IBENS - ENS

Coraline Chapperon

Alexandra Louis (équipe Roest Crollius) — 2026-04-23T09:07:17Z

Ingénieure de Recherche CNRS

Equipe DYOGEN
CNRS UMR8197
Ecole Normale Supérieure
46 rue d'Ulm
75005 Paris, France

email : coraline.chapperon chez bio.ens.psl.eu

Kamil Szafranski

Alexandra Louis (équipe Roest Crollius) — 2023-08-23T12:52:55Z

Ingénieur de Recherche CNRS

Equipe DYOGEN
CNRS UMR8197
Ecole Normale Supérieure
46 rue d'Ulm
75005 Paris, France

email : kamil.szafranski chez bio.ens.psl.eu

Present work
I have been hired as the manager of the "ATLASea - Atlas of Marine Genomes" programme since the beginning of May. At IBENS, I am part of the DyoGen team, led by Hugues Roest Crollius, co-director of the ATLASea programme.

ATLASea is one of the Priority Research Programmes and Equipment (PEPR) funded by the France 2030 investment plan. Supported by the CNRS and the CEA, it aims to sequence the genome of more than 4,500 marine species from the French exclusive economic zone (EEZ).

Previous work
Previously, I completed my master's degree in molecular and cellular biology and prepared my PhD thesis in marine microbiology at Sorbonne University, where I studied the life cycles of symbionts in bivalves from chemosynthesis-based environments in the deep ocean. After a two-year post-doc in microbial ecology at Paris-Sud I oriented my career towards project management and scientific diplomacy. Since 2017 I have worked as the coordinator of the "InterRidge" programme hosted at the Institut de Physique du Globe de Paris, I carried out a Polish-French scientific collaboration mission at the Scientific Centre of the Polish Academy of Sciences in Paris and I was the project manager of the EU-funded H2020 project "GROOM II" led by ARMINES.

Axelle Brulport

Alexandra Louis (équipe Roest Crollius) — 2020-10-28T15:35:15Z

PostDoc INSERM

Equipe DYOGEN
CNRS UMR8197 – INSERM U1024
Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris Cedex 05

Presentation

After an initial health-related training (physiotherapy) and 8 years of work experience in this field and vocational retraining, I obtained a PhD in Physiology in 2019.
During my PhD, I have been interested in the impacts of endocrine disruptors on energy metabolism in mice using physiological, transcriptomic and epigenetic approaches.

For my post-doc, I wanted to work on a project combining clinical issues and fundamental research. I joined DYOGEN group to work on the molecular evolution of menstruation in primates under the supervision of Camille Berthelot (ERC Strating Grant EvoMens).

The aim of this project is to use evolutive genomics to better understand the physiological basis of menstruation, a trait at the origin of many gynaecological disorders like endometriosis affecting 10% of women of reproductive age. As for the EvoMens project, I will be in charge of the collection of samples, the technical aspects of wet lab experiments and functional genomics analyses, which will be an opportunity for me to acquire skills in bioinformatics.

Nous recherchons des donneuses !

Alexandra Louis (équipe Roest Crollius) — 2020-10-15T09:00:44Z

Appel à Volontaires SAINS

Etude de la menstruation chez les femmes

Conditions de participation à l'étude :

Vous êtes âgée de 18 à 45 ans
Vous êtes en bonne santé (absence de traitement)
Vous n'utilisez pas de contraception hormonale ou interne (DIU) ü Vous utilisez une coupe menstruelle

Dans le cadre d'un projet de recherche mené par l'Institut National de la Santé et de la Recherche Médicale (INSERM), nous recherchons des volontaires saines pour réaliser un don de fluide menstruel dans le cadre de l'étude EVOMENS, qui porte sur les mécanismes de la menstruation chez la femme.

La compréhension de ces mécanismes constitue un enjeu scientifique majeur pour la santé des femmes.

Cette étude ne présente aucun risque pour vous et dure au maximum 45 minutes.

