Former seminars

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Former seminars


Seminar
Signatures of ecological processes in microbial community time series – Karoline Faust
Thu 4 Oct 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Nowadays, a number of densely sampled microbial community time series is available, where the abundance of community members is tracked over several months through sequencing. These data allow exploring community dynamics by investigating signatures of underlying ecological processes that are present in the community time series. In this seminar, I will present our work on the exploitation of time series properties to distinguish between different ecological processes behind the observed dynamics



Seminar
Integrated and spatial-temporal multiscale modeling of liver guide in vivo experiments in healthy & chronic disease states: a blue print for systems medicine? – Dirk Drasdo
Thu 20 Sep 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Conclusion:Refined multi-scale models increasingly permit realistic prediction of liver function as well as of toxic injury in acute and chronic damage states. Those models can integrate data from various sources, in vitro, different animal models or human data. The direct representation of liver micro-architecture in those models will open up the future perspective to feed these models with patient-specific data, hence generating a virtual twin of a patients’ liver to guide personalized diagnosis and therapy planning.



Seminar
Viral phylodynamic inference: from ancient evolutionary histories to contemporary outbreaks – Philippe Lemey
Thu 6 Sep 2018 02:00 pm Institut Pasteur Auditorium Jaques Monod – MONOD (66)

The field of computational phylodynamics has witnessed a rich development of statistical inference tools with increasing levels of sophistication that can be applied to address a variety of questions about the evolution and epidemiology of viruses. The central premise of the field is that viruses generally evolve so rapidly that epidemic processes leave an imprint in their genomes. When focusing on deep phylogenies, a rich substitution history may confound time-measured evolutionary analyses, whereas for short-term outbreaks, it may be questioned whether the imprint provides the necessary resolution for insightful evolutionary reconstructions. Here, I will illustrate these aspects on different viral examples. The Hepatitis B virus represents an example of a deep evolutionary history that has been difficult to date accurately using sequences sampled over the last decades. Recently, ancient DNA work has resulted in the first HBV samples dating back thousands of years. Using molecular clock modeling that accommodates time-dependent evolutionary rates, I will show how recent rapid evolutionary rate estimates can be reconciled with the long-term evolutionary dynamics of the virus. The 2013-2016 West African Ebola epidemic marked the start of real-time genomic sequencing. Using this example, I will illustrate that short-term outbreak dynamics can be investigated using viral genome sequences, but integrating various sources of information with genomic data promises to deliver more precise insights in infectious diseases. Finally, using recent work on Lassa virus in West Africa, I will further highlight how in-field, real-time molecular epidemiology may impact outbreak responses.



Seminar
Profiling epitranscriptomic RNA modifications by Next-Generation Sequencing – Yuri Motorin
Thu 14 Jun 2018 11:00 am Institut Pasteur Auditorium Jaques Monod – MONOD (66)

RNA modifications are emerging players in the field of posttranscriptional regulation of gene expression, and are attracting a comparable degree of research interest to DNA and histone modifications in the field of epigenetics. The true potential of only a handful out of more than 100 RNA modifications is currently emerging as the consequence of a leap in detection technology, principally associated with high-throughput sequencing. In the seminar I will outline the major developments in this field with thorougful discussion of detection principles, advantages and drawbacks of new high-throughput approaches, with particular focus on 2′-O-methylations in rRNA and tRNA.



Seminar
Network Medicine: From Cellular Networks to the Human Diseasome – Lazlo-Albert Barbasi
Tue 12 Jun 2018 02:00 am Institut Pasteur Auditorium Francois Jacob – BIME (26)

Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular network. The emerging tools of network medicine offer a platform to explore systematically not only the molecular complexity of a particular disease, leading to the identification of disease modules and pathways, but also the molecular relationships between apparently distinct (patho) phenotypes. Advances in this direction are essential to identify new disease genes, to uncover the biological significance of disease-associated mutations identified by genome-wide association studies and full genome sequencing, and to identify drug targets and biomarkers for complex diseases.



Seminar
How to extract important features and observations in large scale multivariate analyses – Constraining the Singular Value Decomposition. – Hervé Abdi
Thu 31 May 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

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



Seminar
MixMD: Mapping Protein Surfaces to Discover Druggable Allosteric Sites – Heather Carlson
Thu 17 May 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Research in the Carlson lab focuses broadly on the molecular recognition between ligands and proteins, from the fundamental biophysics of ligand binding to applied inhibitor design. Understanding protein flexibility, allosteric control, and ligand binding all require dynamic information at the atomic level. The technique that we prefer is molecular dynamics (MD) simulations. Our most recent projects have focused on developing mixed-solvent MD (MixMD), a surface-mapping technique which samples protein motion in a solution of water and organic probe molecules. This technique identifies possible binding hotspots for ligands and protein-protein interactions. It requires many MD simulations, typically 10-20 independent simulations of 20-100ns, to properly sample the possible configurations. This series of MD simulations must be done for each possible probe types. It is a resource intensive method, but it has the promise of identifying previously unknown regulatory sites on proteins. This could significantly increase the number of drug targets available to treat a wide variety of medical disorders.



Seminar
Learning tumor phylogenies from single-cell data – Niko Beerenwinkel
Thu 19 Apr 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

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



Unit Seminar
Unit Seminar – Gaël Millot & Anthony Cousien (Bioinformatics & Biostatistics HUB & Mathematical modelling of infectious diseases)
Thu 12 Apr 2018 02:00 pm Institut Pasteur Auditorium Jaques Monod – MONOD (66)





Seminar
Hierarchical functional genomics to interpret genome variation and dissect complex disease architecture – Emmanouil Dermitzakis
Thu 5 Apr 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Molecular phenotypes inform us about genetic and environmental effects on cellular and tissue state. The elucidation of the genetic basis of gene expression and other cellular phenotypes is highly informative for the impact of genetic variants in the cell and the subsequent consequences in the organism. In this talk I will discuss recent advances in key areas of the analysis and integration of the genomics of gene expression, chromatin and cellular phenotypes in human populations and multiple tissues from various cohorts including the GTEx consortium and how this assists in the interpretation of regulatory networks and human disease variants. I will also discuss how these recent advances are informing us about the impact of regulatory variation in cancer.



