
Institut Curie
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
Structure(s)
Unit:
Website
CurieScientific leader(s)
Technical leader(s)
Certificat(s)
Team
- Barillot Emmanuel
- Hupe Philippe
- Servant Nicolas
- Girard Elodie
- Syx Laurène
- Tessandie Aurélie
- Brito Isabel
- Gestraud Pierre
- Martignetti Loredana
- Poullet Patrick
- Liva Stéphane
- La Rosa Philippe
- Lucotte Georges
- Chanas Laetitia
- De Soyres Henri
- Kamoun Choumouss
- Romejon Julien
- Jarlier Frédéric
- Andrianteranagna Mamy jean de dieu
Infrastructure
Effective storage
Cluster: cores number
CPU/hours a year
Bioinformatic tools number
Users number (last year)
Servers description
- 3 web servers
- 3 database servers
- 60 computation servers
![]() No website documentedAnnual visits: 2 815 653 an
Unique visits: 7 384 an
Quotes: 7
Downloads: Not documented
NebulaDescriptionServeur Galaxy dédié aux analyses de ChIP-seq Access conditionsAcadémiques |
![]() No website documentedAnnual visits: 208 752 an
Unique visits: 136 an
Quotes: Not documented
Downloads: Not documented
Galaxy-publicDescriptionServeur Galaxy général Access conditionsAcadémiques |
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 documentedTrainees: 25 trainees / year
Training time: Not documented
No upcoming session scheduled
R Biostats NetworkDescriptionThe 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 conditionsAucun |
![]() No website documentedTrainees: 12 trainees / year
Training time: Not documented
No upcoming session scheduled
Introduction to data analysis with RDescriptionThe program includes an introduction:
Access conditionsAucune |
![]() No website documentedTrainees: 15 trainees / year
Training time: Not documented
No upcoming session scheduled
Partek WorkshopDescriptionIntroduction 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 conditionsAucune |
![]() No website documentedTrainees: 30 trainees / year
Training time: Not documented
No upcoming session scheduled
Ingenuiy Pathways Analysis WorkshopDescriptionThe 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 conditionsAucune |
![]() No website documentedTrainees: 10 trainees / year
Training time: Not documented
No upcoming session scheduled
InSilicoDb Analysis TrainingDescriptionInterrogating 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 conditionsAucune |
Formation universitaire
![]() No website documentedTrainees: 300 trainees / year
Training time: Not documented
No upcoming session scheduled
DU "séquençage haut débit et maladies génétiques"DescriptionAcquérir 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 conditionsAucune |
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
Explanation about this distribution:
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
Provision of services not founded through an external organism
Animations (Workshops, Work-groups, seminars, conferences ... )
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