Integrative Bioinformatics

Paoli Calmettes Institute

Ghislain Bidaut

Platform manager

Samuel Granjeaud

Platform manager

Estelle Duprez

Scientific Director / Team leader / Researcher

Bertrand Llorente

Scientific Director / Team leader / Researcher

Pierre Bertrand

Engineer

Paraskevi Kousteridou

Engineer

Julien Vernerey

Engineer

Eugénie Lohmann

Engineer

Benoit Goutorbe

Engineer

The Cibi platform offers a wide range of expertise and services in bioinformatics (data integration, development of customized biological analyses) and develops cutting-edge bioinformatics pipelines. Our engineers also develop biologically-oriented databases for data storage and management.

The Cibi platform offers the following services:
- Analysis and integration of NGS data (Next Generation Sequencing): ChIP-Seq, RNA-Seq, single cell RNA-Seq, analysis of genetic variants for research and diagnostic purposes
- Analysis of flow cytometry and mass cytometry data

- Analysis of proteomics data

Our expertise also extends to software development:
- Development of bioinformatics pipelines and databases (Python, R, Bioconductor, PostgreSQL, etc.)
- Project collaboration (INCa, ANR, ARC, etc.)
- Web applications development (RShiny, Django)

Our Pipelines

Featured Publications

09/2024

Genetic deletion of JAM-C in preleukemic cells rewires leukemic stem cell gene expression program in AML.

Grenier JMP , Testut C, Bal M, Bardin F, De Grandis M, Gelsi-Boyer V, Vernerey J, Delahaye M, Granjeaud S, Zemmour C, Spinella JF, Chavakis T, Mancini SJC, Boher JM, Hébert J, Sauvageau G, Vey N, Schwaller J, Hospital MA, Fauriat C, Aurrand-Lions M.

01/2024

DIAgui: a Shiny application to process the output from DIA-NN.

Gerault MA, Camoin L, Granjeaud S.

08/2022

Gut microbiota in systemic lupus erythematosus patients and lupus mouse model: a cross species comparative analysis for biomarker discovery.

Toumi E, Goutorbe B, Plauzolles A, Bonnet M, Mezouar S, Militello M, Mege JL, Chiche L, Halfon P .

10/2024

CXCR4 signaling determines the fate of hematopoietic multipotent progenitors by stimulating mTOR activity and mitochondrial metabolism.

Rondeau V, Kalogeraki M, Roland L, Nader ZA, Gourhand V, Bonaud A, Lemos J, Khamyath M, Moulin C, Schell B, Delord M, Bidaut G, Lecourt S, Freitas C, Anginot A, Mazure N, McDermott DH, Parietti V, Setterblad N, Dulphy N, Bachelerie F, Aurrand-Lions M, Stockholm D, Lobry C, Murphy PM, Espéli M, Mancini SJC, Balabanian K.

04/2022

TET2 regulates immune tolerance in chronically activated mast cells.

Rigo R, Chelbi R, Agopian J, Letard S, Griffon A, Ghamlouch H, Vernerey J, Ladopoulos V, Voisset E, De Sepulveda P , Guittard G, Nunès JA, Bidaut G, Göttgens B, Weber M, Bernard OA, Dubreuil P , Soucie E

01/2024

Macrophages reprogramming driven by cancer-associated fibroblasts under FOLFIRINOX treatment correlates with shorter survival in pancreatic cancer.

Hussain Z, Bertran T, Finetti P , Lohmann E, Mamessier E, Bidaut G, Bertucci F, Rego M, Tomasini R.

All our publications