Seminar
Learning of Ultra High-Dimensional Potts Models for Bacterial Population Genomics – Jukka Corander
Thu 22 Mar 2018 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

The potential for genome-wide modeling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has earlier been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10000-100000 polymorphisms, representing the amount of core genomic variation observed in analyses of many bacterial species. Here we introduce a novel inference method (SuperDCA) which employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 100000 polymorphisms. Using two large population samples of Streptococcus pneumoniae, we demonstrate the ability of SuperDCA to make additional significant biological findings about this major human pathogen. We also show that our method can uncover signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA thus holds considerable potential in building understanding about numerous organisms at a systems biological level.



Unit Seminar
Unit Seminar – Alexander Serov & Antoine Frenoy (Decision and bayesian computation group & Microbial Evolutionary Genomics group)
Thu 15 Mar 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Alexander Serov (Decision and bayesian computation group) : “Robust Conservative Force Detection with the Overdamped Langevin Equation”

Antoine Frenoy (Microbial Evolutionary Genomics group) : “Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria”



Seminar
Some lessons learned during 30 years of biocuration activities – Amos Bairoch
Thu 8 Mar 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

University of Geneva Medical School



Seminar
Inferring causality in complex molecular pathways from live cell movies – Gaundenz Danuser
Thu 22 Feb 2018 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

One of the major limitations in the study of complex molecular pathways is adaptation of the system to experimental perturbation. With ‘complex’ we mean pathways with a significant level of functional redundancy between components and nonlinear interactions. In this scenario, perturbation of one component may lead to an observable phenotype. However, it is impossible to interpret the difference between phenotype and wildtype in terms of the function the targeted component fulfills in the unperturbed system – although this is the predominant approach cell and systems biologists take to dissect molecular functions. Over the past decade my lab has made efforts to circumvent this problem by exploiting the basal fluctuations of molecular activities observed in live cell movies to establish causal functional relations between pathway components. Inspired by the accomplishments of econometrics, where predictive models are built entirely from passive observation of financial fluctuation time series, we have developed a computational framework to determine nonlinear interdependencies between pathway components. This presentation will introduce some of the mathematical, computational, and experimental concepts based on which we can now accurately delineate the functional hierarchy between signaling and mechanical processes that control cellular morphogenesis, which is a prime example of a complex molecular process.



Unit Seminar
Unit Seminar – Lucas Husquin & Jakob Ruess (Human evolutionary genetics unit & InBio : Experimental and computational methods for modeling cellular processes)
Thu 15 Feb 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Lucas Husquin (Human evolutionary genetics unit) : “Dissecting the impact of population variation in DNA methylation on transcriptional responses to immune activation”

Jakob Ruess (InBio : Experimental and computational methods for modeling cellular processes) : “Virtual reality for bacteria”



Seminar
The structural basis of SMS (Short Motif Sequence) – mediated communication between proteins: characterization, modeling and manipulation – Ora Schueler-Furman
Thu 8 Feb 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Many important regulatory interactions are mediated by short linear motif sequences, which are often embedded in disordered protein regions. These interactions tend to be transient, and therefore pose special experimental challenges. In order to develop precise tools for the manipulation and study of such interactions, accurate structural models are needed. However, due to weak binding affinity and the considerable flexibility of the peptide, structural modeling of peptide-mediated interactions presents a considerable challenge. In my talk I will present an overview of our research on peptide-mediated interactions. I will describe Rosetta FlexPepDock, the suite of protocols that we have developed, and applied, for the structure-based characterization and manipulation of peptide-mediated interactions. FlexPepDock is guided by observations of peptide binding strategies revealed from solved complex crystal structures. Efficient but focused sampling strategies have opened the way to model these interactions at high, atom-level accuracy, starting from a receptor structure and the peptide sequence. Using these starting models, we were able to study binding affinity and specificity, and detect novel substrates for a range of peptide-binding receptors as well as peptide-modifying enzymes. Overall, successful modeling strategies have revealed principles of peptide-mediated interactions that can explain how these interactions are established, and provide a starting point for the extension and specification of the peptide-protein interaction repertoire.



Unit Seminar
Unit Seminar – Frédéric Lemoine & Lyam Baudry (Bioinformatique Evolutive & Spatial Regulation of Genomes Unit)
Thu 18 Jan 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Frederic Lemoine (Bioinformatique Evolutive) : “Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data”

Lyam Baudry (Spatial Regulation of Genomes) : “Metagenome binning using chromosome conformation capture (3C) data”



Seminar
The molecular anatomy of the human body – Roderic Guigo
Thu 11 Jan 2018 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

The relationship between the transcriptomes of tissues and the transcriptomes of the constituent primary cells, and how these impact tissue phenotypes has not been well established. Here we have produced RNA sequencing data for a number of primary cells from multiple human body locations. The analysis of this data, together with additional epigenetic data also produced by the ENCODE project for a total of 146 primary cells, indicate that most cells in the human body belong to five major cell types:  epithelial, endothelial, mesenchymal, neural and blood cells.  These redefine, based on gene expression, the basic histological types in which tissues are usually classified. We identified genes specific to these cell types, including a core set of transcription factors (TFs). Cell type specific genes, particularly when lying in open chromatin domains, are enriched for motifs for these cell type specific TFs, suggesting that they are potential candidates to drive cell type specificity. We estimated the relative proportion in tissues of the different cell types based on the transcriptional profiles obtained from bulk tissue sections from the GTEx project. This inferred cellular composition is a characteristic signature of tissues and reflects tissue histology. We identified changes in tissue composition associated with age and sex, and we found that departures from the normal cellular composition are a characteristic of different cancer types and correlate with histological phenotypes associated to diseases



Seminar
Seminars – From Genome to Pan Genome – Paul Kersey
Thu 21 Dec 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Since the advent of genomics, the Genome Browser has proven an enduring and successful way of representing genomic information, using the paradigm of a linear map; and well-assembled and annotated genomes of experimental organisms have served as references for broader taxonomic groups. Ensembl, developed by EMBL-EBI, is one of the most widely used software platforms organising and serving data according tot his model.  But large scale projects to sequence populations of major species, and to more fully sample the taxonomy, are already commonplace, and accelerating in their ambitions. The logical ay to represent many (related) genome sequences is a graph; but graph-based visualisations may be confusing to users, and the majority of experimental discovery still takes lace in a small number of species.  In this talk, I will present how Ensembl is experimenting with new models to organise and display genomic data, more suited to a world where sequence is ubiquitous (with examples from vertebrates, vectors, pathogens and plants); and will explore not just technological, but also sociological and political aspects to developing a suitable data infrastructure for an era of genomic plenty.



