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Associated laboratories : ENS Paris

Institut de Biologie de l’École normale supérieure – IBENS

IMaLiS students are welcome to inquire to any of research groups at IBENS about training opportunities. Our research is organized into four thematic sections :


Developmental Biology

Development and evolution of neural circuits

Research theme : development and evolution of the autonomic nervous system of vertebrates (that controls blood circulation, digestion and breathing) ; Formation of epibranchial, sympathetic, parasympathetic and enteric ganglia ; Cell differentiation, connectivity and fuction of neuronal subtypes in the hindbrain.
Methods : mouse genetics, conditional kockouts, intersectional genetics, histology and anatomy on sections and cleared 3D samples, transcriptomics, connectomics.
Contact : Jean-François Brunet

Development of the Nervous System

Research theme : analysis of the molecular basis of vertebrate hindbrain segmentation. Systems biology approach to patterning during the development. Study of central nervous system adult stem cells. Characterization of novel populations of peripheral nervous system adult stem cells. Techniques and methodologies : functional genetics and genomics, molecular biology, transgenesis, cell and tissue culture, modelling. Animal models : zebrafish, chick embryo and mouse.
Contact : Patrick Charnay

Dynamic analysis of the molecular control of oriented cell divisions

Research theme : molecular mechanisms of oriented cell divisions ; dynamic distribution and regulation of molecules regulating spindle orientation in time and space ; relationship with cell polarity ; Methods : development of simple standardized models of oriented cell division using microfabricated adhesive patterns ; high resolution live imaging of the dynamics of spindle orientation regulators ; development of optogenetic tools to control cell polarization and spindle orientation.
Contact : Xavier Morin

From development to behaviour

Research fields : Moleculat analysis of the development of organs and structures and cell interactions involved. We also develop a behavioural analysis of the establishment of taste preference. All our experiments are carried out using zebrafish, for its optical clarity, its genetic tools and its manipulability.
Contact : Frédéric Rosa

Développement et fonctions des cellules ciliées

Thèmes de recherche : Identifier les mécanismes moléculaires, cellulaires et physiques du développement des cellules ciliées du cerveau. Rôles des cils dans les communications intercellulaires impliqués dans la biologie des cellules souches neurales. Approches utilisées : génétique, transgénèse, modèles physiques, imagerie. Modèle : souris.
Contact : Nathalie Spassky

Ecology and Evolutionary Biology

Evolution of Caenorhabditis

The team combines evolutionary, ecological and quantitative approaches to the biology of a major model organism, the nematode worm Caenorhabditis elegans. The projects of the team are broadly divided in two parts, the first concerning the robustness, evolution and evolvability of C. elegans vulva development ; the second concerning the study of natural Caenorhabditis populations and their viral pathogens.
Contact : Marie-Anne Felix

Genome responses to environmental signals in photosynthetic organisms

The ability to respond appropriately to a variable environment is essential for the survival of photosynthetic organisms in both terrestrial and aquatic environments.
The mechanisms by which the environment can influence genome structure and dynamics are also likely to be important in driving adaptation and evolution. To investigate these processes we use Arabidopsis thaliana as a higher plant model, and the diatom Phaeodactylum tricornutum as a model marine phytoplankton. In Arabidopsis we are examining the influence of light on chromatin-level regulation. We are exploring the dynamic changes in genome structure mediated by morphogenic light signals during the dark to light transition in young seedlings. In parallel we are using Phaeodactylum to explore the role of epigenetic phenomena in regulating phytoplankton life histories, in particular during the rise and fall of seasonal blooms.
The laboratory is a member of the Tara Oceans consortium and is exploring worldwide patterns of diatom biodiversity and abundance in a functional context.
Contact : Chris Bowler

Eco-Evolutionary Mathematics
Research themes : The Eco-Evolutionary Mathematics (EEM) team explores how ecology and evolution interplay, how ecological interactions shape selective pressures acting on individual traits, and how in return adaptive evolution influences population dynamics, community structure and diversity, and ecosystem function. Research in EEM involves three levels of investigation.
  • Mathematical foundations of eco-evolutionary modelling : deriving ‘macroscopic’ models of quantitative traits evolution starting from ‘microscopic’ models of individual interactions and heritable variation.
  • Applications of the general theory to major issues in evolutionary ecology and developmental biology, including the evolution of parasitic and cooperative interactions at the gene, cell, organism and population levels ; life history evolution ; evolution of virulence and eco-evolutionary dynamics of pathogens ; evolution of species interactions and community structure and diversity ; and eco-evolutionary responses of populations, communities and ecosystems to environmental change.
  • Empirical tests of the theory. We use several model systems to integrate theory and experiments, including microorganisms in the lab ; global plankton communities in the world oceans ; and flu, dengue and HIV as model pathogens.

