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About

The Systems Biology group builds computational approaches to discover causal paths in complex diseases that connect their genetic or environmental causes to their higher-level effects.

Previous research

The rapid development of new measurement technologies provides unprecendented opportunities to observe complex disease at a large scale, and at different levels, including molecular (e.g., transcriptomic, proteomic, and metabolomic) networks. Much of our research is therefore based on machine learning tools. Better understanding of the causal disease paths will lead to better treatment choices, and, ultimately, to medicine that prevents disease instead of reacting to it. Our group is probably best known for discovering the ‘guilt-by-association’ principle in molecular networks, and for creating Cytoscape, an open-source community platform to visualize and analyze molecular networks. We are also member of the national “laboratory of excellence” (LabEx) programs Milieu Intérieur and IBEID. The site researchgate.net now states regularly that “our research items were the most cited research items from their institution”.

Future projects and goals

New developments in this very dynamic area of research are rapidly evolving from three interrelated aspects:

  • new measurement technologies (such as single cell RNA sequencing; Blecher-Gonen et al. 2019), requiring
  • new computational tools (such as Viral-Track; Bost et al. 2020 and LEAN analysis; Gwinner et al. 2017), leading to
  • new biological insights (such as the detailed characterization of COVID 19-infected cells Bost et al. 2020, and a sparse, reproducible, biomarker for severe dengue infection; Nikolayeva et al. 2018), which then leads to new biological questions that need to be addressed with their own measurement and computational tools.

We therefore couple the development of new computational tools closely to the development of new technology, and ambitious biomedical research projects, currently in the areas of single cell sequencing technology, autoimmune disease and cancer. If you might be interested to join our research team, please check out the Jobs section below.

Former Members

2000
2000
Name
Position
2016
2020
Pierre Bost
Postdoc, ETH Zürich
2019
2019
Chiara Facciotto
PhD student, U. Helsinki
2019
2019
Yanis Bendjelal
MD/PhD student, Sorbonne U
2018
2019
Ozan Özışık
Postdoc, Aix-Marseille U
2018
2018
Aurélie Nerin
Data Scientist, MP data
2016
2017
Mislav Acman
PhD student, UCL
2013
2017
Iryna Nikolayeva
Product manager, CRI
2011
2016
Freddy Cliquet
Research Engineer, Institut Pasteur
2014
2015
Urszula Czerwinska
Data scientist, NLP at Cour de cassation
2014
2015
Sharad Goulam Abas
PhD student, U. Paris Saclay
2011
2015
Oriol Guitart Pla
Software and ML engineer, Team CMP
2011
2015
Xiaoyi Chen
INSERM researcher, Necker hospital
2010
2015
Robin Friedman
Senior Director of Computational Biology, Dragonfly Therapeutics
2010
2014
Frederik Gwinner
Bioinformatics Scientist, Immatics
2006
2012
Mathias Vandenbogaert
Bioinformatics Scientist, Institut Curie
2009
2010
Ashish Anand
Associate Professor, IIT Guwahati
2009
2010
Samuel Drulhe
EU analyst, Brussels
2007
2010
Thomas Rolland
CNRS Researcher, Institut Pasteur
2006
2010
Sébastien Li-Thiao Té
Researcher-Teacher Sorbonne U.
2006
2011
Pascal Bochet
CNRS Researcher, Institut Pasteur
2008
2009
Samad Lotia
Software Engineer, Google
2006
2009
Aurélien Mazurie
Chief data scientist, Starling Trust Sciences
2007
2008
Hans-Michael Kaltenbach
Scientist, ETH Zürich
2007
2007
Ghislain Bidaut
Head, Integrative bioinformatics, Aix-Marseille U
2006
2007
Tero Aittokallio
Professor, FIMM Helsinki/U. Turku/U. Oslo
2005
2006
Melissa Cline
Researcher, UC Santa Cruz
2005
2006
Andrea Splendiani
Data Strategy Director, Novartis
2005
2005
Marc Vincent
Data Scientist, Imagine Institute
2004
2006
Behshad Behzadi
VP Engineering, Google
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Transversal Project

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Contact

Phone: +33 1 4568 8620 Email: benno@pasteur.fr Address 25-28 Rue du Docteur Roux 75015, Paris France To find us, you can enter these Plus codes into Google Maps: “R8R6+57G, Paris” (Campus entrance); “R8R5+G95, Paris” (OMICS building)