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One of the missions of SiRIC Curamus is to foster the integration of bioinformatics platforms to provide multidisciplinary analysis of cancer data around the AP-HP.Sorbonne University Hospital Group.
In order to meet the growing needs in bioinformatics, the CURAMUS SiRIC Bioanalysis Centre was created in 2018 with the aim of providing a single datacenter shared by all CURAMUS programmes and enabling interoperability between SIRIC research, the AP-HP MOABI platform and the AP-HP datacenter.
This research is conducted by researchers and bioinformaticians using high throughput sequencing techniques to characterize genetic, epigenetic and genomic tumour abnormalities.
To carry out its work, the centre has its own computing and storage resources. At the same time, a close partnership has been set up between the SiRIC Curamus centre and the MOABI AP-HP platform in order to pool bioinformatics expertise and to have computing and storage resources that are complementary to those of the centre.
The centre is open to AP-HP.Sorbonne University staff (biologists, bioinformaticians, post-doctoral students, PhD students) wishing to benefit from computing resources and methodological support in the performance of their analysis(s).
Contact
Team
- Managers
Pierre-Yves Boelle, PhD, MD, PU-PH, iPLesp
Vincent Jonchere, PhD, research engineer, AP-HP
- Team leader
Vincent Jonchère – IR
With a Master’s degree in Developmental Biology (Université François Rabelais-Tours), Vincent Jonchère obtained a PhD for this work on the role of uterine proteins in mineral transfer and shell calcification in hens (INRA – Nouzilly). He then carried out a first post PhD experiment at the University of Liverpool on the regulation of tissue growth by MRL proteins (CRUK grant). A second post PhD experience at the Natural History Museum of Paris (MnHn-CNRS) allowed him to work on the cross effect of thyroid hormones and glucocorticoids on the epigenome during amphibian metamorphosis. Since 2016, he has joined the “Microsatellite and cancers” team where he studies the genomics of these cancers using high-throughput approaches. In addition to these research activities, Vincent Jonchère is in charge of coordinating the bioanalysis centre.
- Research engineer and technician
Coralie Gimonnet – IE
Coralie Gimonnet holds a Master’s degree in Genetics, Physiology and Bioinformatics from the University of Clermont for her work on alternative splicing in a Drosophila model of Steinert’s disease. She then continued her career by joining the INRA of Nouzilly where she worked for 2 years on the development of bioinformatics pipelines of epigenetic data (ChIP-Seq, BiSulfite-Seq). Since 2019, her work within the neuro-oncology program of SiRIC has focused on characterizing the genetics and development of brain tumors using various bioinformatics approaches.
Maria Kondili – IE
Maria Kondili holds a Master’s degree in Bioinformatics and Modeling from the Sorbonne University. She first worked at the Max Planck Institute in Frankfurt on the development of a peak annotation pipeline from ChIP-Seq. She then studied the acetylation of the histone marker H3K27ac in pre-diabetic patients at the Cordelier Research Center. Since October 2019, she has been studying the link between microsatellite instability and immunity in different tumor localizations at SiRIC.
Quentin Letourneur – IE
Quentin Letourneur obtained his Master’s degree in Bioinformatics (BIB) at the University Paris Diderot for his work on genome reconstruction in a metagenomic context at the Pasteur Institute. He joined the bioanalysis center of SiRIC CURAMUS in 2019 and is in charge of the management of the computing cluster and the development of bioinformatics and biostatistical analysis pipelines for genomic data.
- Student
Toky Ratovomanana – PhD 2018-2021
Toky Ratovomanana holds a Master’s degree in Bioinformatics (Geniomhe) from the University of Paris-Saclay for his work on the identification of driver mutations in MSH2 Knock Out mice. He is currently pursuing a PhD at Sorbonne University in the field of cancer genetics. Toky’s thesis is on the genomics of instability of metastatic microsatellites in colorectal cancer.
Adress
Hôpital Saint-Antoine
Bâtiment INSERM Kourilsky (2ème Étage)
184, Rue du Faubourg Saint-Antoine
75012 Paris
Recent publications
Decamps C, Privé F, Bacher R, Jost D, Waguet A; HADACA consortium, Houseman EA, Lurie E, Lutsik P, Milosavljevic A, Scherer M, Achard S, Amblard E, Bacher R, Bergmann F, Blum M, Blum Y, Bottaz-Bosson G, Broseus L, Chuffart F, Decamps C, Devijver E, Durif G, Feofanov V, Houseman EA, Gallopin M, Jedynak P, Jonchere V, van de Geer E, Jumentier B, Kaoma T, Lurie E, Lutsik P, Markowski J, Melnykova A, Merlevede J, Nazarov P, Nguyen NH, Permiakova O, Privé F, Richard M, Rolland M, Scherer M, Spill Y, Blum MGB, Richard M. Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software. BMC Bioinformatics. 2020
Jonchere V, Marisa L, Greene M, Virouleau A, Buhard O, Bertrand R, Svrcek M, Cervera P, Goloudina A, Guillerm E, Coulet F, Job S, Ayadi M, Elarouci N, Armenoult L, Merabtene F, Sylvie Dumont S, Parc Y, Lefèvre J, André T, Jean-François Fléjou JF, Agathe Guilloux A, Ada Collura A, De Reyniès A et Duval A. Analysis of both positive and negative selection leads to the identification of driver gene mutations associated with colorectal cancer with microsatellite instability. CMGH. 2018
Marisa L, Svrcek M, Collura A, Becht E, Cervera P, Wanherdrick K, Buhard O, Goloudina A, Jonchere V, Selves J, Milano G, Guenot D, Cohen R, Colas C, Laurent-Puig P, Olschwang S, Lefèvre JH, Parc Y, Boige V, Lepage C, André T, Fléjou JF, Dérangère V, Ghiringhelli F, de Reynies A et Duval A. The Balance Between Cytotoxic T-cell Lymphocytes and Immune Checkpoint Expression in the Prognosis of Colon Tumors. Journal of the National Cancer Institute. 2018
Rosenberg S, Simeonova I, Bielle F, Verreault M, Bance B, Le Roux I, Daniau M, Nadaradjane A, Gleize V, Paris S, Marie Y, Giry M, Polivka M, Figarella-Branger D, Aubriot-Lorton MH, Villa C, Vasiljevic A, Lechapt-Zalcman E, Kalamarides M, Sharif A, Mokhtari KM, Pagnotta SM, Iavarone A, Lasorella A, Huillard E, Sanson M. A recurrent point mutation in PRKCA is a hallmark of Chordoid Gliomas. Nat Commun, 2018.
Labreche K, Kinnersley B, Berzero G, Di Stefano AL, Rahimian A, Detrait I, Marie Y, Grenier-Boley B, Hoang-Xuan K, Delattre JY, Idbaih A, Houlston RS, Sanson M. Diffuse gliomas classified by 1p/19q co-deletion, TERT promoter and IDH mutation status are associated with specific genetic risk loci. Acta Neuropathol. 2018.