Contacts : Regis Ferriere

and Silvia De Monte

Modelling Biodiversity

The team combines models and large datasets to understand biodiversity as we see it around us today. We are experts in the development of phylogenetic comparative methods, and we are particularly interested in understanding the ecological and evolutionary factors that have shaped the diversification (speciation and extinction) and phenotypic evolution of species over millions of years.
Contact : Hélène Morlon

Functional Genomics

Computational Systems Biology

The incorporation of molecular genetic data into predictive dynamic models is a key component of the emerging fields of systems biology. In this respect, we focus on the development of computational methods (logical simulations, attractor identification, feedback circuit analysis, model reduction, etc.) to enable the design and the analysis of comprehensive models of molecular regulatory networks.
In parallel, we are developing sequence analysis tools to process large-scale functional genomic data (obtained with ChiP-seq and related techniques) and decipher cis-regulatory mechanisms.
In collaboration with experimental groups, we use these methods to address fundamental questions regarding the mechanisms underlying cell fate decisions, e.g. between alternative cell differentiation pathways, proliferation, or programmed death.
Contact : Denis Thieffry

Réplication des Chromosomes Eucaryotes

Thèmes de recherche : Programme spatiotemporel de réplication du génome chez le xénope et l’homme. Identification des origines de réplication, détermination de leur moment d’activation, mécanismes qui coordonnent leur fonctionnement pour assurer la réplication complète et la stabilité du génome. Interactions entre réplication, structure chromatinienne et expression des gènes. Influence de la réplication sur les mutations et l’évolution des génomes. Modèles stochastiques dynamiques. Peignage moléculaire de l’ADN.
Contact : Olivier Hyrien

Dynamique et Organisation des Génomes

Thèmes de recherche : Approches Bioinformatiques pour l’Analyse des Génomes de Vertébrés. Analyse de la sélection naturelle récente chez les primates humain et non-humain, étude de séquences de positionnement du nucléosome en aval du site d’initiation de la transcripition, reconstruction de génome ancestraux, organisation topologique des gènes le long des chromosomes en relation avec la régulation de leur expression, influence de ce phénomène dans les maladies neurologiques liées au chromosome X ; la connaissance préalable d’un language de programmation (awk, perl, python) est préférable.
Contact : Hugues Roest Crollius

Expression of Eukaryotic messenger RNAs

Packed into RNP particles, nascent messenger RNAs (mRNAs) are covered by a myriad of proteins that specify their functional outcome. Our group is studying the assembly of these particles and their importance for gene expression regulation in several cellular environments in mammals (i.e. HeLa, myoblasts, neural stem cells).
We have particular interests in understanding the function of RNA helicases as molecular motors. To this aim, we combine multiple approaches including, biochemistry, structural biology, single-molecule (magnetic-tweezers), molecular biology and transcriptomics (mRNA-seq and CLIP-seq).
Contact : Hervé Le Hir

Bacterial Infection & RNA Destiny

During bacterial infection of eukaryotic cells, a large part of the host-pathogen dialogue relies on the gene expression reprogramming of both organisms. Our team explores the post-transcriptional mechanisms affecting host gene expression during infection by the model food-borne pathogen Listeria monocytogenes. To this end, we combine RNA-seq based technologies with more classical approaches in cellular microbiology, molecular biology and biochemistry.
Contact : Alice Lebreton


Our group aims to understand the operation and function of one particular brain region, the cerebellum, basing our research upon a multidisciplinary characterization of the neural networks it contains. We study cerebellar function using three principal approaches :
  • The in vitro characterization of the network, neurons and synapses of the cerebellum, using patch-clamp recording and imaging in slices.
  • In vivo recordings of cerebellar activity during behavior, using tetrodes to monitor the behavior of multiple neurons simultaneously.
  • Theoretical analysis and numerical modeling (often in collaboration with theoretical physicists).

Contact : Boris Barbour

Cortical dynamics

Research projects : Study of the cortical representation of somatosensory information (whiskers). Neuronal population dynamics evoked by single or multiple whisker stimulation. Study of natural tactile stimuli and of audio-tactile interaction. The main technique used is in-vivo two photon microscopy. Technical developments in two photon microscopy include fast scanning using acousto-optic deflectors and deep imaging using adaptive optics.
Contact : Laurent Bourdieu

Transmission inhibitrice

Thèmes de recherche : Rôle des neurones inhibiteurs dans le traitement de l’information au sein des microcircuits du cervelet. Propriétés émergentes des réseaux neuronaux dans des paradigmes d’activation in vitro et modélisation. Etude de l’intégration synaptique dans les cellules de Purkinje du cervelet, signalisation calcique, plasticité. Développement de modèles explicites permettant de rendre compte de l’intégration dendritique dans ces cellules. Techniques électrophysiologiques et optiques de suivi de l’activité neuronale.
Contact : Stéphane Dieudonné

Modélisation de la biologie cellulaire

Thèmes de recherche : Modélisation du trafficking cellulaire. Modélisation de la phototransduction. Modélisation de la cassure des axones. Méthodes : théoriques et computationelles.
Contact : David Holcman

