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Membres de l’Équipe

The Computational Systems Biology team currently encompasses three faculty members, one postdoc, one software engineer/PhD student, two PhD students and an apprentice.

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Denis THIEFFRY Group leader, Prof. ENS
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Assoc. Prof. ENS, IUF Junior Member
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Assoc. Prof. ENS and head of the IBENS computing plateform
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Olivier COLLIN
Assoc. Prof. ENS
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Aurélien NALDI Post doc
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Post doc
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Céline HERNANDEZ Bioinformatics Engineer / PhD student
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Swann Floc’hlay PhD student
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Nathalie LEHMANN Engineer
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Geoffray Brelurut
Master2 student / apprentice
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Hatim El Jazouli Master1 student
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Sylvie Sylvie HERMANN-LE DENMAT Visiting scientist

Former members

Samuel Collombet - Master + PhD Student (2012-2017)
Past at IBENS : I am working on the reconstruction of the regulatory network controlling hematopoietic lineages specification, and its dynamical modelling in order to understand how is normal differentiation regulated, and how is cellular reprogramming possible. Then : Postdoc in the lab of Edith Heard (Institut Curie)

Otoniel Rodríguez Jorge - visiting PhD student (UAEM, Mexico) (2013-2017)
I am a PhD student working on neonatal T cell activation and differentiation using experimental and in silico approaches. My visits in Paris aims at learning logical modeling and computational analysis of ChIP-seq data. Then : Lecturer at UAEM in Morelos, Mexico.

Wassim ABOU-JAOUDE - Postdoc (2013-2016)
Past at IBENS : My research works are essentially devoted to the modeling and analysis of cellular regulatory networks using complementary modeling frameworks (logical modeling, continuous and hybrid differential equations, stochastic framework).

Cédric Michaud - M1 Student (2016)
Past at IBENS:I am working on the extension of the Eoulsan ChIP-seq pipeline in collaboration with the genomic facility directed by Stéphane Le Crom. My final goal is to compare different experimental ChIP-seq protocols.

Pauline TRAYNARD - PhD Student (2013-2016)
Past at IBENS : I am pursuing a PhD, working on continous and discrete models explaining cell fate decisions, in particular regarding the links between the cell cycle and the circadian clock.

Roberto Tirado Magallanes - M2 Student (2015)
Past at IBENS:I am a Mexican student doing my master’s thesis here at the CSB lab. My project focuses on the computational analysis and integration of
osteoporotic genome-wide data.

Swann Floc’hlay - M1 Student (2015)
Past at IBENS:My internship project in the CSB lab concerns the axis specification of the sea urchin embryo (Paracentrotus Lividus). I work on Boolean Gene Regulatory Networks using GINsim and I also collaborate with the team of T.Lepage at the Valrose Institute.

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CSB Lab - 2014

Pierre-Marie Chiaroni - M2 Student (2014)
Past at IBENS:I am working on the epigenomic networks regulating bone formation, focusing on molecular mapping and functional genomic data analysis, in order to better understand age-related osteoporosis.

Benoît Noël - M1 student (2014)
Past at IBENS : Preparation of a UCSC Trackhub and ChIP-seq processing of data from zebrafish.

Amhed Missael Vargas Velazquez - M2 student (2014)
Past at IBENS:I am a Mexican M2 student with background in genomics and passion for science. My project is devoted to the modelling of chromatin marking mechanisms and its relation with gene expression. What’s really appealing to me are the regulatory processes that underline the environmental and genetic context of each cell.

Anna Niarakis - Post-doc (2011-2013)
Past at IBENS : I am working on the computational modeling of FcERI signaling during mast cell activation. Based on a manual curation of scientific papers and reviews, we built and annotated a comprehensive and detailed molecular map that consists of the main signaling pathways involved in mast cell activation.

Jonas Ibn-Salem - M2 student (ERASMUS with Freie Universiteit Berlin, 2013)
Past at IBENS : I work on the regulatory interaction of transcription factors and their binding sites in DNA by analysing genome-wide ChIP-seq and ChIP-exo data sets. Collaboration with S. Meijsing (MPIMG, Berlin).

Luca Grieco - PhD student (2009-2012)
Past at IBENS : I spent seven months in Denis Thieffry’s group at IBENS (from March to September 2012), working on the logical modelling of the influence of Mitogen-Activated Protein Kinase (MAPK) network on cell fate decision. In that period, I also contributed to the iSA project by identifying over-expressed protease-coding genes in mastocytes through DNA-microarray data analysis.

Elisabetta Cacace - Medical student (2013-2016)
Elisabetta is a medical student from Scuola Superiore Sant’Anna in Pisa, Italy, and she has focused on the gene regulatory network underlying the early phases of T-cells differentiation and exclusion of alternative fates. She has been working here within an exchange programme between the École Normale Supérieure and her institution.

Charles Girardot - PhD student (2011-1013)
Charles is currently Head of Genome Biology Computational Support at EMBL, Heidelberg, Germany.