An 18-month post-doctoral position is available in the “Chemoinformatics and Proteochemometrics”

EVENT : C3BI Available position

Contact : Olivier Sperandio Date : 18-09-2018  Location : Institut Pasteur, Paris

An 18-month post-doctoral position is available in the “Chemoinformatics and Proteochemometrics” group (Dr O. Sperandio) of the Structural Bioinformatics unit (Pr M. Nilges) within the Structural Biology and Chemistry department, available immediately. Research project: Molecular modeling and protein-protein docking to characterize key molecular mechanisms that underlay the pathophysiology of osteoporosis. The position is offered in the framework of the ANR-funded Targetbone collaborative project that brings together the complementary expertise of the groups of Professor Martine Cohen-Solal (Hôpital Lariboisière, project coordinator), Professor Giovanni Levi (Museum National d’Histoire Naturelle) and of the “Chemoinformatics and Proteochemometrics” group of Dr Olivier Sperandio at Institut Pasteur. The overall goal of the project is to provide an integrated understanding of the cellular and molecular mechanisms that underlay the pathophysiology of osteoporosis focusing on the differentiation process of Bone Marrow Mesenchymal Stem Cells (BM-MSC) and bone marrow progenitors towards the osteoblastic lineage. Key transcription factors, playing an important role in osteogenesis, are expressed by BM-MSC and are upstream regulators of master genes involved in the induction of osteoblast differentiation. The general aim of the project is to characterize the cellular and molecular factors that promote BM-MSCs differentiation modifying directly the function of transcription factors in BM-MSCs or in more differentiated progenitors in vivo and in vitro. The contribution of our group to this project is to use molecular modeling and protein-protein docking to characterize the molecular interactions that those key transcription factors have with their known partners to promote BM-MSCs differentiation at the molecular level. A tight collaboration is ongoing with the Pole Protein of Institut Pasteur for this project. This will bring precious crystal structures to validate the modeling approach with one or several generated structures. The expected results are the functional and structural characterization of the interactions that those transcription factors make with some of their key partners in the context of osteoporosis. This opens new perspectives to identify druggable binding cavities, which will pave the way for future drug design projects. Who are we looking for: The candidate must have a strong background in structural bioinformatics, homology modeling and protein-protein docking, ideally using the techniques based on evolutionary information. The candidate should be familiar with the concept of druggable pockets and the various software that can profile them. The candidate must be highly motivated, have good communication skills in english, and be willing and able to work with a team-spirit in a highly interactive research consortium. What are we offering: Funding for 18 months, with the possibility to extend the contract by applying to further funding. The possibility to be involved in other protein-protein docking projects, a highly-demanded topic on the Pasteur campus. A fruitful and highly cooperative environment with the rest of the department, the structural bioinformatics unit, and the bioinformatics center (C3BI) which contain numerous talented structural biologists and bioinformaticians. Salary will be commensurate with experience according to the Institut Pasteur guidelines. A first contact is usually established through a Skype interview, followed by an invitation to give an informal 30 minute talk to the team at the Institut Pasteur, and half a day discussing with the members of the lab. A decision to hire is then taken after discussion with the team. Qualified applicants should send their CV, a statement of research interests and two letters of recommendation to

Software Engineer – 8 months contract – Institut Pasteur

EVENT : C3BI Available position

Software Engineer – 8 months contract – Institut Pasteur


We are hiring a software engineer for a 8 months period. This person will contribute to two different software development projects:

  • software development to enable the support of CWL [1] tools and workflows on the Galaxy platform
  • development of the next version of MacSyFinder [2], a software to model and search for macromolecular systems in bacterial genomes.
  • Masters degree in computer science, software engineering, or bioinformatics,
  • Good knowledge of the Python programming language and Object Oriented Programming,
  • Knowledge of data serialization formats such as XML, JSON and/or YAML,
  • Working knowledge of HTTP APIs (development and usage),
  • Familiarity with bioinformatics tools and data,
  • Familiarity with integrated environments such as Galaxy (
  • Familiarity with concurrent versioning system (git) would be a plus
The successful candidate will participate in two different projects:
  • a collaboration to unify the annotation of eukaryotic transcriptomes from MMETSP and Tara Oceans Project through interoperable workflows. The goal of this project will be to work on enabling the execution of CWL workflows in Galaxy, in close collaboration with international collaborators from ELIXIR and the Galaxy community.
  • the MacSyFinder project: MacSyFinder is an open source program to model and detect macromolecular systems and molecular pathways from protein sequence datasets ( MacsyFinder has now been used by bioinformaticians for several years and will be updated:
  • to ensure its technical sustainability
  • to make it more intuitive of use by biologists
  • to add new features

The new version of MacSyFinder is developed in collaboration by two research laboratories: the Microbial Evolutionary Genomics group at the Pasteur Institute ( and the GEM group at the TIMC-IMAG department (

On the first project, the main mission is to contribute to the development of the Galaxy platform to enable the direct execution of CWL tools and workflows. On the second project, the mission of the candidate will be to participate to the design and implementation of the new MacSyfinder version, through the implementation of new features, the creation of unit tests, the migration from python 2 to python 3, etc.

