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About

The Bioinformatics and Biostatistics Hub is a team of research engineers led By Marie-Agnès Dillies and Hervé Ménager, dedicated to bringing support in computational biology to Institut Pasteur’s research units and platforms. The Hub is organized around seven expert poles:

Hub also has expertise outside of these poles like:

The above list of expertise is not exhaustive. Do not hesitate to visit the Poles web pages or contact the Hub directors if you don’t find the one you need. The Hub can help Institut Pasteur’s scientists in many ways:

  • By direct interaction during the open-desk sessions. Every Tuesday morning (now on Teams or in real life in Yersin building)
  • By answering short questions submitted through our web site or using the mail alias hub@pasteur.fr.
  • By collaborating to research projects. The Hub support is:
    • Free of charge for projects lasting less than 3 months of full-time equivalent effective working time – short projects
    • Half of the full salary of an Engineer (3k€/month) for projects of 4 months or more – long projects

In any case projects must be submitted on our website with as much detail as possible : Submit a project.
All short projects are accepted if the required expertise is available in the Hub within a reasonable time. Long projects are examined by the Hub executive steering committee who meets three times a year: the second Thursday of March, June and December. For the year 2024, these are on March 14, June 13 and December 12.
A specific template is available for long projects and has to be sent to Marie-Agnes Dillies and Hervé Ménager two weeks before the steering committee meeting. Some discussions and exchanges with the Hub are encouraged before submitting long projects. A detachment of an Hub engineer is also possible for very long projects. See below the detached section for more information.
These different possibilities are summarized in the table below:

TypeCostDescriptiondecision process
Long project
  • Half of the charged salary
  • about 3k€/month
  • 1.5 k/month for strategic projects
  • no HR affiliation
  • not included into ETM
  • Half the cost of a post-doc
  • Duration adapted to the project
  • no hiring
Validated by Executive steering committee after reviewing request using this template
Detachment
  • Included into the Unit package
  • HR affiliation
  • Included into ETM
  • from 2 to 5 years, renewable
  • Hiring or internal mobility
Validated by IP’s Direction and Executive steering committee
Detachment on Grant
  • 80% of the salary
  • on external grant, typically ERC
  • HR affiliation
  • Included into ETM f
  • from 2 to 5 years, renewable
  • Hiring or internal mobility
Validated by IP’s Direction and Executive steering committee

The Hub is also involved in two other activities:

  • Software development: Hub engineers have developed many tools to help data analyses such as Shaman, JASS. More details in the software section
  • Teaching and training: Hub engineers are deeply involved into sharing their knowledge with PhD students, post-docs or permanent scientists from IP in Paris and in the RIIP. More information in the courses section

Services

Newsletter

The Hub’s communications group publishes a newsletter containing information on the latest publications from Hub members, updates on tools under development, specific content on the Hub’s expertise and organization, and much more. Previous newsletters: […]

Open Desk of the Hub of Bioinformatics and Biostatistics

Every Tuesday mornings from 10am to 12am, Hub engineers are enlisted to provide a direct support to any members of Institut Pasteur seeking help on bioinformatics or biostatistics related subjects. You can come directly […]

