturgeon Genome Sequence and the Mechanisms of Segmental Rediploidization. Nature Ecology & Evolution 2020, 4 (6), 841–852. https://doi.org/10.1038/s41559-020-1166-x
Perrier, F.; Bertucci, A.; Pierron, F.; Feurtet‐Mazel, A.; Simon, O.; Klopp, C.; Candaudap, F.; Pokrovski, O.; Etcheverria, B.; Mornet, S.; Baudrimont, M. Transfer and Transcriptomic Profiling in Liver and Brain of European Eels ( Anguilla Anguilla ) After Diet‐borne Exposure to Gold Nanoparticles. Environ Toxicol Chem 2020, 39 (12), 2450–2461. https://doi.org/10.1002/etc.4858
Touchard, A.; Aili, S. R.; Téné, N.; Barassé, V.; Klopp, C.; Dejean, A.; Kini, R. M.; Mrinalini; Coquet, L.; Jouenne, T.; Lefranc, B.; Leprince, J.; Escoubas, P.; Nicholson, G. M.; Treilhou, M.; Bonnafé, E. Venom Peptide Repertoire of the European Myrmicine Ant Manica Rubida : Identification of Insecticidal Toxins. J. Proteome Res. 2020, 19 (4), 1800–1811. https://doi.org/10.1021/acs.jproteome.0c00048
Payton, L.; Hüppe, L.; Noirot, C.; Hoede, C.; Last, K. S.; Wilcockson, D.; Ershova, E.; Valière, S.; Meyer, B. Widely Rhythmic Transcriptome in Calanus Finmarchicus during the High Arctic Summer Solstice. iScience 2020, 101927. https://doi.org/10.1016/j.isci.2020.101927
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.
Acknowledgement
Publications 2017 : http://bioinfo.genotoul.fr/index.php/about-us/publications-2/2017-2/
Publications 2018 : http://bioinfo.genotoul.fr/index.php/about-us/publications-2/2018-2/
Users distribution
International
1 %
National
24 %
Regional
53 %
Local
22%
Explanation about this distribution:
Not documented
Platform's own projects
(8)
3 actives and 5 in the maintenance
Collaborations
National projets
(4)
Currently 3 ANR projects et 1 Labex project. 1 project Region occitanie / FEDER, 1 project PIA ANR (IFB).
International and European projects
(1)
Salhostrop accepted in 2016
Projets with industry
(1)
Some CPU and storage rentals and the SeqOccIN project co-sponsored with get-plage (Occitanie / FEDER project in partnership with industry)
Collaboration projects not founded through an external organism
(20)
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 and in 2020)
⁃ JOBIM '13 (Participation of the whole team in the organization of this event)
⁃ Workshop "Bioinformatics of ncRNA"
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