BioComputing Hub
Missions
The Biocomputing Hub goal is to lead and promote bioinformatics in the LBMC. The center actions are organized around 3 axes:
1. the development of standards for the laboratory
The Biocomputing Hub provides guides and toolboxes to facilitate collaboration between members of the laboratory.
For example, the Hub Biocomputing established:
- a guide of good practices to standardize the format of the projects.
- a data management guide to back up and share more easily the data generated in the laboratory
- a Gitlab server to share codes and scripts
2. the training
To make these tools accessible to all members of the laboratory and promote the sharing of methods, the Biocomputing Hub organizes training.
These training courses are often given in collaboration with the other laboratories of SFR-Bioscience and its Conseil d’Analyse Numérique (CAN).
3. Increasing the number projects between biologists and bioinformaticians
Benefiting from the axes 1 and 2, the members of the Biocomputing Hub are also involved in projects supported by members of the laboratory.
These projects are of three types:
- Support to biologists in the processing and analysis of their data
- Co-supervision of bioinformatics students
- Emergency interventions for deadlines related to publications
Projects
2021 Bernard team: Developpment of a normalization method for calibrated Chip-Seq data
To be able to analyze global variations of condesine occupancy on the whole genome of S. pombe we have developed a nextflow pipeline implementing the normalization proposed by Hu et al. We improved this normalization by proposing a calibrated normalization using the input data. This improvement allowed us to take into account the variations of chromatin accessibility in the observed signal as well as to be able to look at the condensin occupation at the repeated regions of the genome.
2019 ECBN team: Genome analysis of Mesorhabditis belari:
To better understand the mechanisms behind the reproductive strategy of the worm Mesorhabditis belari, which produces 9% of males, we have produced a hybrid assembly of its genome from WGS paired-end sequence (100 bp) at 200x as well as from long read at 10x (nanopore). The annotation of this genome was made using RNA-Seq data for the genes and DNA-Seq data for the repeated elements. We then used this assembly to identify sex-specific regions of the genome, as well as sex-specific SNPs. These SNPs and regions could then be used to design PCR probes or perform DNA FISH experiments.
2017 PRIO team: Automatic analysis of FACS data
Writing of an R package for the analysis of the stability of the TAL1 protein, involved in the development of acute T cell leukemia. This study was carried out by establishing T lymphocyte lines (Jurkat) expressing two fluorescent proteins: GFP and RFP fused to our protein, from the same mRNA (use of “self-cleaving sequences”). The RFP to GFP fluorescence ratio is used to assess the stability of the protein fused to RFP. The R package to be developed allows you to directly analyze FACS output files, and to perform automatic gating steps before analyzing data from dozens of different proteins for thousands of cells with a linear model.
You can consult the list of projects on which the members of the Hub Biocomputing intervene.
Internships
You can consult the list of internship subjects co-supervised or supervised by the Hub Biocomputing
Composition
The Biocomputing Hub is composed of 5 permanent members under the direction of Daniel Jost, Franck Mortreux and Laurent Modolo:
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Ghislain DURIF, IR CNRS (100%)
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David CLUET, IR CNRS (20%)
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Nicolas Fontrodona, IE, ENS (30%)
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Stéphane JANCZARSKI, IE CNRS (20%)
- Stève de BOSSOREILLE, IR CNRS (20%)
The Hub members are in charge of the executing the missions of the Biocomputing Hub such as training and the implementation of standards as well as accompanying or co-supervising projects, hold by LBMC members’.
Biocomputing Committee
The Biocomputing Committee is made up of 15 members, meeting several times a year to decide on the future actions of the Hub Biocomputing.
members | ||
---|---|---|
Audrey Lapendry | Aurèle Piazza | Cecile Bedet |
Daniel Jost | David Cluet | Fabien Duveau |
Franck Mortreux | Franck Picard | Helene Polveche |
Laurent Modolo | Marie Semon | Maxime Lepetit |
Nicolas Fontrodona | Stéphane Janczarski | Steve de Bossoreille |
During these meetings, the Committee will:
- Create surveys to identify the needs of the members of the laboratory
- Plan training courses
- Create animations around bioinformatics
The minutes of the meetings of the Committee are available online
Steering Committee
A Steering Committee, made up of team leaders, is responsible for evaluating and awarding projects supported by members of the laboratory.
members | ||
---|---|---|
Daniel Jost | Didier Auboeuf | Gaël Yvert |
Marie Semon | Pascal Bernard | Franck Mortreux |
These projects are then attributed to the members of the Hub Biocomputing.
The list of these projects is available online
Biocomputing Hub Publications
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- 2022 Titration of Apparent In-Cellula Affinities of Protein-Protein Interactions.
Journal : Chembiochem - Link to PubMed entry
- 2021 Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny.
Journal : Wiley Interdiscip Rev RNA - Link to PubMed entry
- 2020 Gradient in cytoplasmic pressure in germline cells controls overlying epithelial cell morphogenesis
Journal : PLoS Biol -
- 2020 Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans.
Journal : Commun Biol - Link to PubMed entry
- 2020 Spen modulates lipid droplet content in adult Drosophila glial cells and protects against paraquat toxicity.
Journal : Sci Rep - Link to PubMed entry
- 2020 A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities
Journal : Molecular & Cellular Proteomics -
- 2019 Characterizing the interplay between gene nucleotide composition bias and splicing
Journal : Genome Biol -
- 2019 Interplay between coding and exonic splicing regulatory sequences
Journal : Genome Res -
- 2019 Males as somatic investment in a parthenogenetic nematode.
Journal : Science - Link to PubMed entry
- 2018 Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription.
Journal : Elife - Link to PubMed entry
- 2018 The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation.
Journal : Nucleic Acids Res - Link to PubMed entry
- 2018 Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3 HDAC complex
Journal : bioRxiv -
- 2017 Identification of protein features encoded by alternative exons using Exon Ontology
Journal : Genome Res -
- 2017 Nerve Growth Factor Signaling from Membrane Microdomains to the Nucleus: Differential Regulation by Caveolins.
Journal : Int J Mol Sci - Link to PubMed entry
- 2017 The C. elegans SET-2/SET1 histone H3 Lys4 (H3K4) methyltransferase preserves genome stability in the germline.
Journal : DNA Repair (Amst) - Link to PubMed entry
- 2022 Titration of Apparent In-Cellula Affinities of Protein-Protein Interactions.