Software

Members

Groups

Former Members

2000
2000
Name
Position
2014
2022
Christophe Malabat
Head Member - Research Engineer - permanent position
2018
2021
Dmitry Erchov
Research Engineer - permanent position
2021
2021
Junhanlu Zhang
Undergraduate Student
2017
2021
Emna Achouri
Research Engineer - permanent position
2020
2020
Naima Bessaoud
Undergraduate Student
2020
2020
Julie Leborgne
Undergraduate Student
2018
2020
Laurent Bourri
Engineer - short term contract
2015
2020
Varun Khanna
Research Engineer - permanent position
2019
2019
Valentin Marcon
Engineer - short term contract
2017
2019
Maëlle Daunesse
Undergraduate Student
2019
2019
Sulyvan Dollin
Undergraduate Student
2019
2019
Ahmed Keceli
Undergraduate Student
2019
2019
Andrei Furtuna
Undergraduate Student
2019
2019
Antoine Ménard
Undergraduate Student
2019
2019
Olivier Merzeau
Engineer - short term contract
2019
2019
Tom Gutman
Undergraduate Student
2015
2019
Christophe Becavin
Research Engineer - permanent position
2016
2018
Kenzo-Hugo Hillion
Engineer - short term contract
2017
2018
Quentin Letourneur
Engineer - short term contract
2016
2018
Olivia Doppelt-Azeroual
Research Engineer - permanent position
2017
2018
Jérôme Raciazek
Engineer - short terme contract
2017
2017
Paul Stretenovitch
Undergraduate Student
2015
2017
Louis Jones
Research Engineer - permanent position
2015
2016
Harindra Arachchi
Research Engineer - permanent position
2016
2016
Anita Annamale
Undergraduate Student
2015
2015
Mélaine Vanderbroucke
Undergraduate Student
Show all

Courses

12ème Ecole de bioinformatique AVIESAN – IFB – Inserm Niveau1 (2023)

Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next Generation Sequencing” (NGS). Cette édition de l’école aborde les nouveaux enjeux technologiques: elle s’articulera autour de trois ateliers thématiques en session […]

2023-11-05 18:00:00 2023-11-11 14:00:00 Europe/Paris 12ème Ecole de bioinformatique AVIESAN – IFB – Inserm Niveau1 (2023) Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next Generation Sequencing” (NGS). Cette édition de l’école aborde les nouveaux enjeux technologiques: elle s’articulera autour de trois ateliers thématiques en session […] Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France

Bioinformatics program for PhD students 2023 2024

This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]

2023-10-23 09:30:00 2024-06-28 17:00:00 Europe/Paris Bioinformatics program for PhD students 2023 2024 This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […] 25-28 Rue du Docteur Roux, Paris, France

2ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2

Initiation au traitement des données de génomique obtenues par séquençage à haut débit Bulk RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq, niveau 2 Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next Generation […]

2023-06-05 08:00:00 2023-06-09 16:00:00 Europe/Paris 2ème Ecole de Bioinformatique AVIESAN – IFB – INSERM Niveau 2 Initiation au traitement des données de génomique obtenues par séquençage à haut débit Bulk RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq, niveau 2 Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next Generation […] Station Biologique De Roscoff, Place Georges Teissier, Roscoff, France

11ème école de bioinformatique AVIESAN-INSERM-IFB

Initiation au traitement des données de génomique obtenues par séquençage à haut débit Bulk RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq, single-cell RNA-Seq, niveau 1 Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets […]

2022-11-13 18:00:00 2022-11-18 13:00:00 Europe/Paris 11ème école de bioinformatique AVIESAN-INSERM-IFB Initiation au traitement des données de génomique obtenues par séquençage à haut débit Bulk RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq, single-cell RNA-Seq, niveau 1 Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets […] Station Biologique De Roscoff, Place Georges Teissier, Roscoff, France

PHINDaccess – Functional OMICs

This course will explore state-of-the-art knowledge and experiences to better understand complex biological systems. The main objective is to provide participants with a solid foundation on the current bioinformatics approaches and tools to better […]

2022-05-23 09:00:00 2022-05-27 17:00:00 Europe/Paris PHINDaccess – Functional OMICs This course will explore state-of-the-art knowledge and experiences to better understand complex biological systems. The main objective is to provide participants with a solid foundation on the current bioinformatics approaches and tools to better […] Institut Pasteur، Tunis, Tunisia

1ere école EBAII Assemblage & Annotation

Initiation au traitement des données de génomique obtenues par séquençage à haut débit Assemblage et annotation de novo de génomes   Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next […]