Unit Seminar
Unit Seminar – Axel Cournac & Anna Zhukova (Spatial Regulation of Genomes Unit – Head Romain Koszul & Unité de Bioinformatique évolutive – Head Olivier Gascuel)
Thu 14 Dec 2017 02:00 pm Institut Pasteur Jean-Paul Aubert room – FERNBACH (68)

Axel Cournac (Spatial Regulation of Genomes Unit – Head Romain Koszul) : “The multi-scale spatial organization of the Escherichia coli chromosome”

Anna Zhukova (Unité de Bioinformatique évolutive – Head Olivier Gascuel) : “Modeling emergence and transmission of drug resistance in HIV”



Seminar
Seminars – Statistical design and analysis of reproducible quantitative mass spectrometry-based experiments – Olga Vitek
Thu 7 Dec 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Statistical methodology is key for quantitative proteomics, as it helps reduce bias and inefficiencies,  distinguish the systematic variation from random artifacts, and maximize the reproducibility of the results. This talk will overview the statistical methodology implemented in MSstats, an open-source R package for statistical relative quantification of proteins and peptides. MSstats supports experiments with complex designs, such as comparisons of multiple groups or time course comparisons. It handles quantitative shotgun DDA (data-dependent acquisition) experiments, targeted SRM (selected reaction monitoring), and SWATH/DIA (data independent acquisition) experiments. It can be used in conjunction with label-free experimental workflows, or with workflows that utilize stable isotope reference proteins or peptides. MSstats contains functionalities for data processing, model-based statistical analysis (including testing proteins and peptides for differential abundance, or estimating protein abundance on a relative scale), and model-based calculation of a sample size for a future experiment. It also contains functionalities for systems suitability and statistical process control, and for quantification of figures of merit (such as limit of detection) of mass spectrometric assays. MSstats is available stand-alone or via graphical user interface as an external tool in the software framework Skyline. It can be interfaced with numerous spectral processing tools, such as MaxQuant.



Seminar
Seminars – Genome in 3D: models of chromosome folding – Leonid Mirny
Thu 23 Nov 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

DNA of the human genome is 2m long and is folded into chromosomes that fit in 10-micron cellular nucleus. How are these long polymers of DNA folded and organized in 3D inside the nucleus? How can proteins that are much smaller than chromosomes drive chromosome compaction, segregation or control functional interactions at much larger scales? Recently developed Chromosome Conformation Capture technique (Hi-C) provides comprehensive information about frequencies of spatial interactions between genomic loci. Inferring principles and mechanisms of 3D organization of chromosomes from these and imaging data is a challenging biophysical problem. Recently we proposed that chromosomes are organized by an active, motor-driven process of loop extrusion. Loop extrusion can be a universal mechanism responsible for formation of domains and facilitation on enhancer-promoter interaction during interphase [1], and chromosome compaction and segregation in metaphase [2]. I will review recent experimental studies [3-5] that provide strong support to loop extrusion as a universal mechanism of chromosome folding.



Unit Seminar
Unit Seminar – Jorge André Sousa & Matthieu Domenech de Celles (Microbial Evolutionary Genomics Unit & Pharmacopepidemiology and infectious diseases Unit)
Thu 16 Nov 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Jorge André Sousa: “Studying the eco-evolutionary dynamics of horizontal gene transfer with an individual-based model”

Matthieu Domenech de Celles: “Untangling pneumococcal seasonality using mechanistic transmission models”



Seminar
Seminars – Emergence of de novo protein coding genes from ‘dark genomic matter’ — fact or fiction? – Erich Bornberg-Bauer
Thu 9 Nov 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Proteins are the workhorses of the cell and, over billions of years, they have evolved an amazing plethora of extremely diverse and versatile structures with equally diverse functions. Therefore, their evolution echoes the evolution of all forms of life. Evolutionary emergence of new proteins and transitions between existing ones are widely believed to be rare or even impossible. However, recent advances in comparative genomics have repeatedly called some 10%-30% of all genes without any detectable similarity to existing proteins. Even after careful scrutiny, some of those “orphan” genes contain protein coding reading frames with detectable transcription and translation. Thus some proteins seem to have emerged from previously non-coding ‘dark genomic matter’. These ‘de novo’ proteins tend to be disordered, fast evolving, weakly expressed but also rapidly assuming novel and physiologically important functions. I will review mechanisms by which ‘de novo’ proteins might be created, under which circumstances they may become fixed and why they are elusive. I will present a couple of studies which mostly focus on metazoan genomes.



Seminar
Seminars – A leap forward in biological link prediction – Itsvan Kovacs
Thu 19 Oct 2017 02:00 pm Institut Pasteur Module 1-2-3 – SOCIAL BUILDING (06)

Biological function emerges from the complex interplay between molecules in our cells, comprising the human interactome. While interactions between proteins play a central role in the interactome, current maps are still missing the majority of these interactions. State-of-the-art network-based link prediction tools rely on the triadic closure principle, stating that proteins are likely to interact if they share many of their interaction partners, utilizing network paths of length l=2. We show that this principle is valid only for the small fraction of self-interacting proteins, while it fails completely for the rest of the network. Supported by both evolutionary and protein structural arguments, we identify missing protein interactions based on l=3 paths. Our top predictions validate as well experimentally as known protein-protein interactions, outperforming previous methods at least 2-3 fold. Our Length 3 Association Prediction (L3AP) approach provides a fundamental biological principle with a broad potential applicability, including also protein associations (i.e. co-complex membership) information, enabling us to better understand the emergence of biological function under both healthy and pathological conditions.