He/she will be affiliated to the “Bioinformatics Hub” and the “Microbial Evolutionary Genomics” research laboratory of the C3BI at the Institut Pasteur, and will work with the same core team of engineers that also works on both projects.

Please send your application (resume, supporting statement) by email to, and

[1] Amstutz P, Crusoe M R, Tijanić N, Chapman B, Chilton J, Heuer M, Kartashov A, Leehr D, Ménager H, Nedeljkovich M, Scales M, Soiland-Reyes S, Stojanovic L. Common Workflow Language v1.0. Figshare. 2016
[2] Abby, S. S., Neron, B., Menager, H., Touchon, M. & Rocha, E. P. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9, e110726 (2014).

Inception project: Call for applications for the creation of five-year groups

EVENT : C3BI Available position

Inception project: Call for applications for the creation of five-year groups

Institut Pasteur has launched an international call for junior candidates wishing to establish new independent research groups in the cutting edge interdisciplinary environment of its campus in Paris, France. This year the call will be focused on the topics associated with the INstitut Convergence entitled “Emergence of Pathologies Through Individuals and populatiONs” (Inception program).

The Inception program would particularly welcome projects in the following fields:
– Sequence analysis
– Machine learning
– Data management and analysis
– Systems biology
– Phylodynamics
– Metagenomics
– Precision medicine

The primary focus of the call is on computational and statistical analysis of biological “big data”, typically produced by New Generation Sequencing (NGS) and -omics technologies. Nevertheless, all modeling and computational approaches addressing biological questions closely related to the Inception program areas are eligible.

Successful candidates will possess the following qualifications:
– Significant achievements in bioinformatics/biostatistics/biomathematics,
– Broad experience in methodological development and data analysis,
– Relevant publication record of cutting-edge research as senior/first author,
– Demonstrated ability to collaborate with experimental and computational biologists.

The successful junior candidate* will be appointed with a permanent position, heading a group of six persons at the Institut Pasteur of Paris. This group will be created for a period of five years. Thereafter, the group may compete for full research group status.

A highly attractive package matching the experience of the successful candidate will be provided, including salaries (principal investigator, permanent bioinformatician/biostatistician, post-doctoral fellowships), a substantial contribution to equipment and computing facilities and annual running costs. Support for relocation expenses will also be provided.

Applications must be submitted online at:

The deadline for application submission is January 14, 2018, 12:00 pm CET.
Shortlisted applicants will be notified by the end of March 2018 and will be invited for interviews to take place in May 2018 (please set aside 2-4 May). The final ranking will be established by the Pasteur Scientific Council during its June 2018 session (please set aside 05-06 May, when applicants will be interviewed).
Informal inquiries related to the INCEPTION program should be addressed to

* Institut Pasteur is an equal opportunity employer. Junior group leaders are eligible to apply within eight years of receiving their PhD at the time of submission. Women are eligible to apply as junior group leaders up to 10 years after receiving their PhD if they have one child and up to 12 years after their PhD if they have two or more children.

Inception Call G5 – Available positions

  • Candidate information

  • Keywords

  • PhD

  • Publication records

  • Application summary

  • Selected publications

  • Selected publications

  • Upload your complete application document

  • In a single file (pdf, 1.5 spacing, 25MB max):
    · Description of past and present research activities (4 pages)
    · Proposed research project (6 pages)
    · Detailed CV and full publication list
    · Three scientists from whom letters of recommendation can be sought
    · The names of scientists with a potential conflict of interest
  • Accepted file types: pdf.

C3BI Deputy director job offer

Directeur/Directrice adjoint(e) du centre de bioinformatique (C3BI) de l’Institut Pasteur

