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PACA-Bioinfo

PACA-Bioinfo

Adress
Case 934
163 Avenue de Luminy 13009 Marseille
Structure(s)
CNRS
Unit:
CNRS UMR7256
[field_pole_regional_de_rattachem]
Website
PACA Bioinfo
Scientific leader(s)
Scientific leader
Not documented
Technical leader(s)
Technical leader
Not documented
Certificat(s)
  • Label IBiSA
  • CATI / CTAI
Check the website
Annual visits:
8 982 an
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
02-01-2019

Gbrowse virus géants

Description

Genomes références des principaux virus géants

Access conditions

Libre accès
Check the website
Annual visits:
800 000 an
Unique visits:
100 000 an
Quotes:
2 200
Downloads:
Not documented

Phylogeny.fr/ Blast-Explorer

Description

Robust Phylogenetic Analysis For The Non-Specialist

Access conditions

Gratuit
No website documented
Annual visits:
11 271 an
Unique visits:
Not documented
Quotes:
315
Downloads:
Not documented

Tcoffee

Description
Access conditions

Gratuit
Check the website
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
1 900
Downloads:
Not documented

ACD Tools 2.0

Description

A web-server for the generic analysis of large data sets of counts

Access conditions

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

Génomique procaryote et virale. Transcriptomique. Métagénomique. Protéomique. Biologie Structurale (EM and X-ray crystallography)

Keywords:
  • NGS data analysis
  • Sequence analysis
  • Structural bioinformatics
  • Biostatistics
  • Cartography
  • Evolution and phylogeny
  • Comparative genomics
  • Proteomics
  • No relevant terms in the list above

Formation professionnelle

No website documented
Trainees:
3 trainees / year
Training time:
Not documented
No upcoming session scheduled

Projet AMIDEX "spongex"

Description
Not documented
Access conditions

Accès en local aux différents clusters

Formation universitaire

No website documented
Trainees:
2 trainees / year
Training time:
Not documented
No upcoming session scheduled

Master STIC pour la Santé

Description
Not documented
Access conditions

Accès en local aux différents clusters
Internal publications
Mozar M. & Claverie J-M. (2014) Enlarging the Mimiviridae family using asparagine synthase as a sequence bait. Virology, 2014 Oct;466-467:112-22.
External publications
Berney C, Romac S, Mahé F, Santini S, Siano R, Bass D(2013) Vampires in the oceans: predatory cercozoan amoebae in marine habitats. ISME J.7:2387-99, PMID:23864128

Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, Herman EK, Lin YC, Napier J, Ogata H, Sarno AF, Shmutz J, Schroeder D, de Vargas C, Verret F, von Dassow P, Valentin K, Van de Peer Y, Wheeler G, Dacks JB, Delwiche CF, Dyhrman ST, Glockner G, John U, Richards T, Worden AZ, Zhang X, Grigoriev IV, Allen AE, Bidle K, Borodovsky M, Bowler C, Brownlee C, Cock JM, Elias M, Gladyshev VN, Groth M, Guda C, Hadaegh A, Iglesias-Rodriguez MD, Jenkins J, Jones BM, Lawson T, Leese F, Lindquist E, Lobanov A, Lomsadze A, Malik SB, Marsh ME, Mackinder L, Mock T, Mueller-Roeber B, Pagarete A, Parker M, Probert I, Quesneville H, Raines C, Rensing SA, Riano-Pachon DM, Richier S, Rokitta S, Shiraiwa Y, Soanes DM, van der Giezen M, Wahlund TM, Williams B, Wilson W, Wolfe G, Wurch LL(2013) Pan genome of the phytoplankton Emiliania underpins its global distribution.Nature.499 ;7457:209-13, PMID:23760476

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H(2013) Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.ISME J. ; :,2013 Apr 11 - PMID:23575371

Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C(2013) Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.Mol Ecol. ; :,2013 Jan 22 - PMID:23163508

Jeanniard A, Dunigan DD, Gurnon JR, Agarkova IV, Kang M, Vitek J, Duncan G, McClung OW, Larsen M, Claverie JM, Van Etten JL, Blanc G(2013) Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses.BMC Genomics.14 ;1:158,2013 Mar 8 - PMID:23497343
Publications with the hosting laboratory
Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4274-9. PMID:24591590

Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C(2013) Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.Science.341 ;6143:281-6,2013 Jul 19 - PMID:23869018

Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM(2013) Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. Proc Natl Acad Sci U S A.110 ;26:10800-5,2013 Jun 25 - PMID:23754393

Legendre M, et al. (2018). Diversity and evolution of the emerging Pandoraviridae family. Nat Commun. 9(1):2285. doi: 10.1038/s41467-018-04698-4. PubMed PMID: 29891839; PubMed Central PMCID: PMC5995976.

 


Belahbib H, Renard E, Santini S, Jourda C, Claverie JM, Borchiellini C, Le Bivic A. New genomic data and analyses challenge the traditional vision of animal epithelium evolution. BMC Genomics. 2018 May 24;19(1):393. doi: 10.1186/s12864-018-4715-9. PubMed PMID: 29793430;
Users distribution
International
50 %
National
50 %
Regional
0 %
Local
0%
Explanation about this distribution:

Approximativement 50% internationaux.

Pas de traçabilité régionale/locale.
Platform's own projects

Nouvelle technologie de séquençage, long read • Oxford Nanopore Technologies Ltd • Oxford Science Park, Oxford, UK. OX4 4GA • Nouvelle techniques de prospections des bases de données à l'aide de l'information phylogénétique (Pplacer+)
Collaborations
National projets

Tara-Oceans, Permagenomics (France-Génomique), Spongex (IDEX-AMU).

International and European projects

Tara-Oceans, Oceanomics, MicroB3, BioMarks

Projects with industry

Oceanomics, MicroB3

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 ... )

EMBO Practical course: Bioinformatics and genomes analyses (Athène, 5-17 mai 2014).
(chaque année: 2012: Casablanca, 2013: La Réunion).
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