Seminar
Seminars – Perturbing the interactome: multi-omics and personalized methods for network medicine – Marc Santolini
Thu 19 Oct 2017 03:00 pm Institut Pasteur Module 1-2-3 – SOCIAL BUILDING (06)

In this talk, I will describe several recently developed methods to study disease perturbations through the lens of network science. First I will present an investigation of the personalized gene expression responses when inducing hypertrophy and heart failure in 100+ strains of genetically distinct mice from the Hybrid Mouse Diversity Panel (HMDP). I will show that genes whose expression change significantly correlates with the severity of the disease are either up- or down-regulated across strains, and therefore missed by traditional population-wide analyses of differential gene expression. These uncovered personalised genes are enriched in human cardiac disease genes and form a dense co-regulated module strongly interacting with the cardiac hypertrophic signaling network in the human interactome, the set of molecular interactions in the cell. We validate our approach by showing that the knockdown of Hes1, predicted as a strong candidate, induces a dramatic reduction of hypertrophy by 80-90% in neonatal rat ventricular myocytes, demonstrating that individualized approaches are crucial to identify genes underlying complex diseases as well as to develop personalized therapies. Then, I will present a novel approach to identify the collective impact of miRNAs in disease. Instead of focusing on the magnitude of miRNA differential expression, here we address the secondary consequences for the interactome. We developed the Impact of Differential Expression Across Layers (IDEAL), a network-based algorithm to prioritize disease-relevant miRNAs based on the central role of their targets in the molecular interactome. This method was used in the context of asthmatic Th2 inflammation and identified five Th2-related miRNAs (mir27b, mir206, mir106b, mir203, and mir23b) whose antagonization led to a sharp reduction of the Th2 phenotype. This result offers novel approaches for therapeutic interventions. Finally, I will present evidence that one can accurately predict perturbation patterns from the topology of biological networks, even when lacking measurements on the kinetic parameters governing the dynamics of these interactions. Using 87 biochemical networks with experimentally measured kinetic parameters, we show that a knowledge of the network topology offers 65% to 80% accuracy in predicting the impact of perturbations. In other words, we can use the increasingly accurate topological models to approximate perturbation patterns, bypassing expensive kinetic constant measurement. These results open new avenues in modeling drug action, and in identifying drug targets relying on the human interactome only.



Seminar
Seminars – Big data in biology : challenges and opportunities – Ewan Birney
Thu 5 Oct 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Ewan Birney:  Co-director of the European Bioinformatic Institute and played a vital role in annotating the genome sequences of human, mouse, chicken and several other organisms. He was one of the founder of the Ensembl Genome Browser and the head of the Encode data analysis group. Ewan is a non-executive Director of Genomics England, and is a consultant and advisor to a number of companies, including Oxford Nanopore Technologies and GSK. Abstract: Molecular biology is now a leading example of a data intensive science, with both pragmatic and theoretical challenges being raised by data volumes and dimensionality of the data. These changes are present in both “large scale” consortia science and small scale science, and across now a broad range of applications – from human health, through to agriculture and ecosystems. All of molecular life science is feeling this effect. This shift in modality is creating a wealth of new opportunities and has some accompanying challenges. In particular there is a continued need for a robust information infrastructure for molecular biology. This ranges from the physical aspects of dealing with data volume through to the more statistically challenging aspects of interpreting it. A particular problem is finding causal relationships in the high level of correlative data. Drawing on recent experience I will explore both the “blue collar” challenges of data volume and the “white collar” challenges of interpretation. I will end with exploration of linear traits in cardiac biology using large scale cohorts.



Seminar
Seminars – Computer Vision & Computational Optics for Bioimage Informatics – Gene Myers
Thu 21 Sep 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Eugene Myers: Best known for contributing to the early development of the BLAST tool for sequence analysis. His 1990 paper (with Stephen Altschul and others) describing BLAST has received over 62,000+ citations making it amongst the most highly cited papers ever. Myers was also the Vice President of Informatics Research at Celera Genomics, where he was involved in the sequencing of the human genome, as well as the genomes of Drosophila and mouse. In 2012, Myers moved to Dresden to lead a new center for systems biology. Abstract: Our group has been actively pursuing the idea that with great microscopes and great informatics we will be able to truly digitize models of cells, tissues, and organisms through time with information about the genetic and proteomic states of each cell layered there on. The belief is that these atlases combined with optical observations of labeled entities will accelerate the life sciences by allowing us to visualize these systems from any vantage point and as a system, thus leading to many discoveries such as the nature of the genetic control of fly wing development. Since arriving in Dresden five years ago we have made significant progress on hard segmentation and tracking problems with the use of AI techniques developed in the computer vision community. We will present several examples of current projects that exemplify various such techniques and present the quality of results we obtain with them. Despite these improvements we still find ourselves at the limit of what can be determined because of the limited resolution and contrast of the imagery. Fortunately, advances in microscope componentry such as adaptive optics, spatial light modulators, and ultra high-speed cameras present opportunities for improving the underlying imagery. We will report on two microscope development projects in our lab, where the aim is to improve resolution by making multiple observations of a volume and from them computing a better reconstruction of the object under observation using deep neural networks. We think better microscopy through computation and dynamic onboard control of acquisitions is an emerging trend that we generally call computational optics.



Seminar
Seminars – Linking gene and function by integrated approaches: how to improve the poor annotation status of sequenced genomes – Valérie de Crécy-Lagard
Thu 7 Sep 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Linking gene and function by integrated approaches: how to improve the poor annotation status of sequenced genomes Identifying the function of every gene in all sequenced organisms is the major challenge of the post-genomic era and an obligate step for any systems biology approach. This objective is far from reached. By various estimates, at least 30-50% of the genes of any given organism are of unknown function, incorrectly annotated, or have only a generic annotation such as “ATPase”. Moreover, with ~8000 genomes sequenced and ~80,000 in the pipeline (http://www.genomeson.line.org), the numbers of unknown genes are increasing, and annotation errors are proliferating rapidly. For some gene families, 40% of the annotations are wrong. On the other side of the coin, there are still ~1,900 known enzyme activities for which no corresponding gene has been identified and these numbers are also increasing. This biochemical knowledge is yet to be captured in genome annotations. Using mainly a comparative genomic approach, we have linked gene and function for around 50 gene families related mainly to the fields of coenzyme metabolism, tRNA modification, protein modification and more recently metabolite repair. This approach integrates several types of data and uses filters, sieves, and associations to make predictions that can then be tested experimentally. An unknown gene’s function may thus be predicted from those of its associates: the ‘guilt by association’ principle. Associations that can be derived from whole genome datasets include: gene clustering, gene fusion events, phylogenetic occurrence profiles or signatures and shared regulatory sites. Post-genomic experimental sources such as protein interaction networks, gene expression profiles and phenomics data can also be used to find associations. In practice it is often ‘guilt by multiple association’ as genes can be associated in several ways, and analyzing more than one of these improves the accuracy of predictions. If these types of comparative genomic approaches were systematically used to annotate genomes, the quality of annotations would greatly improve. Also the experimentalists need to be more involved in the annotation process, as without expert knowledge the curation effort is beyond what annotation resources such as Uniprot or NCBI can do alone.



