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Institut Curie

Institut Curie

Infrastructure
Propriétaire
Effective storage
2 000.00 To
Cluster: cores number
2 000 cores
CPU/hours a year
1 000 000 H / an
Bioinformatic tools number
80
Users number (last year)
1 656
Servers description
  • 3 web servers
  • 3 database servers
  • 60 computation servers
No website documented
Annual visits:
2 815 653 an
Unique visits:
7 384 an
Quotes:
7
Downloads:
Not documented

Nebula

Description

Serveur Galaxy dédié aux analyses de ChIP-seq

Access conditions

Académiques
No website documented
Annual visits:
208 752 an
Unique visits:
136 an
Quotes:
Not documented
Downloads:
Not documented

Galaxy-public

Description

Serveur Galaxy général

Access conditions

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

The expertise of the platform is versatile on many aspects of high-throughput data management, processing, integration and statistical and functional analysis in biology and in clinics.
Many data types are treated:

  • Microarrays: expression, copy number, SNP, ChIP
  • NanoString
  • NGS: Exome-seq, targeted-seq, WGS, RNA-seq, smallRNA-seq, 5C, HiC, ChIP-seq …
  • RPPA,
  • Mass spectometry, classical and SILAC, SWATH
  • low-throughput biological data.

The expertise covers fundamental, translational and clinical research, including clinical trials.
In all these domain, the platform also develop appropriate methods, implement tools and automatic pipelines, and package and release them publicly or grant on-line access to the community.
Software optimisation for high-performance computing is also part of our know-how.
Finally the platform has developed an experience in training biologists, clinicians and bioinformaticians in all above-mentionned fields

Keywords:
  • NGS data analysis
  • Biostatistics
  • Information and communication technology developments
  • Genomics: Chips

Formation professionnelle

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

R Biostats Network

Description

The program provides an introduction to biostatistical approaches. The principles, methodologies, uses, and applications of statistical methods in biological and clinical research will be presented. Practical trainings on computer with the R software are planned. The bases of the R programming language will be introduced and statistical approaches presented in the theoretical session will be applied.

Access conditions

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

Introduction to data analysis with R

Description

The program includes an introduction:

  • Approaches in biostatistics and research, explaining to participants the principles, methodologies, use of statistical methods and applications in biology and clinical research.
  • Courses on software R will be delivered in the form of additional exercises. The basis of the programming language R will be discussed and statistical approaches presented in the theoretical part will be implemented.
  • Application of skills acquired over a personal dataset
Access conditions

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

Partek Workshop

Description

Introduction to Partek® software and the principles of RNA-seq data analysis DNA-Seq analysis and annotations with Partek® Genomics Suite® Hands on analysis in Partek® Flow® including: Data import and sample annotation, Pre and post alignment quality control, Gene and transcript quantification, Detection of differential expression using powerful gene specific modeling

Access conditions

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

Ingenuiy Pathways Analysis Workshop

Description

The User Group Meeting will consist of talks, customer case studies and interactive feedback sessions where new and existing users of QIAGEN’s Ingenuity products can learn about product updates, usability tips & tricks and best practices. Take advantage of this opportunity to engage with other users from the scientific community.

Access conditions

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

InSilicoDb Analysis Training

Description

Interrogating public and private gene expression datasets for bio-medical researchers. This workshop will you  teach about two subjects: 1- Genomics data management for the lab (efficiently store and make accessible microarray and NGS data), 2- Interrogation of your expression data and comparison and combination of your data with public data.

Access conditions

Aucune

Formation universitaire

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

DU "séquençage haut débit et maladies génétiques"

Description

Acquérir une formation en séquençage nouvelle génération appliqué aux maladies génétiques mendéliennes,des technologies de séquençage et approches expérimentales possibles aux outils bio-informatiques utilisés pour le traitement des données brutes, l'identification de variations génétiques et l'interprétation des résultats. Se familiariser avec le système Unix/Linux, la ligne de commande et la gestion et l'analyse de données sur un serveur à distance. Connaître et savoir utiliser les principaux logiciels dédiés à l'analyse de données de séquençage nouvelle génération, de l'alignement des séquences brutes à l'annotation de variations génétiques. Maîtriser les principaux navigateurs, bases de données et outils de prédiction couramment utilisés en génétique humaine et médicale. Connaître les différentes applications possibles du séquençage nouvelle génération pour le diagnostic de maladies génétiques, les principales règles à suivre et paramètres à considérer pour assurer la qualité des données produites dans un contexte de laboratoire médical, et les considérations éthiques que soulève le séquençage nouvelle génération pour l'interprétation et le rendu des résultats.