La direction de l’Institut Pasteur a défini la bioinformatique et la biologie des systèmes comme priorités stratégiques. Un “Centre de bioinformatique, biostatistique et biologie intégrative” (C3BI – a vu le jour en 2015 sur le campus parisien. L’objectif de ce centre est de fédérer/renforcer les activités bioinformatiques et biostatistiques dans les divers domaines de recherche de l’institut, autour de la biologie de la santé. Il regroupe aujourd’hui une vingtaine d’ingénieurs bioinformaticiens et biostatisticiens, une quarantaine à terme, et neuf unités de recherche, avec des objectifs de service comme de recherche, y compris fondamentale. Depuis le 1er janvier 2016 le C3BI est une unité mixte avec le CNRS (USR 3756). Dans ce contexte, l’Institut Pasteur prévoit de recruter en CDI un(e) Directeur/Directrice adjoint(e). Les missions du poste sont diverses, avec l’objectif général de participer aux tâches inhérentes à la direction d’un centre important et ambitieux comme le C3BI. Notamment :
  • prendre en charge/participer au montage de grands projets (Investissements d’Avenir, Europe …)
  • assurer la visibilité et gérer les collaborations du C3BI au niveau national (IFB, FG, grands organismes) et international (ELIXIR, EBI et EMBL, SIB …)
  • développer les synergies au sein du C3BI et avec les autres entités de l’Institut Pasteur et du CNRS
  • contribuer à la mise en place de formations en bioinformatique/biostatistique, destinées au campus parisien comme à l’international
  • gérer le fonctionnement (communication, rapport d’activités, budget, RH …) du C3BI au sein de l’Institut Pasteur et du CNRS
Le (la) candidat(e) retenu(e) apportera une aide décisive dans tout ou partie de ces différentes activités. Il/elle devra justifier d’une carrière scientifique solide en bioinformatique/biostatistique (thèse, postdoc, liste de publications, collaborations internationales) et d’une expérience de management d’équipe. Il conservera un lien fort avec la recherche en participant à certains des projets du C3BI. Il aura des capacités évidentes à interagir avec le milieu de la recherche et ses différentes composantes, tant scientifiques qu’administratives ou de service. Un très bon niveau en Anglais parlé et écrit est indispensable, de même qu’en Français pour les non-francophones. Pour candidater vous rédigerez un document (pdf) unique comportant (dans cet ordre) :
  1. Un CV résumé d’un page
  2. Une lettre de motivation de 2-3 pages expliquant comment vous vous inscrivez dans les différentes tâches propres à ce poste (en Français, le reste du dossier peut être en Anglais)
  3. Un CV détaillé
  4. Trois références (minimum) à contacter pour avoir des avis sur votre candidature
  5. Vos prétentions salariales (possibilité de joindre le dernier bulletin de salaire)
Ce document est à déposer avant le 15 Mai sur : La date de clôture des candidatures est fixée au 15 Mai 2016. Contact :

Available Positions – C3BI 2016 – Job Application

CIB Team – CDD Job application

CDD en Bioinformatique au sein de la Cellule Informatique pour la Biologie

Le CIB (Cellule Informatique pour la Biologie) est une composante majeure du nouveau centre de Bioinformatique, de Biostatistiques et de Biologie intégrative (C3BI) de l’Institut Pasteur. Son rôle est de répondre aux besoins informatiques des scientifiques du campus par le développement, la mise à disposition et le déploiement d’outils bioinformatique. Son pôle “Intégration Web et Développement Logiciel” recrute un Ingénieur (Bio-)Informatique dans le cadre d’un CDD (6 mois, du 01 novembre au 15 mai 2015). → Vous assurerez, en collaboration avec le reste de l’équipe de la plate-forme Galaxy de l’Institut Pasteur: L’évolution de celle-ci (mises à jour, modifications de la configuration) Le développement et la maintenance d’interfaces pour des outils bioinformatique Le support et la formation aux utilisateurs → Vous participerez aussi à l’étude de faisabilité de la mise en place d’un serveur public Galaxy.

Compétences requises

De formation BAC+5, type Master Informatique/Bioinformatique, vous maitrisez le langage de programmation Python ainsi qu’au moins un logiciel de gestion de versions. Vous avez des connaissances des formats XML, JSON et de préférence, une première expérience de Galaxy. Maîtrise de l’anglais (lu et écrit). Esprit d’équipe, ouverture d’esprit et autonomie sont des qualités recherchées.   English version below

Support engineer for Galaxy at the CIB in the Institut Pasteur

The CIB (Informatics cell for Biology) is a major component of the new Institut Pasteur Center of Bioinformatics, Biostatistics and Integrative Biology. Its role is to fulfill the scientific computational needs of the campus with software implementation, bioinformatics software providing and/or their deployment. Its group “Web Integration and Software Development group” is hiring an (Bio-)informatics engineer for a 6 month contract (from November 1st to May 15th 2015) In collaboration with the rest of Institut Pasteur’s Galaxy Team, he will insure:
  • The evolution of our Galaxy instance (updates, configuration modifications, …)
  • The implementation and the maintenance of Galaxy tools
  • The support and training for Galaxy users
→ He will also participate in the study of the possibility to create a public Galaxy instance hosted in the Institut Pasteur. The engineer has to be familiar with Python, as well as a versioning tool such as git, or svn, … He will have working knowledge of XML, Json formats. Previous experience on Galaxy is a plus. An open mind, autonomy and teamwork skills are mandatory for this position. Proficiency in written and spoken English as well as minimal notions of French (for support and training tasks) are required. If interested, send your application to and