PRABI-G

Adress
17 avenue des Martyrs 38054 GRENOBLE Cedex 9
Structure(s)
CEA, CNRS, INRIA, INSERM
Unit:
Laboratoire BGE (INSERM/CEA/UGA)
Regional Center
Prabi, Rhône-Alpes
Website
Prabig
Scientific leader
Vandenbrouck Yves
Technical leader
Coissac Eric
Certificat(s)
Not documented
No website documented
Annual visits:
25 920 an
Unique visits:
36 961 an
Quotes:
40
Latest update:
01-01-2014

UNIPATHWAY

Description

UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. The Unipathway project is a joint collaboration between INRIA (Rhône-alpes) and SIB (Swiss Insitute of Bioinformatics, Geneva)

Access conditions

http://www.grenoble.prabi.fr/obiwarehouse/unipathway

Annual visits:
2 247 an
Unique visits:
1 725 an
Quotes:
238
Latest update:
01-01-2015

Arabidopsis chloroplast database (AT_CHLORO)

Description

The AT_CHLORO database stores sub-plastidial (envelope, stroma, thylakoids) and sub-thylakoidal (Grana, stroma-lamellae) localization of Arabidopsis thaliana chloroplast proteins obtained from MS-based quantitative proteomics experiments as well as curated function and localization of proteins. Furthermore, the AT_CHLORO database links to other public web sites (TAIR, PPDB, AtProteome, SUBA, POGs, Aramemnon)

Access conditions

http://at-chloro.prabi.fr/at_chloro/

No website documented
Annual visits:
14 657 an
Unique visits:
9 827 an
Quotes:
Not documented
Downloads:
Not documented

Metabarcoding

Description
Access conditions

http://metabarcoding.org

Domains of activity
  • Biomedical
  • Environment
  • Biotechnology
  • Biology
Description of expertise domains

Computational biology for MS-based proteomics (basic science and biomedical research) and metagenomics (environment, ecology and evolution)

Keywords:
  • NGS data analysis
  • Metagenomics, metatranscriptomics
  • Sequence analysis
  • Data curation
  • Ecology
  • Population genetics
  • Biodiversity
  • Proteomics
Users distribution
International
90 %
National
10 %
Regional
0 %
Local
0%
Explanation about this distribution:

Calculé sur l'utilisation d'Unipathway à partir du nombre de hits par noms de domaine (pour ceux qui sont identifiables). L'origine est essentiellement US (40%) puis Europe (Suisse, Allemagne, France).

Platform's own projects

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 ... )

Christophe Bruley et Yves Vandenbrouck sont partenaires du projet « Prospectom » (Coordinateur G. Bisson, Laboratoire LIG, Grenoble). Ce programme d’animation scientifique en « bioinformatique pour l’analyse protéomique » bénéficie du soutien de la Mission Interdisciplinarité CNRS « MASTODONS Grandes masses de données scientifiques» (2011-2015). 2 Séminaires organisés (29-30/11/2012 et 19-21/11/2014, Grenoble, http://prospectom.liglab.fr/).

Internal publications

Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A. UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. 2012;40 (Database issue):D761-9. PMID: 22102589.

Bruley C, Dupierris V, Salvi D, Rolland N and Ferro M. AT_CHLORO - A chloroplast database dedicated to sub-plastidial localization. Frontiers in Plant Science, 2012, 3: 205. PMID: 22973284

External publications
Tomizioli M, Lazar C, Brugiere S, Burger T, Salvi D, Gatto L, Moyet L, Breckels LM, Hesse AM, Lilley KS, Seigneurin-Berny D, Finazzi G, Rolland N*, Ferro M*. Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Mol Cell Proteomics. 2014. 13(8): 2147-2167. PMID: 24872594.

Casabona MG, Vandenbrouck Y, Attree I, Couté Y. Proteomic characterization of Pseudomonas aeruginosa PAO1 inner membrane. Proteomics, 2013, 13(16): 2419-2423. PMID: 23744604

Bruley C, Dupierris V, Salvi D, Rolland N and Ferro M. AT_CHLORO - A chloroplast database dedicated to sub-plastidial localization. Frontiers in Plant Science, 2012, 3: 205. PMID: 22973284

Journet A, Klein G, Brugiere S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C and Aubry L. Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry. Proteomics, 2012, 12(2): 241-245. PMID: 22120990

Ferro M, Brugiere S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C and Rolland N. AT_CHLORO: A comprehensive chloroplast proteome database with subplastidiallocalization and curated information on envelope proteins. Molecular and Cellular Proteomics, 2010, 9(1): 1063-1084.

Després L, Stalinski R, Faucon F, Navratil V, Viari A, Paris M, Tetreau G, Poupardin R, Riaz MA, Bonin A, Reynaud S, David JP. Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito. Biol Lett. 2014 Dec;10(12):20140716. doi: 10.1098/rsbl.2014.0716. PMID: 25540155

Smith AA, Belda E, Viari A, Medigue C, Vallenet D. The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol. 2012 May;8(5):e1002540. doi: 10.1371/journal.pcbi.1002540. Epub 2012 May 31. PMID: 22693442

Sorn S, Sok T, Ly S, Rith S, Tung N, Viari A, Gavotte L, Holl D, Seng H, Asgari N, Richner B, Laurent D, Chea N, Duong V, Toyoda T, Yasuda CY, Kitsutani P, Zhou P, Bing S, Deubel V, Donis R, Frutos R, Buchy P. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infect Genet Evol. 2013 Apr;15:87-94. doi: 10.1016/j.meegid.2012.05.013. Epub 2012 Jun 7. PMID: 22683363

Duong V, Henn MR, Simmons C, Ngan C, Y B, Gavotte L, Viari A, Ong S, Huy R, Lennon NJ, Ly S, Vong S, Birren BW, Farrar JJ, Deubel V, Frutos R, Buchy P.  Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. Infect Genet Evol. 2013 Apr;15:77-86. doi: 10.1016/j.meegid.2012.05.012. Epub 2012 Jun 5. PMID: 22677620
Publications with the hosting laboratory
Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse AM, Couté Y, Ferro M, Bruley C, Burger T. DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. Bioinformatics. 2017; 33(1):135-136.PMID: 27605098.
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