GenScale is a bioinformatics research team. Its main goal is to develop scalable methods, tools, and software for
processing genomic data. Our research is motivated by the fast development of next-generation sequencing (NGS) and third-generation (TGS) technologies that provide very challenging problems both in terms of bioinformatics and computer sciences.
processing genomic data. Our research is motivated by the fast development of next-generation sequencing (NGS) and third-generation (TGS) technologies that provide very challenging problems both in terms of bioinformatics and computer sciences.
GenScale research is organized along four main axes:
- Data structures
- Indexing the mass of genomic data
- Focus on the de-Bruijn graph structure.
- Provide end-user and optimized library
- Algorithms
- Optimized (time and memory) tools dedicated to NGS processing
- Data compression, genome assembly, variant detection, metagenomics, GWAS (genome-wide association Study)
- Parallelism
- Combine several levels of parallelism
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Use existing techniques such as multithreading or MapReduce
- Constrained algorithmic development, in particular, targeting hardware accelerators
- Applications
- Participate in biology-oriented projects
- INRAe, CEA, National Museum, Hospitals, …
Previously
Photos of GenScale through the Ages
Members
Administrative assistant
- Marie Le Roïc
Academic and research staff
- Susete Alves-Carvalho, IE INRAE
- Rumen Andonov, Prof. univ. Rennes 1
- Karel Brinda, ISFP, Inria
- Charles Deltel, IR Inria
- Dominique Lavenier, DR CNRS
- Claire Lemaitre, CR Inria
- Fabrice Legeai, IR INRAE
- Jacques Nicolas, DR Inria
- Pierre Peterlongo, DR Inria (team leader)
- Emeline Roux, Ass. Prof., Univ. Rennes1
- Riccardo Vicedomini, CR CNRS
Post Doc
- Loren Dejoies, Post-doc Inria, AEx Barde
Visitors
- Francesca Brunetti – Visiting Ph.D. student from the Sapienza University of Rome
Former members
Ph.D. students
- Léo Ackerman, Inria
- Lune Angevin, Univ. Rennes/NuMeCan
- Siegfried Dubois, Inria/INRAe, PEPR AgroDiv
- Roland Faure, UR1
- Khodor Hannoush, ITN Alpaca
- Victor Levallois, Défi Inria OmicFinder
- Nicolas Maurice, Inria, PEPR Mistic
- Meven Mognol, CIFRE , UPMEM
- Alix Régnier, PEPR AgroDiv
- Sandra Romain, ANR Divalps
- Mélody Temperville, Univ. Rennes
Engineers
- Olivier Boullé, IE Inria, MolecularXiv
- Julien Leblanc, IE CNRS, dnarXiv
- Florestan De Moor, IE CNRS, BioPIM
- Erwan Drezen, Institut Pasteur ( collaborator)
2024-2025 internship Students
- Amory Antao (ENS)
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Inria
IRISA