Seminars – Network biology and Salmonella infection mechanisms

EVENT : C3BI Seminars – Methodological

Network biology approaches to uncover the mechanisms of Salmonella infection and its autophagy modulating features in the gut

Speaker : Tamas Korcsmaros, Research Leader from TGAC, The Genome Analysis Centre, Norwich Research Park, Norwich, UK – Institute of Food Research, Norwich Research Park, Norwich, UK      Time : 02:00 pm      Starting Date : 07/12/2015     

Location : Retrovirus room – LWOFF (22), Institut Pasteur, Paris

In the last decade, networks became a novel approach in understanding how changes in cellular processes can lead to diseases, such as cancer, infection and inflammatory bowel disease (IBD). In our studies we focus on autophagy (cellular self-degradation) and its regulation. Autophagy is a stress response mechanism also important in development, immune regulation, ageing and cancer, where it could act as both pro- and anti-tumorigenic. Autophagy malfunction is also known to be related to IBD, and it is often manipulated by intestinal pathogenic bacteria, such as Salmonella.

To investigate how Salmonella is modulating autophagy we developed the first large-scale network resource for Salmonella enterica, integrating known and predicted regulatory, metabolic and signalling interactions. We investigated the variation and commonality in the networks of Salmonella serovars with either a predominantly intestinal or extra-intestinal pathogenicity. We analysed the differences (e.g., regulatory connections) for 10 strains of two niche groups (intestinal / extraintestinal), as well as defined a “core” Salmonella consensus network. Then, built on the combination of earlier identified Salmonella-host interactions and our recently published Autophagy Regulatory Network resource (, we predicted novel genes responsible for autophagy modulation in the gut using the intestine specific Salmonella networks. Finally, we have designed a fluorescence reporter system to monitor autophagy of Salmonella and to validate the role of predicted genes. The developed bioinformatics workflows and experimental validation system could be used for other strains or pathogens to iteratively predict genes for biological validation with the potential to provide additional insight or model refinement.

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Available Positions – C3BI 2016 – Job Application

Performance evaluation of DNA copy number segmentation methods

Thursday 3rd of December, Pierre Neuvial will talk about performance evaluation of DNA copy number segmentation methods. #C3BIPasteur

EVENT : C3BI Seminars – Large audience

Performance evaluation of DNA copy number segmentation methods

Speaker : Pierre Neuvial, CNRS researcher from Laboratoire de Mathématiques et Modélisation d’Evry (LaMME) – Équipe Statistique & Génome – Université d’Evry Val d’Essonne      Time : 02:00 pm      Starting Date : 03/12/2015     

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris

A number of bioinformatic or biostatistical methods are available for segmenting DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these methods is generally assessed using unrealistic simulation studies, or based on small real data analyses.

In order to make an objective and reproducible performance assessment, we have designed and implemented a resampling-based framework to generate realistic DNA copy number profiles of cancer samples with known truth. In this talk, I will describe this framework and its application to a comparison study between methods for segmenting DNA copy number profiles from SNP microarrays.

This study indicates that no single method is uniformly better than all others. It also helps identifying pros and cons of the compared methods as a function of biologically informative parameters, such as the fraction of tumor cells in the sample and the proportion of heterozygous markers.

Reference: M. Pierre-Jean, G. Rigaill and P. Neuvial Performance evaluation of DNA copy number segmentation methods. Briefings in Bioinformatics (2015)

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Protein superfamily evolution: algorithms and applications

Kimmen Sjölander will present “Protein superfamily evolution: algorithms and applications” in Institut Pasteur, Paris #C3BISeminars 22 Oct15

EVENT : C3BI Seminars – Large audience

Protein superfamily evolution: algorithms and applications

Speaker : Kimmen Sjölander, Professor from Department of Bioengineering, University of California, Berkeley  Time : 02:00 pm Starting Date : 22/10/2015

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris

Protein superfamilies evolve through diverse mechanisms, including insertions, deletions, point mutations, gene duplications and domain architecture rearrangements.   Each of these events can modify the function or structure of the encoded protein. It is not surprising, therefore, that bioinformatics algorithms for virtually every conceivable task depend on accurately reconstructed phylogenetic trees.    In this talk, I will present the SATCHMO (Simultaneous Alignment and Tree Construction using Hidden Markov mOdels) algorithm. SATCHMO is designed to handle extreme levels of sequence and structural divergence, using Hidden Markov Models and other statistical modeling techniques to model the conserved structure within nested subgroups, and HMM-HMM scoring and alignment to construct a hierarchical tree and output a multiple sequence alignment. On benchmark datasets of structurally aligned proteins, SATCHMO outperforms MUSCLE, MAFFT, and ClustalW algorithms.    In the second half of this talk, I will present phylogenomic methods for ortholog identification. Ortholog identification is fundamental to phylogenetic tree estimation as well as automatic function prediction. While most standard orthology prediction methods employ computationally efficient graph-based approaches, their accuracy is generally lower than phylogenomic approaches.   Benchmark experiments using the TreeFam dataset show the superior performance of our methods, particularly in cases where proteins contain “promiscuous” domains.

