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 c3bi-ask@pasteur.fr

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.

 

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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 c3bi-ask@pasteur.fr

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 : http://what-health.org

C3BI

Seminars – Large audience – From Genomics to Medicine: Uncovering and targeting the genetic circuits underlying GWAS and cancer

@manoliskellis will talk @institut_curie, 08-31-2015 at 11AM, about Uncovering and targeting the genetic circuits underlying GWAS and cancer

Upcoming Events : C3BI Seminars – Large audience – 08/31/2015 at 11:00 am in

Date : 08/31/2015 at 11:00 am Location : Institut Curie, Centre de Recherche – Paris – Amphithéâtre Biologie du développement et cancer Speakers/Trainers : Manolis Kellis, Professor , MIT Computer Science and Artificial Intelligence Lab from Broad Institute of MIT and Harvard For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at  c3bi-ask@pasteur.fr

From Genomics to Medicine: Uncovering and targeting the genetic circuits underlying GWAS and cancer

Perhaps the greatest surprise of genome-wide association studies (GWAS) of human disease is that 90% of top-scoring disease-associated loci lie outside protein-coding regions. This has increased the urgency of mapping non-coding DNA elements and regulatory circuits, in order to understand the molecular basis of human disease. To address this challenge, we have developed and applying new methods to systematically characterize the epigenomic landscape of diverse primary human cells and tissues, resulting in the annotation of 2.3M enhancer elements across 127 primary human tissues and cell types. We also predicted tissue-specific regulatory networks linking these enhancers to their upstream regulators and target genes, and enable us to weave genetic information from GWAS through these networks to recognize preferentially-disrupted genes, regulators, and biological processes. In this talk, I will describe the use of non-coding annotations and circuits for understanding the molecular basis of genetic differences underlying common disease and cancer: (1) We uncover the mechanistic basis of GWAS hits, predicting and experimentally validating the causal variants, cell types of action, upstream regulators, downstream genes, and their molecular, cellular and organismal phenotypes in the context of obesity. (2) We combine genetic and epigenomic evidence to prioritize and experimentally validate weakly-associated variants in the context of cardiac repolarization phenotypes, showing that epigenomic data enables robust discovery with much smaller cohorts. (3) We use our regulatory predictions to identify new cancer genes based on recurrent somatic mutations in their linked upstream regulatory elements, revealing out-of-context de-repression as a common cancer strategy in the context of prostate cancer. These three applications, spanning the spectrum of common, rare, and somatic variants, illustrate the power and broad applicability of epigenomic annotations and regulatory networks for understanding human disease and cancer. More Manolis Kellis is a Professor of Computer Science at MIT, where he directs the MIT Computational Biology Group (compbio.mit.edu). He has helped direct several large-scale genomics projects, including the NIH Roadmap Epigenomics project, the comparative analysis of 29 mammals, the Encyclopedia of DNA Elements (ENCODE) project, and the Genotype Tissue-Expression (GTEx) project. He received the US Presidential Early Career Award in Science and Engineering (PECASE), the NSF CAREER award, the Alfred P. Sloan Fellowship. He obtained his Ph.D. from MIT, where he received the Sprowls award for the best doctorate thesis in computer science. He lived in Greece and France before moving to the US.

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First Fiocruz-IP-USP Hands-on Course Bioinformatics and Biostatistics

Upcoming Events : First Fiocruz-IP-USP Hands-on Course Bioinformatics and Biostatistics. 19-30th October 2015 in Ribeirão Preto, Brazil

Date : 19-30th October 2015 Location : Ribeirão Preto, Brazil Speakers/Trainers : Institut Pasteur International Network (RIIP) and the University of Sao Paulo.

First Fiocruz-IP-USP Hands-on Course Bioinformatics and Biostatistics

The aim of this course is to provide students with theory and practical tools to analyze Next Generation Sequencing (NGS) data.  The course is composed of a theory and practice lessons . In the first week theory sessions will cover the main kind of HTS analyses (re-sequencing and variant analysis, de-novo sequencing, transcriptomics, ChIP-Seq, metagenomics), in addition to some general bioinformatics tools and Biostatistics. The second week is dedicated to practice, in which the students work with their own data in small groups with a mentor that guides them. The practice week is designed so the course is of immediate use to each student. We expect the students to go back to their countries with the necessary knowledge to continue working on their own data. Lastly, this course will also promote interactions through bioinformatics between Fiocruz, the Institut Pasteur International Network (RIIP) and the University of Sao Paulo. The course will take place from the 19-30th October in Ribeirão Preto, Brazil. For more information and to apply visit: http://bioinformatics.fmrp.usp.br/curso2015/

Sponsors: Logo-Course_First_Tripartite_USP_Fiocruz_IP

C3BI

INDA Hands-on NGS-GWAS course, 10 – 19 September, 2015. Senegal

The INDA Hands-on NGS-GWAS course

Upcoming Events : INDA Hands-on NGS-GWAS course. 10 – 19 September, 2015

Date : 10 – 19 September, 2015 Location : Gaston Berger University, Saint-Louis, Senegal Speakers/Trainers : INDA and IP Dakar

INDA Hands-on NGS-GWAS course

We are happy to announce the International Network for Data Analysis (INDA) Hands-on course in NGS and GWAS. The objective of the course is to provide to each student the knowledge and tools necessary to understand and analyze Next Generation Sequencing (NGS) data, as well as Genome-wide association studies (GWAS), no matter the dataset they have or where they come from in the RIIP. The course is around two weeks long. First week is devoted to theory sessions that will include the basis of NGS technologies, quality analysis, algorithms for mapping and assembling, different kinds of biological experiments and a strong focus on the corresponding statistical techniques. We will also offer and introduction to GWAS, Genotypic variation and linkage disequilibrium, and SNP array design, with some model cases. The second week is dedicated to practice, in which the students work with their own data in small groups with a mentor that guides them. The practice week is designed so the course is of immediate use to each student. We expect the students to go back to their countries with the necessary knowledge to continue working on their own data. Lastly, this course will also promote interactions through bioinformatics between different Institut Pasteur in the RIIP.