Dédommagement : Les frais de transport seront pris en charge dans le cadre de
cette étude, sur présentation des justificatifs.

Déroulement de la recherche : cette étude se déroulera à l'Institut de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris.

Si vous souhaitez participer à cette recherche et si vous remplissez les conditions, contactez-nous :

e-mail : evomens chez biologie.ens.fr

Responsable de l'étude : Madame Camille Berthelot.

Małgorzata Anna Gazda

Alexandra Louis (équipe Roest Crollius) — 2020-10-08T16:23:35Z

PostDoc INSERM

Equipe DYOGEN
CNRS UMR8197 – INSERM U1024
Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris Cedex 05

Presentation

My name is Małgorzata Anna Gazda (nickname Gosia) and main research interest consists of applying omics methods to answer questions of general interest in evolutionary biology.

For my Postdoc at DYOGEN group under the supervision of Camille Berthelot I will address the molecular evolution of menstruation using state-of-the-art comparative and functional genomic assays. I will carry out a genome-wide analysis at two different time scales (within primates and across mammals) to identify genes and regulatory elements controlling menstruation, as well as the evolutionary forces driving the evolution of this trait. Determining how evolution shaped menstruation is critical for advancing the fields of medicine and human reproduction.
For my PhD at CIBIO, University of Porto, Portugal, I used next generation sequencing to undercover genes underlying traits of general importance in avian biology and evolution, such as coloration and singing in canary birds as well as flying performance and orientation in racing pigeons. I used domestic species, what facilitated possibility to find genes causing extreme phenotypic variation, which resulted from the strong artificial selection. I had a unique opportunity to find out which genes are responsible for the traits under study and also to provide insights into the evolutionary processes that created those traits. The most important goal of my research so far was understanding of the complete evolutionary mechanism of trait generation, from causative genetic change to specific phenotype.
Prior to my PhD studies, I graduated from the Jagiellonian University in Cracow, Poland with a MSc thesis about heterozygosity-fitness correlations, supervised by Aleksandra Biedrzycka and Jacek Radwan. Afterwards I gained experience working 2 years in the Museum and Institute of Zoology PAN, Warsaw, Poland and Technical University of Munchen, Germany as a research assistant. I worked in the molecular laboratory, developed set of microsatellites and sexing markers for birds. I have extended fieldwork experience : tropical biology courses (Venezuela and Madagascar), followed 4 months ornithological field work in New Caledonia.

List of publications
ORCID
Twitter

Postdoc position in Bioinformatics/Computational Biology

Alexandra Louis (équipe Roest Crollius) — 2020-10-08T16:20:39Z

Applications are invited for a postdoctoral research position at the Institute of Biology of the Ecole Normale Superieure in Paris, France.

We are seeking an enthusiastic postdoc to work on computational developments for functional interpretation of human genetic variation. This project is part of a nation-wide collaborative effort to analyse and interpret genetic variation in an extensively phenotyped sample of the French population. The postdoc will explore machine-learning and statistical approaches to (i) integrate functional and population genomics data in order to identify non-coding genetic variants with an impact on gene expression, (ii) infer tissue-specific outcomes of allelic variation in humans, and (iii) interpret molecular impacts of allelic variants associated with well-characterized phenotypes studied by collaborators.

Applicants must have a PhD degree or equivalent, or have submitted their thesis at the time of application. The ideal applicant will have experience with computational analysis of genomics data, methodological developments for genomics, machine-learning for biological applications, biostatistics and/or population genetics ; however, we will also consider applicants coming from computer science, physics and mathematics with relevant experience with machine-learning or big data problems and a strong interest for biology. Programming skills in a relevant bioinformatics language (Python, R, etc) are a requisite. Candidates will also be expected to write manuscripts, deliver research presentations and be involved in the daily life and management of the laboratory.

