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Bioinfo seminars

Every two weeks on Thursday at 11 a.m in Favard room (46, Ulm street), except on holidays, the Bioinformatics platform and the "Computational Bioimaging and Bioinformatics" team organize a bioinformatic seminar (topics are algorithmic, methodology, technology, software, work in progress, etc.).

To be reminded of the upcoming seminar, ask admin-bioclust at to add you to ’bioinfo-ens’ mailing list.

Most of the past seminar presentation supports are available through a link on the title.

Be careful, the first time you need to:
- Create an account on the mailing list manager (with the address first_name.last_name at for ENS people)
- Subscribe to the mailing list (even if you already receive the mails)

Once connected, you will find the document you want through the button Documents partagés.

Upcoming seminars


Past seminars



Date Speaker(s) Team Title Video
23/05/2023 Jean-Philippe Proux GENCI GENCI Presentation Video
23/03/2023 Julien Mozziconacci MNHN Deep learning for genomics Video
02/03/2023 Manon Connault IBENS Presentation of Labex MemoLife cluster: Bioclust Video
16/02/2023 Alexandra Louis IBENS Introduction au Plan de Gestion de Données : Pourquoi et Comment? Video



Date Speaker(s) Team Title Video
01/12/2022 Simon Tournier Inserm U53 (UAR CNRS 2030, Université de Paris Cité) Toward practical transparent verifiable and long-term
reproducible research using Guix
17/11/2022 Christophe Blanchet IFB (Institut Français de Bioinformatique Les Services Numériques de l’IFB pour les Sciences de la Vie Video
16/06/2022 Jeanne Bauduin IBENS - Genome Organization and Dynamics Team (Hugues Roest Crollius) (M2-rehearsal) Identification of conserved Regulatory Sequences in Ray-finned Fishes Video
16/06/2022 Ali Hamraoui IBENS - Genomics Facility Team (Morgane Thomas-Chollier) (M2-Rehearsal) -scRNA-seq with Nanopore sequencing: benchmark of approaches based on hybrid sequencing Video
02/06/2022 Julien Kot IBENS - Experimental Evolutionary Genetics Team (Henrique Teotónio) (M2- Rehearsal) - Determination and analysis of chromosomal rearrangements in the nematode worm Caenorhabditis elegans Video
19/05/2022 Nicolas Servant Institut Curie CUBIC : bioinformatics support for cancer biology Video
21/04/2022 Laurent Lacroix IBENS ECR Team Evaluating replication fork speed using nanopore sequencing Video
07/04/2022 Louna de Oliviera IBENS GDEV Team De Novo assembly of Arabidopsis thaliana genomes using Nanopore technology Video
24/03/2022 Anis Bourou IBENS Bio Comp Team Overview of Parallel Computing on GPUs Video
10/03/2022 Anthony Bretaudeau (INRIA) FAIR data analysis with Galaxy Video



Date Speaker(s) Team Title Video
28/10/2021 Ignacio Quintero (BioDiv Team) Using Julia for efficient numeric computations Video
09/09/2021 Anne-Cécile Orgerie (Myriads team - IRISA) Efficacité énergétique des infrastructures de calcul et de communication
24/06/2021 Lynda Messad IBENS - RCE Group (O.Hyrien) Use of nanopore sequencing for stalled/paused replication fork detection in yeast
03/06/2021 Etienne Jean IBENS - RCE Group (O.Hyrien) Workflow management with Nextflow Video
20/05/2021 Sophia Lambert IBENS - BioDiv Group (Hélène Morlon) Challenges in studying the macroevolution of microorganisms.
07/05/2021 Emilie Villar & Nathanaël Zweig IBENS - MPB Group (Chris Bowler) "Challenges and Technical choices on DiatOmicBase, an online tool to mine diatom omics" Video
15/04/2021 Ninon Burgos Paris Brain Institute (ICM) - ARAMIS Lab "Reproducible computer-aided diagnosis of Alzheimer’s disease using deep learning"
01/04/2021 Christophe Zimmer Pasteur Institute - Department of Computational Biology Computational imaging and modeling approaches for high resolution cell biology
18/03/2021 Leandro Quadrana IBENS - A2E Team(Vincent Colot) "Investigating transposable elements mobilization using population genomics data" Video
04/03/2021 Franklin Delehelle IBENS - DYOGEN When R & Python are not enough:
high-performance bioinformatics with Rust"
12/02/2021 Hervé Turlier CIRB - Multiscale Physics of Morphogenesis A reverse-engineering program of early embryo development combining computational and physical approaches
21/01/2021 Leandro Agudelo MIT - Computer Science & Artificial Intelligence Lab Disease resilience through tuning of genome plasticity
07/01/2021 Maël Lefeuvre IBENS - Plateforme Informatique Presentation of the Labex Memolife cluster and how to use it (simple and advanced usage of HT-Condor). Video