We will only accept candidates coming from the Institut Pasteur International Network , Fiocruz, University of Sao Paulo (USP) and the University Gaston Berger (UGB). International candidates can apply for a travel grant. Candidates must fill and send the application form (here), a short CV (2 pages max) and a letter of support from your head of laboratory or mentor to the following email: inda_training@pasteur.fr

See course flyer for more information (here) and syllabus (here). Deadline for the application is July 31st, 2015 at midnight (Paris time).

Sponsors:   LOGO_INDA   Logo UGB Senegal   CEA-MITIC   Logo IP Dakar   RIIP_en

C3BI

C3BI News – REGATE, REGISTRATION OF GALAXY TOOLS IN ELIXIR

ReGaTE is a software component enabling the automated publication of Galaxy tools into the ELIXIR Tools and Data Services Registry

Upcoming Events : C3BI News – Galaxy Community Conference 2015

Date : 6-8th July 2015 Location : The Sainsbury Laboratory, Norwich, UK

REGATE, REGISTRATION OF GALAXY TOOLS IN ELIXIR

Olivia Doppelt-Azeroual1, Fabien Mareuil1, Eric Deveaud1, Matus Kalas2, Hervé Menager1 1 Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France 2 Computational Biology Unit, University of Bergen, Norway ReGaTE is a software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry (https://elixir-registry.cbs.dtu.dk/#/). This registry is a web portal for the exploration of bioinformatics resources, such as software packages, web services, websites, or reference databases. Through a dedicated interface, its users can search and locate relevant tools and data resources, and bioinformatics resource providers can enhance the visibility of their services. The registration of resources in the registry can be performed either manually, by filling a form on a web user interface, and providing the required description elements, or automatically by using the registry API. ReGaTE uses the BioBlend API and the Registry API to completely automate the registration of the tools installed on any given Galaxy portal. Central to the development of this tool is the mapping of the Galaxy datatype system to the EDAM Ontology. EDAM provides a controlled vocabulary for the description of scientific topics, software operations, types of data and data formats and it is used to describe the contents of the ELIXIR Registry. This mapping enables the automation of the registration of Galaxy tools by describing the format of their input and output data in the controlled vocabulary of the registry. This mapping is being developed in collaboration with members of the Galaxy team, the EDAM ontology and the Common Workflow Language project. ReGaTE is available at http://github.com/bioinfo-center-pasteur-fr/ReGaTE

C3BI

C3BI News – JOBIM 2015

Most of HUB Team members are attending to JOBIM conference this week.

Upcoming Events : C3BI News – JOBIM 2015 – Clermont Ferrand

Date : From Monday 6th July 2015 to Thursday 9th July 2015 Location : Polydome – Clermont-Ferrand

JOBIM 2015

Most of HUB Team members are attending to JOBIM conference this week. You can have a look to our poster n°116 PosterHubC3BI

C3BI

C3BI Seminars – Large audience – Comparative genomics in vertebrates: from models to applications.

Hugues Roest Crollius @ENS_ULM will talk about Comparative genomics in vertebrates: from models to applications. #C3BIPasteur #LargeAudience

Upcoming Events : C3BI Seminars – Large audience – 07/02/2015 at 02:00 pm in Retrovirus room – LWOFF (22)

Date : 07/02/2015 at 02:00 pm Location : Retrovirus room – LWOFF (22) Speakers/Trainers : Hugues Roest Crollius, Head of the Genome Evolution and Dynamics Group (DYOGEN) from Ecole Normale Supérieure For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at bioinfo-hub@pasteur.fr

Comparative genomics in vertebrates: from models to applications.

Genomic rearrangements, first observed more than a century ago, are one of the most obvious differences between genomes of closely related eukaryotes. Genomic rearrangements modify the order and organisation of genes because of evolutionary breakpoints caused by chromosome inversions, translocations, fusions or fissions. They do not occur randomly in genomes and are known to be associated with specific genomic features, yet the forces that promote them have remained elusive. Importantly, chromosome breakpoints are mutational events that may cause or may be associated with human pathologies. I will present two facets of comparative genomics in vertebrates that exploit the properties of genome rearrangements. The first illustrates how considering breakpoints in an evolutionary framework can lead to statistical models that formulate strong and plausible explanations for the mechanisms that cause breakpoints. The second postulates that genomic regions that do not rearrange during evolution are likely to be under strong functional constraints, thus revealing potential long-range cis-regulatory domains. Methods to identify such regions were experimentally tested both in model organisms and with respect to their involvement in human developmental disorders. Comparative genomics is a powerful multidisciplinary approach to decipher genome biology, and the recent acceleration in genome sequence production is paving the way for exciting discoveries. Website

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