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

C3BI Seminars – Large audience – Species interactions from a mathematical modelling and algorithmic perspective

Marie-France Sagot will present “Species interactions from a mathematical modelling and algorithmic perspective”#C3BISeminars #LargeAudience

Upcoming Events : C3BI Seminars – Large audience – 01/10/2015 at 02:00 pm in Auditorium Francois Jacob – BIME (26)

Date : 01/10/2015 at 02:00 pm Location : Auditorium François Jacob – BIME (26) Speakers/Trainers : Marie-France Sagot, Directeur de recherche, Head from Inria European Team Erable and of the LBBE-UMR5558 Team Baobab, Lyon For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at

Species interactions from a mathematical modelling and algorithmic perspective

At its extreme, one could see life as one collection, or a collection of collections of genetically identical or distinct self-replicating cells who interact, sometimes closely and for long periods of evolutionary time, with same or distinct functional objectives. The interaction may be beneficial or neutral to all, or it may be or become at some time beneficial only to some and detrimental to other cells or collections of cells. The interaction may also involve systems that have been described as being at the edge of life such as viruses, or else genetic or inorganic material such as, respectively, transposable elements and chemical compounds. In this talk, I will briefly present some of the models and algorithms we have recently been developing with the goal of better understanding some such close and often persistent interactions. I will also mention a much longer term objective of this work that would be to become able in some cases to suggest the means of controlling for equilibrium in an interacting community. The complexity of all this means that the use of mathematical models and algorithmic investigations may be crucial for obtaining any initial hints and insights on the potential of such an approach. Two points are critical here. One is the capacity to computationally handle the problems in an efficient way. A second is to be “accurate” in the answers provided. Both concerns are recurrent and, I believe, essential. Website :


C3BI Training – – Introduction à la phylogénie moléculaire

Upcoming Events : C3BI Training – Phylogeny – 29/09/2015 at 09:30 am in Retrovirus room

Date : 29/09/2015 at 09:30 am Location : Retrovirus (Lwoff) Speakers/Trainers : , from C3BI For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at

Introduction à la phylogénie moléculaire

Le C3BI propose des cours pour acquérir les notions théoriques de phylogénie et maitriser les outils et logiciels. Les cours d'”Introduction à la phylogénie moléculaire” sont ouverts EN ACCES LIBRE à tous les Pasteuriens et dispensés en langue française (pas d’inscription). Ils auront lieu du 29 septembre 2015 au 02 octobre 2015 en salle Rétrovirus du bâtiment Lwoff (sauf le 29/09 après-midi : salle Duclaux 2e étage). ** Mardi 29 septembre – 9h30-11h : Méthodes de distance (A. Criscuolo) – 14h-15h30 : Méthodes de Maximum de Parcimonie (O. Gascuel) ** Mercredi 30 septembre – 9h30-11h : Modèles d’évolution (O. Gascuel) – 14h-15h30 : Méthodes de Maximum de Vraisemblance (O. Gascuel) ** Jeudi 1er octobre – 9h30-11h : Méthodes Bayesiennes (G. Perriere) – 14h-15h30 : Inférences des forces sélectives (G. Perriere) Website : more details


C3BI Seminars – Methodological – Le Cloud Académique IFB pour les Sciences du Vivant

“Le Cloud Académique IFB pour les Sciences du Vivant”, présénté par Christophe Blanchet. #IFBCloud #C3BISeminars

Le Cloud Académique IFB pour les Sciences du Vivant, Retrovirus Room, LWOFF Building

Time : 2 PM       Starting Date : 24/09/2015        Ending Date : 24/09/2015

Location : Retrovirus Room, LWOFF Building, Institut Pasteur, Paris

Ces dernières années, beaucoup d’Infrastructures de Recherche dédiées aux sciences du vivant, ont été mises en place à l’échelle nationale et européenne, et produisent d’énormes quantités de données expérimentales hétérogènes à analyser. Leur analyse demande un grand nombre d’outils logiciels et souvent la comparaison avec des collections de données de références. De la même manière, les interfaces requises couvrent un spectre large : de la ligne de commande au portail web, en passant par des logiciels graphiques. L’objectif de l’Institut Français de Bioinformatique (IFB) est de fournir aux scientifiques et ingénieurs, utilisateurs comme développeurs, les capacités de stockage et de calculs requises dans une solution flexible, simple d’utilisation et facilement adaptable. Pour simplifier l’utilisation des logiciels bioinformatiques pertinents, nous les avons intégrés dans des machines virtuelles préconfigurées (les appliances), prêtes à l’emploi sur le cloud de l’IFB. Le modèle d’organisation envisagé vise un équilibre entre les mouvements de données, qui peuvent être très couteux et dans certains cas impossible pour les données confidentielles, et le déploiement automatique des appliances sur des clouds locaux, au plus près des dépôts de données mais nécessitant une infrastructure locale compatible. Pour répondre aux besoins les plus courants, nous avons installé une sélection de plusieurs logiciels scientifiques dans des appliances pour différents domaines des sciences du vivant. L’IFB référence les outils des machines virtuelles dans un catalogue, disponible en ligne, et contenant déjà vingt appliances pour différents sujets comme l’analyse de séquence, l’écologie et la dynamique de populations, la génomique avec le portail Galaxy et des outils comme Stacks pour le RAD-seq, la bio-imagerie, les statistiques avec la suite R, le portail R-studio et l’API web Shiny, etc.

