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Membres de l’Équipe

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Denis THIEFFRY Group leader, Prof. ENS
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Research Scientist CNRS (CR)
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Assoc. Prof. ENS and head of the IBENS computing plateform
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Marika Kapsimali Research Scientist INSERM (CR)
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Nathalie LEHMANN Engineer/PhD student
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Claire Lansonneur PhD student FRM
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Geert-Jan Huizing PhD student
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Touati Benoukraf Invited Scientist ENS
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Olivier COLLIN
Assoc. Prof. ENS

Former members

Morgane Thomas-Chollier - MCU ENS (2012-2021)

Yoonjee KANG - M2 (2020)

Pr. Thomas Höfer - Invited Scientist ENS in 2019-2020
Univ Heidelberg

Swann Floc’hlay - PhD Student (2016-2020)
Past at IBENS : I was pursuing a PhD, working in collaboration with the Furlong Lab (EMBL, Heidelberg) on the impact of natural genetic variations on transcriptional regulation in Drosophila embryos.

Andrea Checcoli - M2 (2019)

Walter SANTANA - M2 + engineer (2019)
Past at IBENS : methodological developments to enhance the assembly of words into matrices in RSAT

Aurélien NALDI - Post-doc (2016-2019)
Past at IBENS : I did my PhD on methods and software for qualitative modeling in Marseilles with Denis Thieffry and Claudine Chaouiya. I also did some data analysis for microarrays, ChIP-seq, and phospho-proteomics data during previous postdocs. My main project is the study of the heterogeneous profiles of IFN production in dendritic cells, combining modeling and single-cell RNA-seq data.

Hatim El Jazouli - Master2 student /Apprentice (2018-2019)

Celine Hernandez - Engineer + PhD Student (2014-2018)
Past at IBENS : My main projects in the CSB group focused on immunology related to cancer. The focus of my work was mainly CD4+ T cells, their CTLA4 and PD-1 co-inhibitory receptors and the downstream concurrent intracellular processes. In this context, I used various approaches linked to dynamical modelling whether logic-based (GINsim) or rule-based (Kappa). I am also particularly interested in applying techniques inherited from software development to model definition and parametrisation. Then : Postdoc in the lab of Emmanuel Barillot (Institut Curie)

Sylvie HERMANN-LE DENMAT - Visiting scientists (2017)
Past at IBENS : I am a Geneticist, studying mainly the connexions between mitochondria and the rest of the cell in various model organisms by using genetics, cell biology and also -omics approaches. As a visiting scientist, I was learning about the basics of bioInformatics to gain autonomy and skills in the -omics analyses.

Karla CORRAL JARA - Postdoc (2016-2018)
Past at IBENS : I have a background in Biochemical Engineering and a PhD in Genomic Medicine, with a specialisation in the study of immunological cells during viral infection. My work focuses on the effects of miRNAs on intracellular signaling networks controlling the differentiation of T-helper lympocutes. This work relied on a computational modeling approach, using Cell Designer and GINsim software, in collaboration with the team of Vassili Soumelis at the Institute Curie.

Geoffray Brelurut - Paster student in apprenticeship (2015-2018)
Past at IBENS : I am a Master student in Bioinformatics from Université de Rouen. I have been working on the analysis of single cell RNA-Seq data. Then : engineer in V. Soumelis team (Institut Curie)

Samuel Collombet - Master + PhD Student (2012-2017)
Past at IBENS : I was 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)
Past at IBENS : I was a PhD student working on neonatal T cell activation and differentiation using experimental and in silico approaches. My visits in Paris aimed 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 was 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 was 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 was 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 was a Mexican student doing my master’s thesis at the CSB lab. My project focused 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 concerned the axis specification of the sea urchin embryo (Paracentrotus Lividus). I worked on Boolean Gene Regulatory Networks using GINsim and I also collaborated 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 was 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 was a Mexican M2 student with background in genomics and passion for science. My project was 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 was 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 worked 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)
Past at IBENS : Elisabetta was 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.