Date Speaker(s) Team Title Video
10/12/2020 Thomas Denecker Institut Français de Bioinformatique Les principes FAIR appliqués à la bioinformatique. (FAIR data principles applied to bioinformatics) Video
24/06/2020 Yoonjee Kang IBENS Cell type specific characterization of subtyped Colorectal Cancer using single cell RNA-seq
18/06/2020 Claire Lansonneur
Myriam Hanna
Computational study of T-cells lineage specification at single-cell resolution
Replication fork speed analysis using nanopore sequencing
11/06/2020 Louna De Oliveira IBENS Analyse bioinformatique de l’épivariation naturelle à l’aide des données de séquençage bisulfite du projet 1001 génomes d’Arabidopsis Thaliana
05/03/2020 Laurent Jourdren / Sophie Lemoine IBENS Oxford Nanopore data analysis at IBENS Genomics core facility
06/02/2020 Swann Floc’hlay / Elise Parey IBENS / IBENS Introduction to Snakemake workflow management
23/01/2020 Mathieu Bahin IBENS Bioclust & HTCondor: computing cluster at IBENS
09/01/2020 Sébastien Lemaire IBENS Characterizing the interplay between gene nucleotide composition bias and splicing



Date Speaker(s) Team Title
19/12/2019 Gilles Cottrell IRD Histoire, pratique et raisonnement des tests statistiques – Faut-il bannir la significativité ?
28/11/2019 Walter Santana Garcia IBENS D3.js: a brief introduction
14/11/2019 Bioinfo Club Bioinformatics career(s)
10/10/2019 Nathalie Lehmann IBENS Deciphering 10xGenomics and SMART-seq2 single-cell RNA-seq data with Eoulsan workflows
19/09/2019 Léa Bellenger ARTbio A galaxy tool suite to analyse Single cell RNAseq data
29/08/2019 Raphaël Bricout IBENS Automatic genome annotation using deep learning
20/06/2019 Walter Santana
Louna De Oliveira
Enhancing motif discovery approach to discover refined DNA binding motifs involved in the early development of Drosophila embryos
Caractérisation et simulation de la mécanique de coupure de la transposase Tn5 lors de la technique ATAC-seq
13/06/2019 Etienne Jean IBENS Vitesses de déplacement des fourches de réplication de l’ADN, obtenues par séquençage Nanopore
23/05/2019 Aurelien Naldi IBENS "High level" programming languages: compromises and hidden costs
11/04/2019 Chloé-Agathe Azencott Curie Institute Feature selection in high-dimensional data sets, with applications to precision medicine
04/04/2019 Bioinformatics Club Code reproducibility/reusability
21/03/2019 B. Jagla Pasteur Single cell RNAseq data analysis using an extendable shiny app
21/02/2019 Mathieu Bahin IBENS Bioclust & HTCondor: computing cluster at IBENS
07/02/2019 Justine Guegan ICM BISTAR : A pipeline for the identification of CpG differentially methylated regions from bisulfite sequencing data



Date Speaker(s) Team Title
13/12/2018 C. Bon MNHN Challenges in NGS analyses of ancient DNA
08/11/2018 Bioinformatics Club Publishing in bioinformatics
11/10/2018 Yoann Dufresne Pasteur 64 BPM (64 bits Beautiful Pattern Matching): When engineering outperform research algorithms
21/06/2018 F. Habibolahi
Guillaume Delevoye
Analysis and Interpretation of short time series gene expression data in the case of Listeria monocytogenes infection
Analyse de la méthylation de l’ADN par séquençage PacBio : résolution molécule unique, brin unique, nucléotide unique chez Paramecium tetraureliae
15/06/2018 Hatim El Jazouli
Geoffray Brelurut
IBENS Single-cell transcriptional analysis (Drop-Seq & SMART-Seq2 protocols) using the workflow engine Eoulsan
Evaluation, intégration et application à des données de cellules immunitaires d’outils d’analyse pour le scRNA-Seq
31/05/2018 Bérengère Laffay IBENS Développement d’outils d’analyse de données RNA-Seq dédiés à la technlogie Oxford Nanopore
17/05/2018 Auréliane Gailliègue MNHN Automatic reconstruction from skeleton point clouds of MNHN Galleries
19/04/2018 Guillaume Louvel IBENS Hypothesis testing with a phylogeny: the challenge of accounting for phylogenetic non-independence (part 2)
05/04/2018 Bioinformatics Club Notebooks
22/03/2018 Guillaume Louvel IBENS Hypothesis testing with a phylogeny: the challenge of accounting for phylogenetic non-independence (part 1)
08/03/2018 Bioinformatics Club Python pandas library
08/02/2018 Nikita Menezes IBENS High throughput imaging of replicating DNA using Nanochannel technology
25/01/2018 Mathieu Bahin IBENS Bioclust & HTCondor: computing cluster at IBENS
11/01/2018 Aurélie Teissandier Curie Institute Analysis of transposable elements within heterogeneous NGS data