The position is funded by the French National Institute for Health and Medical Research (INSERM) for two years. The postdoc will join the Dynamics and Organisation of Genomes laboratory, located at the Institute of Biology of the ENS. ENS is a prestigious university with a vibrant academic life and is part of the Paris Sciences et Lettres (PSL) network of universities and research centers, ranking 1rst in France according to the Times Higher Education's World University Ranking. The institute is located in the heart of Paris, in the Quartier Latin known for its lively student life, restaurants and bars.
This position is in tight collaboration with the Theories and Approaches of Genomic Complexity laboratory (TAGC, Université Aix-Marseille) in Marseille, France, with opportunities for research stays at TAGC.

Salary : € 30,000 to € 48,000/year depending on experience ; includes extensive healthcare and benefits. Funded for 2 years.

Application deadline : February 28th 2020

Start date : from April 15th 2020 (negotiable)

Contact : Please send your application (cover letter, detailed CV) and the names of two referees with your relationship to them to dyogenjobs chez biologie.ens.fr

Three IBENS bioinformatic tools selected to be part of the European Elixir infrastructure

Alexandra Louis (équipe Roest Crollius) — 2020-03-04T14:58:09Z

Elixir is the european infrastructure for bioinformatics. It provides a catalog of key resources selected by each country.
In 2019, the French Elixir node has labelled 26 bioinformatic tools or services after an extended reviewing process.

The eligibility was based on :

impact on French and international communities of research in life sciences
compliance to ELIXIR recommended good practices
sustainability

Three services developed and maintained at IBENS have been labellised.

This selection underlines the importance of these tools for the french and international community. It attests that they are developed according to the Elixir recommendations ensuring large accessibility, major interest, and open science initiative. They are long-term and reliable resources for research community.

- Genomicus (Team Dyogen)
Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions : linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales : local gene order, karyotypes, matrix plots, etc. Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.

- GinSIM (Team CSB)
GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its qualitative dynamical behaviour.

- RSAT (Team CSB)
Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. The tools can be accessed via a Web site (http:rsat.eu/), as Web services, or installed locally on Linux / Mac OS X systems.

Postdoc position in Functional and Evolutionary Genomics

Alexandra Louis (équipe Roest Crollius) — 2020-02-27T14:55:17Z

Applications are invited for an ERC-funded postdoctoral research position at the Institute of Biology of the Ecole Normale Superieure (IBENS) in Paris, France. Position is for two years, with possibilities for extension. Start date : from May 1rst 2020, flexible.

We are hiring an enthusiastic postdoc to work on ERC Starting Grant EVOMENS, which seeks to understand how menstruation evolved in the primate uterus. Menstruation is a recent evolutionary innovation in primates : the trait is present in some species (humans, baboons) but not in closely related others (vervets). The molecular and genetic bases of menstruation are not fully understood, despite its involvement in critical gynecological conditions. EVOMENS aims to profile cellular populations, gene expression and gene regulation in the uterine lining of several primates across the female hormonal cycle to characterize how menstruation evolved at the functional level. The postdoc will be in charge of functional genomics experiments (single-cell transcriptomics, cell sorting, cell population RNA-seq and ATAC-seq) and data analysis.

Applicants must have a PhD degree or equivalent, or have submitted their thesis at the time of application. The applicant should have wet-lab experience relevant to the project such as functional genomics experiments, transcriptomics, experimental genetics, cell sorting and/or cell culture. Computational experience is appreciated, but not required – however, the successful candidate will be expected to develop that skillset and will receive appropriate support. The postdoc will also be expected to write manuscripts, deliver research presentations and be involved in the daily life and management of the laboratory.

The postdoc will join the Dynamics and Organisation of Genomes laboratory, located at the Institute of Biology of the ENS. ENS is a prestigious university with a vibrant academic life and is part of the Paris Sciences et Lettres (PSL) network of universities and research centers, ranking 1rst in France according to the Times Higher Education's World University Ranking. The institute is located in the heart of Paris, in the Quartier Latin known for its lively student life, restaurants and bars.