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

C3BI Seminars – Methodological – Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walks?

Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walk?

Upcoming Events : C3BI Seminars – Methodological – 09/03/2015 at 02:00 pm in Retrovirus room – LWOFF (22)

Date : 09/03/2015 at 02:00 pm Location : Retrovirus room – LWOFF (22) Speakers/Trainers : Jean-Baptiste Masson, Visiting Scientist from Janelia Farm Research Campus, Ashburn, VA, USA For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at

Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walks?

The development during the last 20 years of single biomolecule tagging allows unprecedented access to single biomolecule dynamics. Trajectories are now space filling in 2D and densities in 3D are rapidly rising. Thus, large amount of random walks are now accessible. These random walks bear information on both the biomolecule dynamics and on the environment properties. One of the key questions is how to exploit these random walks to gain quantitative information on the biological processes taking place and the nature of these random walks. Growing number of data being accessible multiple statistical hypothesis can be tested. Bayesian Inference [1] is a natural tool to handle multiple environment models, large amounts of data and multiple statistical hypothesis. We will discuss the use of Bayesian Inference to analyse single biomolecule trajectories[2–4], show various local models to describe biomolecule dynamics, methods to analyse multi-scale dynamics and describe transitions to anomalous dynamics [3]. We will also comment on out-of-equilibrium dynamics and stochastic integrals dilemma. Furthermore, numerous estimators lack robustness regarding linking mistakes of the tracking algorithm. We will show how to remove tracking by efficiently sampling the biomolecules assignment graph between images. We will comment the various methods to perform these sampling and discuss the inference of multi-scale fields. We will show time evolving maps at the full cell scale using high density tagging. We will discuss toxins receptor interactions with lipid platforms and Glycine Receptors dynamics at the full cell scale in both neurons and transfected Hela Cells. Finally, we will quickly introduce InferenceMAP a user-friendly software to analyse random walks trajectories. [1] U. Von Toussaint. 2011. Bayesian inference in physics. Review of Modern Physics 83:943-999. [2] El Beheiry, M., Dahan, M. and J.-B. Masson. 2015. InferenceMAP: Mapping of Single-Molecule Dynamics with Bayesian Inference. Nature Methods (In Press). [3] Masson, J.-B, Dionne, P., Salvatico, C., Renner, M., Specht, C. G. , Triller, A. and M. Dahan. 2014. Mapping the Energy and Diffusion Landscapes of Membrane Proteins at the Cell Surface Using High-Density Single-Molecule Imaging and Bayesian Inference: Application to the Multiscale Dynamics of Glycine Receptors in the Neuronal Membrane. Biophysical Journal 106 (1), 74–83 . [4] Masson,J.-B., Casanova, D. , Tu ̈rkcan, S., Voisinne, G., Popoff, M. R., Vergassola, M. and A. Alexandrou. 2009. Inferring Maps of Forces Inside Cell Membrane Microdomains. Physical Review Letters 102 (4), 048103.



C3BI Seminars – !hacking@pasteur – What Health : Bring to the global health the key of its own digital revolution.

@EnguerrandH will present @whathealthfr association @aiderpasteur Thursday 27th of August 2PM in Lwoff building

Upcoming Events : C3BI Seminars – !hacking@pasteur – 08/27/2015 at 02:00 pm in Retrovirus room – Lwoff building

Date : 08/27/2015 at 02:00 pm Location : Retrovirus room – LWOFF (22) Speakers : Enguerrand Habran, Co-founder & President of What Health Association For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at

What Health : Bring to the global health the key of its own digital revolution.

What Health is an independent association whose mission is to make emerge and support innovation in healthcare, in particular thanks to the potential of the new technologies. Our process is conceived to take innovation at source and bring the right environment for its growing, to allow its establishment in healthcare system. What Health fosters exchanges and the collaborative working between several universe to help them become players in innovation in healthcare system. What Health approach is diverse: • « Bottom-up », the innovation is coming from the ground and borne either by healthcare practitioners or by patients. • Collaborative, each player of our community that is willing to contribute to improving healthcare system can provide his know-how and expertise. • Global, What Health supports innovation from its emergence to implantation in the healthcare system. • Supported, What Health is partner of major players in the healthcare system. • Ethical, What Health supports all projects that can improve health. The What Health process consists of several actions: • The “Cafés”, a meeting and debate place • The Innovation challenge, collaborative events that allow to prototype a solution and validate the proof of its concept; • The Hub, support structure dedicated to the development and establishment of projects. As a facilitator, What Health makes no claim to intellectual property emerging from events and other activities. That applies also for any actor and partner of What Health. Therefore, the ownership of a project belongs to the team that supports it. Website :