Date Speaker(s) Team Title
07/12/2017 Benoit Noel IBENS When make meets Python: building bioinformatic pipelines with Snakemake
23/11/2017 Mandy Cadix Curie Institute 3-SMART: Bioinformatic analysis of intronic polyadenylation regulation
09/11/2017 Amira Kramdi IBENS ATAC-seq technique and data analysis
19/10/2017 Thomas Cokelear Pasteur Institute Sequana: a set of flexible genomics pipelines for processing and reporting NGS analysis
28/09/2017 Lambert Moyon
Felipe Delestro
Predict me if you can: the 80k 2D plots classification challenge
14/09/2017 Ouardia Ait-Mohamed IBENS PacBio data analyses: studying DNA modification
22/06/2017 Baptiste Ameline
Antoine de France
Toward a functional map of the human germline genome
Analyse génétique des TEs chez A. thaliana par l’exploitation du ’1001 Genomes’ Project
15/06/2017 Aurélien Birer
Lionel Ferrato
IBENS Développement d’un outil pour l’analyse de run MinIon
RNA-Seq pipeline for nanopore data analysis: Toullig
01/06/2017 Nathalie Lehmann IBENS Analysis of the diversity of human plasmacytoid pre-dendritic cells (pDC) at a single-cell level
04/05/2017 Sophie Lemoine IBENS MinION: analyses first steps and pitfalls
20/04/2017 Felipe Delestro IBENS Dealing with images: formats and tools for quality results
30/03/2017 Nicolas Lomenie LIPADE Tissue analysis with graphs
16/03/2017 Mohamed Elati Genopole Reconstruction and interrogation of regulatory networks
02/03/2017 Iuliana Ionita-Laza Columbia University Predicting tissue-specific functional effects of noncoding variation
02/02/2017 Mathieu Bahin IBENS Introduction to bioclust and Condor
19/01/2017 Felipe Delestro IBENS Jupyter Notebook
05/01/2017 V. D. Bohler IFB-core Cyber Strategy for Life Sciences Data at the French Institute of Bioinformatique



Date Speaker(s) Team Title
08/12/2016 Laurent Jourdren
Céline Hernandez
Eoulsan new features for RNA-seq and ChIP-seq analyses
24/11/2016 Amine Ghozlane Pasteur Institute SHAMAN: a shiny application for metagenomic analysis
10/11/2016 L. Martignetti
L. Calzone
Institut Curie ROMA: Pathway-Based Analysis of Multi-omics data for tumour subtypes classification
20/10/2016 Alexis Renault IBENS A new interface to monitor bioclust activity
15/09/2016 Benoit Noel IBENS ALFA: Annotation Landscape For Aligned reads
23/06/2016 Geoffray Brelurut IBENS Single Cell RNA-Seq data analysis
09/06/2016 Nikita Menezes
Guillaume Louvel
Improvement of DNA molecule detection using NGM technology
Duplicate genes and adaptation in Vertebrates
26/05/2016 Maud Gautier
Cédric Michaud
Epigenome dynamics during root cell differentiation in Arabidopsis thaliana
Extension d’un workflow d’analyse de ChIP-seq et comparaison de protocoles expérimentaux
12/05/2016 Lambert Moyon IBENS Biological network analysis: using Python ’igraph’ and ’networkx’
14/04/2016 Alexandra Louis IBENS Genomicus: fast and intuitive comparative genomics in eukaryotes
31/03/2016 Quentin Viautour IBENS Comparison of absolute quantification methods for high throughput qPCR Data
17/03/2016 Samuel Collombet IBENS Chromatin Conformation Capture data analysis
18/02/2016 Valentina Boeva Institut Curie Computational analysis of epigenetic landscape and chromatin states in cancer
04/02/2016 Gilles Rigaill URGV Constrained segmentation and supervised penalty learning for peak detection in Chip-seq
21/01/2016 G. Cottrell MERIT Introduction aux tests statistiques: fondements et discussion sur quelques contre-vérités et écueils courants (Video)
07/01/2016 Yves Clément IBENS Hidden Markov Models: detecting regions under selection in phylogenetics