Seminar
– Erich Bornberg-Bauer
Wed 6 Sep 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)



Seminar
Seminars – Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes – Todd Treangen
Wed 5 Jul 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes Metagenomic samples are snapshots of complex ecosystems at work. These samples often involve hundreds of known and unknown species, contain multiple strain variants, and vary greatly both within environments and across environments. Metagenomic assembly is a fundamental tool for elucidating microbial ecology behind these dynamic communities. Specifically, metagenome assembly allows us to reconstruct genes and genomes from metagenomes. Genes and genomes are on two ends of the assembly spectrum, the former often represents the minimal continuous region that is desired, and the later, the optimal result; one contig per replicon. Multiple metagenomic assembly strategies, pipelines, and assemblers have appeared in recent years; several of these have been substantially improved upon the original heuristics and algorithms employed nearly a decade ago designed to solve this challenging computational problem. However, due to the inherent complexity of the metagenome assembly problem, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. In this talk I will cover three main topics: 1) recent progress in de novo assembly of metagenomes, 2) reference-guided assembly of metagenomes with MetaCompass, and 3) de novo metagenomic assembly mis-assembly detection with VALET.



Seminar
Seminars – Between chaos and determinism: the evolution of stochastic gene expression – Julien Dutheil
Thu 15 Jun 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Between chaos and determinism: the evolution of stochastic gene expression While often depicted as finely tuned programs, biochemical processes in the cell are subject to random fluctuations because of the small number of molecules involved. While this phenomenon was long recognised, it was only recently assessed at a genomic scale. In particular, the advent of single cell transcriptomics technologies have provided us with a picture of the amount of each mRNA present in a cell giving us access to a cell-specific measure of gene expression. The comparison of multiple, isogenic cells allows us to measure the variance in gene expression (also called “noise”). Just as average gene expression, expression noise is also subject to natural selection. Housekeeping genes, for instance, have been reported to be less noisy. Conversely, genes involved in stress or immune response are more variable in their expression, an observation which was hypothesised to result from a bet-edging strategy. In order to quantify transcriptional noise, we used single-cell transcriptomes of mouse cells. I will discuss statistical biases in the current measures of noise and introduce a new statistic for its estimation. We compared gene-specific transcriptional noise with other genomic variables, including sequence conservation and 3D genome architecture. Our results demonstrate that the major factors explaining transcriptional noise are linked to gene network architecture, consistent with a multi-level selection model where selection acts at the pathway level to prevent noise propagation.



Seminar
Seminars – Applying identity-by-descent mapping to malaria samples – Melanie Bahlo
Fri 9 Jun 2017 01:30 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Most of the human morbidity and mortality due to malaria is caused by two plasmodium species: falciparum and vivax. Generation of whole genome sequencing data for malaria is now routine. It is generated by extracting the plasmodium DNA from human red blood cells. In countries with a high burden of malaria this can lead to samples with multiple clones, known as multiplicity of infection (MOI). We have developed two algorithms to help detect genetic relatedness, incorporating and leveraging MOI. These two algorithms implement hidden Markov models (HMMs) to identify relatednes, or identity-by-descnet (IBD), between clones within, and between, samples. Using these results we developed an algorithm to detect regions of high relatedness which we postulate as being due to selection pressures. The algorithms also give probability-based measures to distinguish local from imported infections. We demonstrate the algorithm on whole genome sequencing data from P. falciparum from Papua New Guinea and the MalariaGen Pf3K data. We can recapitulate all of the known selection signals as well as identifying some new ones.



Seminar
Seminars – Know Thy Ancestors to Know Thyself: Improving Our Understanding of the Human Genome Using Computational Paleogenomics – Mathieu Blanchette
Thu 8 Jun 2017 02:00 pm Salle CHAMBERLAND – Roux RdC 01

Know Thy Ancestors to Know Thyself: Improving Our Understanding of the Human Genome Using Computational Paleogenomics The genomes of more than one hundred vertebrate genomes are now largely sequenced. How can one make use of this massive amount of evolutionary information to better understand the origin and function of portions of the human genome? In this talk, I will first discuss how the genomes of ancestral mammalian species can be reconstructed with surprisingly high accuracy from the genomes of extant species. I will then present how inferred ancestral sequences can be used to improve the detection of ancient evolutionary events such as transposable element and pseudogene insertions that have shaped mammalian genomes. Finally, I will then introduce algorithmic and machine learning approaches that make use of inferred ancestral DNA sequences to improve the accuracy of transcription factor binding site and micro-RNA target site prediction.



Seminar
Seminars – Genetic basis of gene regulation: genome-wide models and applications to diagnosis. – Julien Gagneur
Thu 1 Jun 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

We are interested in understanding how gene expression is encoded in genomes, and how to leverage this knowledge to understand the basis of genetic diseases. To this end, we employ statistical modeling of ‘omics data and work in close collaboration with experimentalists. I will provide an overview of recent studies from our lab, covering work on RNA metabolism in S. pombe [1] and on mRNA stability in S. cerevisiae [2], and discussing the implications of TT-seq, a novel protocol suited to study nascent transcriptomes in higher eukaryotes [3]. I will also report on a recent pilot study where we established RNA-sequencing as a powerful companion tool to genome sequencing for pinpointing molecular causes of rare genetic disorders [4]. The talk will end with a discussion on future directions in computational modeling of cis-regulatory elements.