Access conditions

Aucune
Internal publications

Ultrahigh dose-rate FLASH irradiation increases the differential response between normal and tumor tissue in mice.
Favaudon V, Caplier L, Monceau V, Pouzoulet F, Sayarath M, Fouillade C, Poupon MF, Brito I, Hupé P, Bourhis J, Hall J, Fontaine JJ, Vozenin MC.
Sci Transl Med. 2014 Jul 16;6(245):245ra93.


Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes JF.
Bioinformatics. 2014 Dec 15;30(24):3443-50.


Biological network modelling and precision medicine in oncology
Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupé P, Zinovyev A, Barillot E.
Bull Cancer. 2014 Jun;101 Suppl 1:S18-21.


Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial.
Servant N, Roméjon J, Gestraud P, La Rosa P, Lucotte G, Lair S, Bernard V, Zeitouni B, Coffin F, Jules-Clément G, Yvon F, Lermine A, Poullet P, Liva S, Pook S, Popova T, Barette C, Prud'homme F, Dick JG, Kamal M, Le Tourneau C, Barillot E, Hupé P.
Front Genet. 2014 May 30;5:152.


Proteomic screening identifies a YAP-driven signaling network linked to tumor cell proliferation in human schwannomas.
Boin A, Couvelard A, Couderc C, Brito I, Filipescu D, Kalamarides M, Bedossa P, De Koning L, Danelsky C, Dubois T, Hupé P, Louvard D, Lallemand D.
Neuro Oncol. 2014 Sep;16(9):1196-209.


Acquired resistance to endocrine treatments is associated with tumor-specific molecular changes in patient-derived luminal breast cancer xenografts.
Cottu P, Bièche I, Assayag F, El Botty R, Chateau-Joubert S, Thuleau A, Bagarre T, Albaud B, Rapinat A, Gentien D, de la Grange P, Sibut V, Vacher S, Hatem R, Servely JL, Fontaine JJ, Decaudin D, Pierga JY, Roman-Roman S, Marangoni E. Clin Cancer Res. 2014 Aug 15;20(16):4314-25.


Challenges for the implementation of high-throughput testing and liquid biopsies in personalized medicine cancer trials.
Verlingue L., Alt M., Kamal M., Sablin MP., Zoubir M., Bousetta N., Pierga JY, Servant N., Paoletti X., Le Tourneau C. et al. Personalized Medicine 2014;11(5), 545-558


Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.
Moarii M., Pinheiro A., Sigal-Zafrani B., Fourquet A., Caly M., Servant N, Stoven V. Vert JP., Reyal F. PLoS One 2014;9:e103986


Combinatorial flexibility of cytokine function during human T helper cell differentiation.
Touzot M., Grandclaudon M., Cappuccio A., Satoh T., Martinez-Cingolani C., Servant N., Manel N., Soumelis V.
Nat Commun 2014;5:3987.


Randomised proof-of-concept phase II trial comparing targeted therapy based on tumour molecular profiling vs conventional therapy in patients with refractory cancer: results of the feasibility part of the SHIVA trial.
Le Tourneau C, Paoletti X, Servant N, Bièche I, Gentien D, Rio Frio T, Vincent-Salomon A., Servois V., Romejon J., Mariani O., Bernard V., Hupé P., Pierron G., Mulot F., Callens C., Wong J., Mauborgne C., Rouleau E., Reyes C., Henry E., Leroy Q., Gestraud P., La Rosa P., Escalup L., Mitry E. Trédan O., Delord JP., Campone M., Goncalves A., Isambert N., Gavoille C., Kamal M.
Br J Cancer 2014;111:17-24.