Date Speaker(s) Team Title
10/12/2015 Morgane Thomas-Chollier IBENS Using RSAT for cis-regulatory element analyses
26/11/2015 Marie-Laure
URGV Differential analysis of RNA-seq data: method comparison with synthetic data
12/11/2015 Mathieu Bahin IBENS Condor: usage and new configuration
15/10/2015 Leïla Bastianelli IBENS Using bioclust to optimize peak detection parameters for CLIP-seq
08/10/2015 Laurent Jourdren IBENS Eoulsan 2: Facilitating expansion to new NGS tools and execution platforms
17/09/2015 S. Perrin IBENS Aozan : Management de séquenceur Nextseq et validation de l’application par test d’intégration
25/06/2015 Benoît Noël
Quentin Viautour
Pipeline d’analyse de Ribosome Profiling pour comparer la traduction de deux contextes cellulaires
Nouvelle méthode d’analyse adaptée au haut débit pour la PCRq
11/06/2015 Swann Floc’hlay
Lambert Moyon
Logical modelling of the regulatory network governing Dorsal-Ventral axis specification in the sea urchin P. Lividus
Regulatory circuits in the human genome from enriched motifs in putative enhancers of co-regulated genes
28/05/2015 Mathieu Bahin IBENS DAGMan: a meta-scheduler for Condor
30/04/2015 L. Al-Shikhley IBENS Genome-wide pathway
analysis: the example of GSEA method
16/04/2015 M. van den Beek UPMC Reproducible research using Galaxy, Docker and the Tool factory
02/04/2015 Joseph Lucas IBENS A custom python API to launch condor jobs
19/03/2015 Achal Rastogi IBENS GFF-Ex: A Genome feature extraction package
05/03/2015 C. Hernandez IBENS Wrapping your own tool in Galaxy: an introduction
19/02/2015 Laurent Jourdren IBENS Docker: The next big thing in application deployment?
05/02/2015 J. Lucas
L. Tittmann
IBENS Magsimus: simulating genome evolution during millions of years
22/01/2015 C. Hernandez IBENS Generating dynamic documents (in R) with knitR
08/01/2015 J. Scheiber BioVariance Analyzing Next generation sequencing data – What to get out of it?



Date Speaker(s) Team Title
11/12/2014 F. Delestro IBENS Setting up a Virtual Environment together with an IPython Notebook workspace
27/11/2014 Elsa Bernard Mines Fast isoform detection from RNA-Seq data with network flow techniques
16/10/2014 Samuel Collombet IBENS ECCB 2014: panorama of new softwares for the analysis of RNA isoforms from RNAseq
02/10/2014 E. Del Nery Institut Curie The BioPhenics screening facility, an exploration of opportunities and challenges facing image-based phenotypic discovery
18/09/2014 V. Sibut Institut Curie How do IPA can help you to discover the interactions between signaling pathways in cancer from omics data
26/06/2014 A. Lermine Institut Curie Galaxy
19/06/2014 P.-M. Chiaroni IBENS Computational analysis of ChIP-seq datasets to decipher the role of epigenetic factors in bone formation
12/06/2014 France Rose IBENS Développement d’algorithmes et d’outils d’analyse d’image pour l’étude de facteurs impliqués dans l’orientation de la division des cellules eucaryotes
05/06/2014 M. Kassam IBENS Introduction of Galaxy at the Computational biology and Bioinformatics platform of IBENS
15/05/2014 Alexandra Louis IBENS The computing cluster of the bioinformatic and computational biology platform at IBENS
03/04/2014 P. Hupé Institut Curie Bioinformatics for Operational Personalized Medicine in Oncology: application to the SHIVA clinical trial
20/03/2014 P.
Institut Curie Managing microscopic image life cycle from acquisition to archiving, and including analysis: experience from Curie Data Center
06/03/2014 F. de Chaumont Pasteur Institut Icy
06/02/2014 Sophie Lemoine IBENS Comptage de lectures en fonction des annotations (par gene, par transcrit, ...)
23/01/2014 Laurent Jourdren IBENS Eoulsan : High Throughput Sequencing Data Analysis at Genomic Paris Centre
09/01/2014 S. Perrin IBENS Aozan: An automated post sequencing data processing pipeline



Date Speaker(s) Team Title
20/12/2013 J. Ibn-Salem Max Planck Institute ChIP-exo data analysis for detecting protein-DNA interactions with high resolution
12/12/2013 Philippe Mailly College de France OMERO: an open-source software for the storage and manipulation of biological microscopy data
28/11/2013 Anne Danckaert Pasteur Institute Image in Microscopy: From Analysis to Statistics
14/11/2013 Samuel Collombet IBENS Circos, a visualization tool for genomic data