Axes de recherche
Big Data Analysis, Artificial Intelligence (AI) and Network Bioscience Research meet in our group: we try to rationalize the comprehension of complex genotype–phenotype interactions through a closed loop AI system, that we call “I3-BioNet”, composed of three building blocks: the Inference (DATA/LEARN), Interrogation (MINE/ANALYSE) and genomic Implementation (DESIGN/TEST) of regulatory networks. We design and develop new algorithms and software for building and analyzing biological networks from 'multi-omics' data, network-based interpretation and integration of biological systems, network causality, network-based hypothesis generation, network optimization and engineering, including integrated pipelines, BioCAD, and visualization tools.
A second scientific/technological challenge is to facilitate the collaboration of AI system with scientists to accelerate systems and synthetic biology models development. Our ambitious goal is the development of a novel framework for semi-automated knowledge discovery “XAI4-BioNet” (Explainable AI for Inference, Interrogation, and genomic Implementation of biological networks). Recent breakthroughs in functional biology and the automation of scientific laboratories (will with no doubt increase in magnitude over the next decade), making the XAI4-BioNet network bioscience automation concept is thus exciting and full of promises for tackling many questions in life sciences, from systems and synthetic biology to personalized medicine.
We particularly pursue multi-disciplinary projects that aim to 1) determine how regulatory networks function and evolve at multiple scales in response to cellular differentiation and proliferation, complex disease heterogeneity, evolution, and resistance to therapies. 2) Cellular engineering of microorganisms for useful purposes.
Since 2013, the group has been working on different stages of the XAI4-BioNet project, which receives significant external funding (> 1000 K€) from the EU (FP7, Chist-Era, Horizon2020) and national science agencies (ANR, ITMO Cancer, INCa, …).
- 2021-2024 : GREENER: Gene and Regulatory Elements Networks Involved in Rice Root Tissue Differentiation. - PRCI ANR/FNR - Coordinators Dr. Christophe Perin (CIRAD, Montpellier), Role : PI Univ. Lille-CANTHER (own funding 195K€).
- 2015-18: Adaptive « Automated Scientific Laboratory - AdaLab » - CHIST-ERA - Coordinators Prof. Larisa Soldatova (Brunel University), Prof. Ross King (Univ. of Manchester) – 1300 K€. Role : ANR coordinateur, PI UEVE-iSSB (198K€).
- 2012-15: “A system biology approach to dissect cilia function and its disruption in human genetic disease” - SYSCILIA (EC FP7 - Health Cooperation programme). Coordinator Dr. Ronald Roepman (Univ of Nigmegen) – €1200K. Role: PI UEVE-iSSB (200K€)
- 2022-24: NETMET: Regulation network of the oncogene addiction triggers by MET receptor in lung cancer, INCa PLBIO. Role PI Univ. Lille-CANTHER (own funding: 58 K€)
- 2018-22: INTEGRIN: Systems biology of integrin inhibition-induced apoptosis for novel glioblastoma treatment, INCa PLBIO, Grant N2017-145. Role PI Univ. Lille-CANTHER (own funding: 115 K€)
- 2015-19: LIONs: Large-scale Integrative approach to unravel the relationships between differentiatiON and tumorigenesiS. ITMO cancer/INSERM 2015 - coordinator: Mohamed Elati 750 K€. Role: coordinator PI Univ Lille-CANTHER (220K€)
- 2016-19: CHASSY: From multi-scale modeling of biological network to engineering metabolic circuits in a biotechnology chassis, Paris-Saclay IDEX, Grant Programme Interdisciplinaire IDI (co-PI), Horizon 2020 No 720824
- 2014-16: « Ingénierie robuste et évolution dirigée de voies métaboliques synthétiques par intégration des approches génomique » coordinator. Dr. François Jean-Marie (INSA Toulouse) – 500€K Rôle: co- PI François Képès (170 K€).
- 2013-14: “Comparaison de Réseaux de régulation par Enumération de PErturbations - CREPE (PEPS CNRS). Coordinator Pr. Etienne Birmelé (Univ. Paris 5) - 20 K€. Rôle: PI UEVE-iSSB (8K€)
- 2011-13: “Search for new therapeutic targets through the Identification of Networks Specifically altered during tumorIGenesis” - INSIGht (INCa). Coordinator Dr. François Radvanyi (Institut Curie) – €464K. Rôle: PI UEVE-iSSB (115 K€)
CANTHER-XAI platform and software packages
- CoRegFlux: R Bioconductor package (Trejo el al., BMC Systems Biology2017, Coutant et al., PNAS 2019). Integrating transcriptional activity in genome-scale models of metabolism.
- LatNet : R package (Dhifli el al., BMC Bioinformatics 2018). Latent
- network-based representations for large-scale gene expression data analysis.
- CoRegNet: is an R bioconductor package, which enables learning of gene regulatory networks from transcriptome data and infers master regulators controlling the transition between phenotypes. (Download stats: https://bioconductor.org/packages/stats/bioc/CoRegNet/).
- PEPPER: is a plugin cytoscape, which enables finding pathways connecting a protein set within a PPI-network using multi-objective optimization. Published in 2014 (Download stats: apps.cytoscape.org/download/stats/pepper/)
- GREAT : The Genome REgulatory and Architecture Tools (GREAT). GREAT is a software suite of related and interconnected tools, currently able to perform systematic analyses of genome regularities (GREAT-Scan-Pattern) as well as improve TFBS prediction based on gene position information (GREATScan- PreCisIon).
- Constantinos Yeles, ANR GREENER
- Maria Kondratova, INCa PLBIO
Current PhD Students
- Geoffrey Palwak (with David Tulasne, ANR AI_PhD@Lille)
- Liangwei YIN (with Christophe Battail, EU Caty)
- Wajdi Dhifli (assistant professor, Lille)
- Daniel Trejo Banos (Researcher, Swiss data science center)
- Konstantinos Koutroumpas (Patent examiner, EU Patent Office)
- Cuong TO (assistant professor, Vietnam)
Former PhD students
- Pauline Trebulle (Post-doc, Crick Institute, London)
- Rémy Nicolle (Team leader INSERM)