2022-09-26 14:00:00 2022-09-30 14:00:00 Europe/Paris 1ere école EBAII Assemblage & Annotation Initiation au traitement des données de génomique obtenues par séquençage à haut débit Assemblage et annotation de novo de génomes   Objectifs La formation s’adresse à des biologistes directement impliqués dans des projets “Next […] Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Ce cours a pour objectif d’enseigner les bases théoriques et pratiques nécessaires à la conduite d’analyses phylogénétiques. Les sessions théoriques seront consacrées aux bases du domaine (représentation et combinatoire des arbres, modèles d’évolution) et […]

2021-12-13 09:00:00 2021-12-17 19:00:00 Europe/Paris Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation Ce cours a pour objectif d’enseigner les bases théoriques et pratiques nécessaires à la conduite d’analyses phylogénétiques. Les sessions théoriques seront consacrées aux bases du domaine (représentation et combinatoire des arbres, modèles d’évolution) et […] 28 Rue du Dr Roux, Paris, France

Analyse de données reproductible

La production de données de plus en plus massives, le développement de méthodes d’analyse de plus en plus complexes, et le nombre en constante augmentation d’outils disponibles amènent les scientifiques à développer des chaines de traitement (workflows) de plus […]

2021-06-21 09:00:00 2021-06-29 17:00:00 Europe/Paris Analyse de données reproductible La production de données de plus en plus massives, le développement de méthodes d’analyse de plus en plus complexes, et le nombre en constante augmentation d’outils disponibles amènent les scientifiques à développer des chaines de traitement (workflows) de plus […] 28 Rue du Dr Roux, Paris, France

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […]

2019-10-07 09:30:00 2019-11-11 17:30:00 Europe/Paris Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […] 28 Rue du Dr Roux, Paris, France

Introduction à l’analyse Bio-informatique de séquences

L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […]

2019-09-23 09:00:00 2019-09-27 17:00:00 Europe/Paris Introduction à l’analyse Bio-informatique de séquences L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […] Institut Pasteur, Rue du Docteur Roux, Paris, France

High Throughput Sequencing Data Analysis on Genomics, Metagenomics and Transcriptomics

The National Center for Aquaculture and Marine Research (CENAIM) of the Polytechnic School of the Litoral (Ecuador), the Computational Biology and Microbial Ecology Group (BCEM) of the Universidad de los Andes (Colombia) and the […]

2018-09-13 09:00:00 2018-09-21 17:00:00 Europe/Paris High Throughput Sequencing Data Analysis on Genomics, Metagenomics and Transcriptomics The National Center for Aquaculture and Marine Research (CENAIM) of the Polytechnic School of the Litoral (Ecuador), the Computational Biology and Microbial Ecology Group (BCEM) of the Universidad de los Andes (Colombia) and the […] Escuela superior politécnica del litoral, Guayaquil, Ecuador

Introduction à la phylogénie moléculaire

Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […]

2019-02-18 09:00:00 2019-02-22 17:00:00 Europe/Paris Introduction à la phylogénie moléculaire Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […] 28 Rue du Dr Roux, Paris, France

Projects

Transversal Project

Tools

Fundings

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Steering committee

Steering Committee

The Hub Steering committee is composed of representatives of all scientific Departments and Directions of Institut Pasteur.

This committee meets once a year for exchanging on Hub advances during the past year.

It is also the opportunity for the Hub to have a direct feedback from departments and to improve its support to the campus.

Executive steering committee

The executive steering committee is in charge of the validation of ressource allocation for long projects. It will focus mainly on the scientific content and perspective of the project. Also it will be garant for a fare share of ressources between research Units of Institut Pasteur.

The executive committee meets three time a year (spring, summer and autumn/winter).
Past meeting:
– December 1st, 2022

Next meeting:
– End of March, 2023

The executive committee is composed of:
– Christophe d’Enfert
– Patrick Trieu-Cuot
– Simonetta Gribaldo
– Roberto Toro
– Olaya Rendueles-Garcia
– Romain Levayer

 

Contact

Phone: +33 (0)1 44 38 93 71 Email: hub@pasteur.fr Address 25-28 Rue du Docteur Roux 75015, Paris France