Seminar
Seminars – Pathogen dynamics through a phylogenetic lens – zooming into the spread of Ebola, Diphtheria, Tuberculosis, Influenza and HIV – Tanja Stadler
Thu 18 May 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Genetic sequencing data contain a fingerprint of past evolutionary and population dynamic processes. Phylogenetic methods infer evolutionary relationships — the phylogenetic tree — between individuals based on their genetic sequences. Phylodynamics aims to understand the population dynamic processes — such as epidemiological processes — giving rise to the phylogenetic tree. I will present the mathematical and computational aspects of our recently developed phylodynamic tools for understanding the evolution and epidemic spread of pathogens. In particular, I will highlight our insights into the evolution and epidemic spread of Ebola, Diphtheria, Tuberculosis, Influenza and HIV. I will end the talk touching upon phylodynamic applications beyond epidemiology, such as immunology, developmental biology, and macroevolution.



Seminar
Seminars – Microbiome diagnostics and biomarker discovery – Dan Knights
Fri 12 May 2017 02:00 pm Institut Pasteur Amphithéâtre Jaques Monod – MONOD (66)

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Seminar
[Cancelled] Seminars – Whole cell model and engineering of Mycoplasma pneumoniae as an universal vaccine – Luis Serrano Pubul
Thu 20 Apr 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Whole cell model and engineering of Mycoplasma pneumoniae as an universal vaccine



Seminar
Seminars – Protein flexibility through in silico approaches – Alexandre de Brevern
Thu 6 Apr 2017 02:00 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Protein flexibility through in silico approaches The function of a protein is directly dependent on its 3-dimensional structure. Visualization tools have oversimplified our views of protein structures. Often, they are considered as macromolecules with repetitive structures as rigid while the connecting loops as flexible or even disordered. in silico approaches are interesting tools to tackle this critical question of protein flexibility. Moreover, it allows applying other criteria than B-factors, to define flexibility [1]. We have previously developed different structural alphabets (SAs) [2], [3]. They are libraries of small protein fragments that are able to approximate every part of protein structures, making them more precise than classical secondary structures. During this talk, I will present: * How a more precise and complete description of protein backbone conformation can be obtained using SAs for the structural analysis? With examples from definition of ligand binding sites to superimposition of protein structures [4]. * How SAs are also well suited to perform prediction of protein flexibility from the sequence [5]? * How have we also used them to analyse the dynamics of protein structures in a case of a transmembrane protein [6] * For integrins implicated in pathologies [7], [8]. * Finally, I will present unpublished results based on a selected a representative set of Molecular Dynamic (MD) performed on 169 protein structures. We show how the SAs can underline specific change of local protein conformations during dynamics [9], especially using PBxplore tool [10]. References 1. Craveur, P., Joseph, A.P., Esque, J., Narwani, T.J., Noël, F., Shinada, N., Goguet, M., Leonard, S., Poulain, P., Bertrand, O., Faure, G., Rebehmed, J., Ghozlane, A., Swapna, L.S., Bhaskara, R.M., Barnoud, J., Télétchéa, S., Jallu, V., Cerny, J., Schneider, B., Etchebest, C., Srinivasan, N., Gelly, J.-C., de Brevern A.G.: Protein flexibility in the light of structural alphabets., Frontiers in Molecular Biosciences – Structural Biology, 2:20. (2015) 2. de Brevern, A.G. , Etchebest, C., Hazout, S.: Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins, 41:271-287. (2000) 3. Bornot, A., Etchebest, C., de Brevern, A.G. : A new prediction strategy for long local protein structures using an original description, Proteins, 76:570-87. (2009) 4. Joseph, A.P., Agarwal, G., Mahajan, S., Gelly, J.-C., Swapna, L.S., Offmann, B., Cadet, F., Bornot, A., Tyagi M., Valadié, H., Schneider, B., Etchebest, C., Srinivasan, N., de, Brevern, A.G. : A short survey on Protein Blocks, Biophysical Reviews, 2:137-145. (2010) 5. de Brevern, A.G., Bornot, A., Craveur, P., Etchebest, C., Gelly, J.-C. : PredyFlexy: Flexibility and Local Structure prediction from sequence, Nucleic Acid Res, 40:W317-22. (2012) 6. de Brevern, A.G., Wong, H., Tournamille, C., Cartron, J.-P., Colin, Y., Le Van Kim, C., Etchebest, C. : A structural model of seven transmembrane helices receptor, Duffy Antigen / Receptor for Chemokines (DARC), Biochem Biophys Acta, 1724:288-306. (2005) 7. Jallu, V., Poulain, P., Fuchs, P.F., Kaplan, C., de Brevern, A.G.: Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIb/β3 Integrin, Plos One, 7:e47304. (2010) 8. Jallu, V., Poulain, P., Fuchs, P.F., Kaplan, C., de Brevern, A.G.: Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants, Biochimie, 105:84-90. (2014) 9. Narwani, T., Craveur, P., Shinada, N., Santuz, H., Rebehmed, J., Etchebest, C., de Brevern, A.G. Dynamics and deformability of α-, 310- and π-helices, submitted. 10.Barnoud, J., Santuz, H., Craveur, P., Joseph, A.P., Jallu, V., de Brevern, A.G., Poulain, P. PBxplore: a tool to analyze local protein 
structure and deformability with Protein 
Blocks, https://github.com/pierrepo/PBxplore, in preparation.



Seminar
Seminars – Inferring antimicrobial resistance from whole genome sequencing – Francois Balloux
Thu 23 Mar 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Inferring antimicrobial resistance from whole genome sequencing



Seminar
Seminars – RNA viruses: characterizing hidden features revealed via comparative genomics – Andrew Firth
Thu 16 Mar 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

RNA viruses: characterizing hidden features revealed via comparative genomics RNA viruses have compact multifunctional genomes. During the course of infection, the genome or its derivatives must direct translation of virus proteins, genome replication and genome packaging. To realize these multiple roles, RNA virus genomes commonly have many overlapping coding and non-coding functional elements. Overlapping functional elements have often escaped detection because it can be difficult to disentangle the multiple roles of the constituent nucleotides via, for example, mutational analysis. On the other hand, RNA viruses evolve very rapidly and there are many sequenced isolates, thus providing potential for powerful comparative genomic analyses, even within single virus species. We have been using comparative genomics to systematically identify ‘hidden’ functional elements in RNA virus genomes. Computationally identified features can then be efficiently targeted for experimental analysis. We are particularly interested in characterizing unusual translation mechanisms – such as ribosomal frameshifting, stop codon readthrough, non-AUG initiation and IRES-mediated initiation – that are so frequently used by RNA viruses for gene expression. Recent work has focused on short overlapping genes identified in the arteriviruses, cardioviruses and potyviruses, and the atypical programmed ribosomal frameshifting and RNA polymerase slippage mechanisms used to express them. To further understand these mechanisms, we have also employed the emerging technique of Ribosome Profiling.