Developmental dynamics and disease potential of random monoallelic gene expression.
Gendrel AV, Attia M, Chen CJ, Diabangouaya P, Servant N, Barillot E, Heard E.
Dev Cell 2014;28:366-80.


Mutational analysis of primary central nervous system lymphoma.
Bruno A, Labrèche K, Boisselier B, Marie Y, Houillier C, Aidaoui B, Daveau R, Hoang Xuan K. Oncotarget. 2014 Jul 15;5(13):5065-75.


Activated Alk triggers prolonged neurogenesis and Ret upregulation providing a therapeutic target in ALK-mutated neuroblastoma. Cazes A, Lopez-Delisle L, Tsarovina K, Pierre-Eugène C, De Preter K, Peuchmaur M, Nicolas A, Provost C, Louis-Brennetot C, Daveau R, Kumps C, Cascone I, Schleiermacher G, Prignon A, Speleman F, Rohrer H, Delattre O, Janoueix-Lerosey I.
Oncotarget. 2014 May 15;5(9):2688-702.


Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes
Anne Biton, Isabelle Bernard-Pierrot, Yinjun Lou, Clémentine Krucker, Elodie Chapeaublanc, Carlota Rubio-Pérez, Nuria López-Bigas, Aurélie Kamoun, Yann Neuzilletn, Pierre Gestraud, Luca Grieco, Sandra Rebouissou, Aurélien de Reyniès, Simone Benhamou, Thierry Lebret, Jennifer Southgate, Emmanuel Barillot, Yves Allory, Andrei Zinovyev, François Radvanyi
Cell Reports, Volume 9, Issue 4, p1235–1245, 20 November 2014


Cdc42 controls the dilation of the exocytotic fusion pore by regulating membrane tension.
Bretou M, Jouannot O, Fanget I, Pierobon P, Larochette N, Gestraud P, Guillon M, Emiliani V, Gasman S, Desnos C, Lennon-Duménil AM, Darchen F.
Mol Biol Cell. 2014 Oct 15;25(20):3195-209.


Human blood BDCA-1 dendritic cells differentiate into Langerhans-like cells with thymic stromal lymphopoietin and TGF-B.
Martínez-Cingolani C, Grandclaudon M, Jeanmougin M, Jouve M, Zollinger R, Soumelis V.
Blood Vol. 124(5).


Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients.
Madic J, Kiialainen A, Bidard FC, Birzele F, Ramey G, Leroy Q, Frio TR, Vaucher I, Raynal V, Bernard V, Lermine A, Clausen I, Giroud N, Schmucki R, Milder M, Horn C, Spleiss O, Lantz O, Stern MH, Pierga JY, Weisser M, Lebofsky R.
Int J Cancer. 2014 Oct 10.


Network Inference in Breast Cancer with Gaussian Graphical Models and extensions, in Probabilistic graphical models for genetics, Oxford University Press (book chapter)
Jeanmougin M, Charbonnier C, Guedj M, Chiquet J.
External publications
Publications with the hosting laboratory
Development

Logiciels libres (Bioconductor, GPL…)

Users distribution
International
15 %
National
10 %
Regional
75 %
Local
5%
Explanation about this distribution:
Not documented
Platform's own projects

Not Documented
Collaborations
National projets
  • France Génomique, 2012-2016
  • Investissement dAvenir, ABS4NGS (Solutions Algorithmiques, Bioinformatiques et Logicielles pour le Séquençage Haut Débit), 2012-2016
  • + projects funded by INSERM, InCA, FRM …
International and European projects

MAARS (EC FP7)
RAIDS (EC FP7)

Projects with industry

Servier, SANOFI, Roche

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 ... )
Coordination WP NGS variants France Génomique
Coordination Groupe de Travail Galaxy IFB:
  • Organisation des Galaxy days 2013 et 2014
  • Organisation des écoles G4B (Galaxy for bioinformatics) 2013 et 2014

Participation au Groupe de Travail VRE IFB

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