Zebrafish neuroethology

Aiming to unravel how the nervous system processes cognitive functions and controls animal behaviour, the laboratory uses the zebrafish larva as the experimental model and a multidisciplinary approach, including two-photon calcium imaging to monitor activity of neural networks, motor behaviours, genetic engineering techniques to label, monitor and manipulate activity of specific neurons or entire circuits and mathematical methods for data analysis. The combination of disciplines, and the use of an intact behaving vertebrate model that enables deciphering complex neuroethological questions such as perception of time, decision making, learning & memory and sensory perception.
Contact : German Sumbre

Cell biology of the synapse

Research theme : Structure and dynamics of pre and postsynaptic membranes.
Methods : multidisciplinary approaches of synapse biology (biology, physics and modelisation). Real-time imaging of neurotransmitter receptors behaviour. Correlation between molecular diffusion dynamics in the membrane and neuronal/synaptic membrane organisation. Real-time study of membrane composition changes during plasticity or in pathologies.
Contact : Antoine Triller

Biology Department (outside IBENS)

Ecology and Evolutionary Biology

Phenotypic Variation and Adaptation
Research themes : The team Phenotypic Variation and Adaptation (VPA) aims to understand how ecological and evolutionary processes structure and shape individual phenotypic variation. Phenotypic differences between individuals in a population are the raw material upon which selective processes act. At the same time, the amount of variation between individuals can itself be tuned by evolution and adaptation to ecological conditions. For example, a certain amount of individual specialization can be adaptive. Our research encompasses three main themes :
  • Individuals can be in different life history stages or other states with different survival and reproductive capacities. We study several systems of structured populations (lizards, springtails, fish), develop theoretical structured population models and fit these to our data.
  • Epigenetic effects that intervene between genotypic state and phenotype are important determinants of constraints or adaptive amounts of variability. We develop adaptive dynamics models with epigenetic structures, and investigate transgenerational epigenetic effects in our empirical model systems.
  • We investigate the control and causation of phenotypic differences in experimental ways, for example by studying plastic developmental response in rapidly changing environments. It is our view that getting the population dynamics of structured populations right is essential to understand ecological and evolutionary responses to climate change. Our work therefore integrates theory and experiments to a large extent. As stated above, we use several empirical model systems, of which we follow the population dynamics in near-natural conditions or by means of experiments in controlled environments. To this end, we make much use of the field station in Saint-Pierre-lès-Nemours and the ECOLAB advanced climate rooms at that site.

Contact : Tom Van Dooren

Chemistry department

Pôle de Chimie Biophysique
UMR 8640 PASTEUR, Département de Chimie, École normale supérieure

When practised at the interface with biology, chemistry produces more than a toolkit for labeling biomolecules or analyzing the composition of biosystems. Chemistry brings a specific molecular point of view, which challenges the quantification of interactions and the kinetic analysis of exquisitely complex networks of reactions.
This is the program of chemical biology, which applies chemical concepts and tools to study and manipulate biological systems. The “Pôle de Chimie Biophysique” addresses methodological questions that are relevant to this field. The “Pôle” members are gathered by a common focus on analysis and control of the dynamics of biomolecules involved in networks of chemical reactions and interactions, up to in vivo.
To reach this goal, one needs tools for properly handling, triggering and/or perturbing biologically significant responses at the molecular scale, while recording their signature in complex environments.
The general goal of the “Pôle de Chimie Biophysique” is presently to achieve remote control of biological responses and selective readouts upon tailoring their actuation via molecular constructs sensitive to light, temperature, or magnetic field.
Contact : Ludovic Jullien

Physics department

Complex networks and cognitive systems

Modeling in biology, cognitive science, complex systems. Notably (but not only) : computational neuroscience (information processing in the brain, neural dynamics), biophysics of neural cells ; biophysics of DNA ; biophysics of simple organisms ; genetics and evolution ; experimental psychophysics (visual memory and perception).
Contacts : Jean-Pierre Nadal

, Vincent Hakim

Photocontrôle de protéines à l’échelle de la cellule unique dans un organisme vivant

Thèmes de recherche : Le contrôle spatio-temporel de l’expression génétique est essentiel en biologie. Nous mettons au point une technologie de libération d’un inducteur non-invasive, rapide, locale et modulable. Elle utilise des impulsions de lumière infra-rouge et une excitation biphotonique pour libérer un inducteur biologiquement actif. Dans notre consortium d’équipes, cette technologie est mise en œuvre afin d’étudier le processus de développement et de régénération chez le poisson zèbre.
Web site 1
Web site 2
Contacts : David Bensimon

, Ludovic Jullien

, Michel Volovitch

, Sophie Vriz

Variabilité phénotypique et Mécanismes de régulation de l’expression génétique

Notre travail porte sur l’étude des variations phénotypiques au sein d’une population bactérienne monoclonale. L’expression génétique est un phénomène stochastique qui implique différentes interactions entre macromolécules. Cependant, le petit nombre de molécules contenues dans une bactérie engendre des fluctuations importantes. Ce thème de recherche bénéficie au sein de notre nouvelle unité de l’apport de biologistes et de physiciens experts dans les domaines de l’optique, la microfluidique et la physique statistique.
Contacts : Jérôme Robert

, Véronique Arluison