Seminar
Seminars – Linking Large-Scale Genomic Rearrangements to 3D Chromatin Structure – Krister Swenson
Thu 9 Mar 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Linking Large-Scale Genomic Rearrangements to 3D Chromatin Structure



Seminar
Seminars – From bacterial gene expression decomposition to Synthetic Biology – Matthieu Jules
Thu 23 Feb 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – RNA-mediated regulation of antibiotics resistance in the human microbiome – Rotem Sorek
Thu 9 Feb 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

RNA-mediated regulation of antibiotics resistance in the human microbiome



Seminar
Seminars – Micro- and nano-fluidic technologies for minute DNA sample analysis: application to genomic analysis of cultured cells and circulating DNA – Aurélien Bancaud
Thu 26 Jan 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Micro- and nano-fluidic technologies for minute DNA sample analysis: application to genomic analysis of cultured cells and circulating DNA



Seminar
Seminars – An integrated, structure- and energy-based view of decoding: translation and cellular homeostasis – Eric Westhof
Thu 12 Jan 2017 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

An integrated, structure- and energy-based view of decoding: translation and cellular homeostasis Abstract:



Seminar
Chemoinformatics and proteochemometrics approaches to the pharmacological modulation of protein-protein interactions. – Olivier Sperandio
Thu 15 Dec 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – Diversity of immune repertoires – Aleksandra Walczak
Thu 1 Dec 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Diversity of immune repertoires



Seminar
Seminars – From Systems Biology to Systems Ecology – Damien Eveillard
Thu 17 Nov 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

From systems biology to systems ecology: a computational journey from genes to ecosystems



Seminar
Seminars – Making data “FAIR” (Findable, Accessible, Interoperable, Reusable): motivation, current implementation and future challenges – Jean-Baptiste Poline
Wed 16 Nov 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

While re-using data from the wider community to validate specific hypotheses or to explore new questions is becoming increasing common, it is still more often than not challenging to efficiently find and access relevant data, and have these sufficiently documented to be safely re-used and integrated. While some journals have started publishing data (i.e their description and scope of use) discoverability, the question of the data publishing incentive and of sustainability are pressing. In this talk, I will review the data sharing and publishing issues in the context of scientific reproducibility and will take the example of neuroscience to demonstrate how data can be made “FAIR”. I will point to current solutions for researchers to link their data with the scientific community and will discuss the remaining technical but also cultural challenges.



Seminar
Seminars – Phylodynamics on local sexual contact networks – David Alan Rasmussen
Tue 15 Nov 2016 03:00 pm Institut Pasteur Jean-Paul Aubert room – FERNBACH (68)

Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks. We present a new framework for phylodynamics on local contact networks based on pairwise epidemiological models that track the status of pairs of nodes in the network rather than just individuals. Shifting our focus from individuals to pairs leads naturally to coalescent models that describe how lineages move through networks and the rate at which lineages coalesce. These pairwise coalescent models not only consider how network structure directly shapes pathogen phylogenies, but also how the relationship between phylogenies and contact networks changes depending on epidemic dynamics and the fraction of infected hosts sampled. By considering pathogen phylogenies in a probabilistic framework, these coalescent models can also be used to estimate the statistical properties of contact networks directly from phylogenies using likelihood-based inference. We use this framework to explore how much information phylogenies retain about the underlying structure of contact networks and to infer the structure of a sexual contact network underlying a large HIV-1 sub-epidemic in Switzerland.



Seminar
Seminars – Authorea: Reinventing the Scientific Article – Karolina Mosiadz
Thu 10 Nov 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

It has been said that in order to cure cancer, we must first cure research. First, we need to improve how researchers work and make breakthrough discoveries by tackling one of the most important parts of the research cycle, which is as important as research itself: scientific communication. The big step is to reinvent the scientific article – the main vehicle of scientific dissemination – that hasn’t changed in format and scope since the birth of the scientific method.



Seminar
Seminars – Mining human contacts: from data gathering to data-driven simulations of infectious diseases – Alain Barat
Thu 3 Nov 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Mining human contacts: from data gathering to data-driven simulations of infectious diseases



Seminar
Seminars – Structural organisation of human replication timing domains – Benjamin Audit
Thu 20 Oct 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Structural organisation of human replication timing domains Understanding how the DNA double helix is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. In this seminar, I will illustrate that when combining concepts and methodologies coming from physics with wavelet-based multi-scale signal processing, we are able to extract original information about the structure/function relationship in the nucleus. I will review some recent analyses of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation (HiC) data that have established some link between the spatio-temporal replication program, gene expression and chromatin structural domains. This provides an analysis framework for the understanding of the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency during cell differentiation in human. The proposed view reconciles the dichotomic picture of early transcriptionally active and late heterochromatin constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the model proposed by our group where U-shaped MRT domains are bordered by ‘‘master’’ replication origins from which a replication wave initiates and propagates toward the domain centre via a cascade of origin firing. I will finally discuss a unified framework based on equilibrium globule models where early euchromatin regions behave as a simple 3D equilibrium globule while, specifically in differentiated cell lines, chromatin folding in heterochromatin regions is compatible with a transition to 2D equilibrium dynamics associated with the nuclear lamina. This transition corresponds to a progressive segregation from 3D dynamics at the nucleus centre of early replicating regions to 2D dynamics confined at the nuclear envelop of late replicating regions. These results shed a new light on replication foci formation and dynamics in human, depending on the cells’ differentiation status.