Salary : € 30,000 to € 48,000/year depending on experience ; includes extensive healthcare and benefits. Position is full-time and funded for two years, with opportunities for extensions.

Application deadline : April 1rst 2020
Start date : from May 1rst 2020 (negotiable)
Application : Please send your cover letter and detailed CV, with the names of two referees and your relationship to them to camille.berthelot chez bio.ens.psl.eu
Informal inquiries welcome.

Recrutements

Hugue Roest Crollius — 2020-01-30T14:11:22Z

François Guidicelli

Morgane Thomas-Chollier — 2019-02-04T11:29:30Z

Après vingt ans passés entre paillasse et microscope à disséquer les interactions réciproques entre régulations moléculaires et développement embryonnaire, je suis arrivé à l'IBENS en octobre 2018, pour examiner le vivant sous un tout nouvel angle, celui de de la génomique comparative, et par de toutes autres méthodes, celles de la bio-informatique.

Originaire de la région parisienne, j'ai suivi une formation initiale d'ingénieur à l'École Polytechnique au milieu des années 90. Puis me suis embarqué dans la recherche expérimentale en biologie en réalisant un travail de thèse au Département de Biologie de l'ENS, dans le laboratoire de Patrick Charnay. J'y ai exploré le rôle de certains facteurs de transcription dans le processus de régionalisation segmentée du cerveau postérieur (rhombencéphale) embryonnaire chez le poulet et la souris. Je suis ensuite parti en stage postdoctoral à Londres, où j'ai découvert grâce à Julian Lewis les formidables possibilités offertes par l'embryon de zebrafish pour la dissection des mécanismes moléculaires du développement. Pendant ces 3 ans, j'ai cherché à comprendre le fonctionnement moléculaire de l'horloge somitogénique, le mécanisme qui assure la formation périodique, régulière et harmonieuse des segments mésodermaux caractéristiques du plan d'organisation des Vertébrés. Recruté à l'INSERM en 2005, je me suis installé au laboratoire de Biologie du Développement de l'Université Pierre et Marie Curie, devenu depuis un Département de l'Institut de Biologie Paris-Seine (IBPS). Là, avec Sylvie Schneider-Maunoury, j'ai continué à développer des projets voués à l'élucidation des liens entre régulation de l'expression génique et processus de développement, particulièrement au cours de la formation du système nerveux, toujours en exploitant la richesse toujours croissantes des approches génétiques expérimentales offertes par le zebrafish, et en cherchant à en inventer de nouvelles. D'abord intéressé par la régulation de la transcription au cours de la régionalisation précoce de la plaque neurale et de la spécification neurogénique, j'ai par la suite tourné mon attention vers la régulation post-trancriptionnelle, en étudiant les ARN messagers localisés et traduits dans les axones tandis que ceux-ci croissent pour atteindre leurs cibles.

Au fil des ans, j'ai pris conscience de ce que le parti-pris forcément réductionniste prévalent dans mon champ de recherches était de plus en plus décalé par rapport à la nécessité de concevoir une vision plus intégrée et globale des liens entre régulation génique et processus biologiques. En parallèle, les progrès technologiques spectaculaires liés au séquençage d'ADN donnaient accès à d'immenses domaines de la génomique jusque là inexplorés. A force de suivre ces progrès et la richesse des concepts - encore en grande partie à inventer - qu'ils appellent, j'ai fini par vouloir y participer moi-même. C'est ainsi que j'ai rejoint la section 'Génomique fonctionnelle' de l'IBENS, dans le laboratoire 'Dyogen' de Hugues Roest Crollius, consacré à la dynamique et l'évolution des génomes. Concrètement, je chercherai à reconstituer des régulations ancestrales à partir d'éléments non codants conservés et de maintien de synténie à travers un large éventail de génomes disponibles. Avec l'ambition d'associer ensuite l'évolution individuelle de certaines de ces régulations ancestrales dans tel ou tel lignage avec les particularités biologiques des espèces concernées.