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PRABI-AMSB

Adress
Université Claude Bernard – Lyon 1
43 boulevard du 11 Novembre 1918 69622 Villeurbanne
Structure(s)
CNRS
Unit:
Université Lyon 1
[field_pole_regional_de_rattachem]
Website
PRABI-AMSB
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • France-Génomique
  • Label IBiSA
Team
Infrastructure
Propriétaire
Effective storage
515.00 To
Cluster: cores number
1 032 cores
CPU/hours a year
3 800 000 H / an
Bioinformatic tools number
30
Users number (last year)
150
Servers description
L’infrastructure informatique de la composante PRABI-AMSB est commune avec celle de la composante PRABI-LBBE. 

Check the website
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
01-03-2020

VirHostNet 2.0

Description

Une base de données dédiée à la biocuration et à l'intégration des interactions protéine-protéine virus/hôte.

Access conditions
Domains of activity
  • Environment
  • Biology
Description of expertise domains

Les domaines de compétences du PRABI-AMSB comprennent la phylogénie moléculaire, les statistiques, l’écologie, la virologie et la microbiologie ainsi que l’analyse de données biomédicales. Par ailleurs les méthodologies utilisées sont celles de la génomique, la transcriptomique, la métagénomique/métatranscriptomique, ainsi que la biologie des systèmes.

Keywords:
  • NGS data analysis
  • Methodology
  • Genome and transcriptome assembly
  • Genomics (DNA-seq)
  • Genome analysis
  • Transcriptomics (RNA-seq)
  • Differential gene expression analysis
  • Transcripts and transcript variants analysis
  • Variant calling
  • Whole genomes
  • Metagenomics, metatranscriptomics
  • Sequence analysis
  • Sequence algorithmics
  • (multiple) Sequence Alignment
  • Sequence annotation
  • Sequence motif discovery
  • Homology/Orthology prediction
  • System biology
  • Complex biological systems functions
  • Regulatory network modelling
  • System modelling
  • Biostatistics
  • Descriptive statistics
  • Statistical tests
  • Regression
  • Multivariate analysis
  • Dimension reduction
  • Data curation
  • Information and communication technology developments
  • Tools
  • Interfaces, web portals
  • Workflows developments
  • Data
  • Databases and information systems
  • Cluster
  • Cloud
  • Parallelisation
  • Ecology
  • Biodiversity
  • Microbial ecology
  • Modelling in ecology
  • Evolution and phylogeny
  • Molecular evolution
  • Genes and genomes
  • Phylogenomics
  • Tree of life
  • Supertrees et reconciliations
  • Selection detection
  • Comparative genomics
  • Genome comparison
  • Genomics: Chips
  • Metabolomics and fluxomics

Formation professionnelle

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Trainees:
10 trainees / year
Training time:
3 day(s) / year
Upcoming session :
18-10-2017

Introduction au logiciel R

Description
Objectifs de la formation
  • Acquérir les compétences nécessaires à l’utilisation du logiciel R
  • Connaître les principales analyses statistiques nécessaires en biologie et les utiliser sous R
  • Réaliser des graphiques sous R
  • Connaitre les bibliothèques R utiles en Biologie
Access conditions

Informations et inscriptions:

http://www.biosciencesco.fr/formation-continue/bio-informatique/formation-au-logiciel-r/

 
Check the website
Trainees:
12 trainees / year
Training time:
Not documented
Upcoming session :
15-11-2017

Analyse de données RNA-seq sous l’environnement Galaxy

Description
Objectifs de la formation
  • Acquérir les connaissances générales sur les méthodes de séquençage à haut-débit.
  • Connaître les caractéristiques des données obtenues dans le cadre de l’analyse du transcriptome (RNA-seq).
  • Savoir planifier une expérience simple de type RNA-seq en fonction de ses objectifs scientifiques et des caractéristiques et contraintes expérimentales.
  • Connaître les principales méthodes et outils d’analyse des données RNA-seq . Pouvoir les mettre en oeuvre dans un cas simple via un serveur web Galaxy.
  • Pouvoir visualiser les résultats dans un navigateur de génome.

Durée de la formation : 2,5 jours

Access conditions

Informations et inscriptions:

http://www.biosciencesco.fr/formation-continue/bio-informatique/analyse-...
Internal publications
External publications
"Global transcriptional response of Dickeya dadantii to environmental stimuli relevant to the plant infection", Environ Microbiol, vol. 18, no. 11, pp. 3651-3672, Nov, 2016.
"Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series", Genome Med, vol. 8, no. 1, pp. 101, Sep, 2016.
"Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches", J Proteome Res, vol. 15, no. 5, pp. 1659-69, May, 2016.
"Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy", Nat Commun, vol. 7, pp. 11067, Apr, 2016.
"Quantitative Molecular Detection of 19 Major Pathogens in the Interdental Biofilm of Periodontally Healthy Young Adults", Front Microbiol, vol. 7, pp. 840, 2016.
"Sample size calculation in metabolic phenotyping studies", Brief Bioinform, vol. 16, no. 5, pp. 813-9, Sep, 2015.
"Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing", Genome Res, vol. 25, no. 9, pp. 1347-59, Sep, 2015.
"Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia", BMC Genomics, vol. 16, pp. 546, Jul, 2015.
"Correction for Galia et al., Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak", Genome Announc, vol. 3, no. 4, Jul, 2015.
"RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements", Nucleic Acids Res, vol. 43, no. 10, pp. 4833-54, May, 2015.
"VirHostNet 2.0: surfing on the web of virus/host molecular interactions data", Nucleic Acids Res, vol. 43, no. Database issue, pp. D583-7, Jan, 2015.
"The InterPro protein families database: the classification resource after 15 years", Nucleic Acids Res, vol. 43, no. Database issue, pp. D213-21, Jan, 2015.
"Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito", Biol Lett, vol. 10, no. 12, pp. 20140716, Dec, 2014.
"Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins", BMC Genomics, vol. 15, pp. 926, Oct, 2014.
"Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence", BMC Genomics, vol. 15, pp. 666, Aug, 2014.
"Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing", BMC Genomics, vol. 15, pp. 174, Mar, 2014.
"Structure homology and interaction redundancy for discovering virus-host protein interactions", EMBO Rep, vol. 14, no. 10, pp. 938-44, Oct, 2013.
"Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes", Environ Microbiol, vol. 15, no. 10, pp. 2829-40, Oct, 2013.
"SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets", Bioinformatics, vol. 29, no. 10, pp. 1348-9, May, 2013.
Publications with the hosting laboratory
Acknowledgement
 
Users distribution
International
0 %
National
100 %
Regional
90 %
Local
80%
Explanation about this distribution:
Not documented
Platform's own projects
(2)

Not Documented
Collaborations
National projets
Not documented
International and European projects
Not documented
Projects with industry
Not documented
Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Not documented
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