Seminar
Seminars – Bayesian Markov models for regulatory motif prediction – Sensitive sequence searching for parallelized analysis of massive data sets – Johannes Soeding
Thu 6 Oct 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Bayesian Markov models consistently outperform PWMs at regulatory motif prediction – Sensitive protein sequence searching for parallelized analysis of massive data sets The talk will cover two very different topics. First I will present Bayesian approach for motif discovery using Markov models in which conditional probabilities of order k − 1 act as priors for those of order k. This Bayesian Markov model (BaMM) training automatically adapts model complexity to the amount of available data. BaMMs improve on PWMs by ~40% in AUC on ~400 ENCODE ChIP-seq data sets and achieves similar improvements in detecting core promoter sequences, poly(A) sites, RNAP pause sites and binding sites for ~20 PAR-CLIPped RNA binding factors. BaMMs never performed worse than PWMs. These robust improvements argue in favour of generally replacing PWMs by BaMMs. Second, I will present our new method MMseqs2 (Many-against-Many sequence searching) for very fast batch protein sequence searches and clustering of huge protein sequence data sets. Protein sequence searching is the main time, cost and quality bottleneck for the analysis of metagenomic datasets. While previous search methods sacrificed sensitivity for speed gains, MMseqs2 is as sensitive as BLAST, more sensitive than PSI-BLAST, and 36 to 1300 times faster. I will explain the ideas that led to this massive improvement. MMseqs2 searching and clustering will considerably increase the fraction of annotatable metagenomic ORFs.



Seminar
Seminars – Hard Problems in Systems Biology – Chris Sander
Thu 29 Sep 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Department of Structural Biology AND Chemistry



Seminar
Seminars – GATB: A Genomic Analysis Tool Box for designing parallel and low memory fingerprint bioinformatics software – Dominique Lavenier
Wed 21 Sep 2016 02:00 pm Institut Pasteur Jules Bordet room – METCHNIKOFF (67)

GATB: A Genomic Analysis Tool Box for designing parallel and low memory fingerprint bioinformatics software Efficient and fast NGS algorithms are essential to analyze the terabytes of data generated by the next generation sequencing machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. We are currently developing an open-source library dedicated to genome analysis to fasten the process of developing efficient software. The library is based on recent optimized de Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with very low memory footprint. The talk will present the algorithm principles of GATB, and its performances through various tools such as genomic assemblers or SNP callers. GATB: http://gatb.inria.fr/



Seminar
Seminars-Computational strategies for the analysis of epigenetic landscape in cancer – Valentina Boeva
Thu 8 Sep 2016 02:00 pm Institut Pasteur Amphithéâtre Jaques Monod – MONOD (66)

Computational strategies for the analysis of epigenetic landscape in cancer and their application to decipher rewiring of transcriptional regulatory networks in neuroblastoma.



Seminar
Seminars – Reconstructing a population’s past demography using whole genomes – 23 June 2016 – Flora Jay
Thu 23 Jun 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars-Gene regulatory network inference from time series: machine learning approaches – Florence D’Alché Buc
Thu 9 Jun 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

We consider the well known problem of gene regulatory network inference from time series measurements (gene expression, protein concentration) under the angle of Machine Learning. We address two different instances of this problem.



Seminar
Seminars – Logical modelling of immune cell specification and reprogramming – 26 May 2016 – Denis Thieffry
Thu 26 May 2016 02:00 pm Institut Pasteur Amphithéâtre Jaques Monod – MONOD (66)

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



Seminar
Seminars – Hierarchical Orthologous Groups – 12 May 2016 – Christophe Dessimoz
Thu 12 May 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

Time : 02:00 pm Starting Date : 12/05/2016     



Seminar
Seminars – From the exposome to the mechanome – 14 April 2016 – Marc Chadeau
Thu 14 Apr 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – Tracking evolutionary changes with ancient DNA time capsules – 7 April 2016 – Ludovic Orlando
Thu 7 Apr 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – Journée i2b2/tranSMART France pour la recherche bio-médicale – Sylvain DEMEY
Mon 4 Apr 2016 09:30 pm Institut Pasteur Auditorium Francois Jacob – BIME (26)

Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris Centre de Recherche des Cordeliers, rue de l’école de médecine, Paris



Seminar
Seminars – Bioinformatics of structured RNAs beyond energy minimization – 24 March 2016 – Yann Ponty
Thu 24 Mar 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – Human population genetics – 4 February 2016 – Lluis Quintana-Murci
Thu 4 Feb 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – P-Metagenomic Analysis Group – Paris – 29 January 2016 – Amine GHOZLANE
Fri 29 Jan 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

    Time : 02:00 pm till 05:00 pm



Seminar
Seminars – Conservation and co-evolution – 21 January 2016 – Alessandra Carbone
Thu 21 Jan 2016 02:00 pm Institut Pasteur Retrovirus room – LWOFF (22)

     Time : 02:00 pm     



Seminar
Seminars – Quality control of the transcription by (NMD) – 7 January 2016
Thu 7 Jan 2016 Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Seminars – Network biology and Salmonella infection mechanisms
Mon 7 Dec 2015 Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
Performance evaluation of DNA copy number segmentation methods
Thu 3 Dec 2015 Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
C3BI Seminars – Methodological – Identification of Novel Cell Types Using Single-Cell Transcriptome Sequencing
Wed 18 Nov 2015 Institut Pasteur

C3BI



Seminar
Protein superfamily evolution: algorithms and applications
Thu 22 Oct 2015 Institut Pasteur Retrovirus room – LWOFF (22)

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



Seminar
C3BI Seminars – Large audience – Species interactions from a mathematical modelling and algorithmic perspective
Thu 1 Oct 2015 Institut Pasteur Auditorium Francois Jacob – BIME (26)

C3BI



Seminar
C3BI Seminars – Methodological – Le Cloud Académique IFB pour les Sciences du Vivant
Thu 24 Sep 2015 Institut Pasteur Retrovirus room – LWOFF (22)

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.



Seminar
C3BI Seminars – Methodological – Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walks?
Thu 3 Sep 2015 Institut Pasteur

C3BI



Seminar
Seminars – Large audience – From Genomics to Medicine: Uncovering and targeting the genetic circuits underlying GWAS and cancer
Mon 31 Aug 2015 Institut Pasteur

C3BI



Seminar
C3BI Seminars – !hacking@pasteur – What Health : Bring to the global health the key of its own digital revolution.
Thu 27 Aug 2015 Institut Pasteur

C3BI



Seminar
C3BI Seminars – Large audience – Comparative genomics in vertebrates: from models to applications.
Thu 2 Jul 2015 Institut Pasteur

C3BI