Bioinformatics & Genetics Team

We create tools, databases, for research

About Us

Our team has been involved for years in different topics.

The analysis of the many variations identified during the sequencing process of genes. In order to identify causative mutations, especially if they are missense mutations or null substitutions that only impact mRNA, we developed two tools: UMD-Predictor® to predict the pathogenicity of missense mutations, and the Human Splicing Finder® (HSF) (http://www.umd.be/HSF3/) to identify splicing signals and evaluate the impact of mutations on splicing. We currently develop the UMD-High Throughput Sequencing system (UMD-HTS®) that integrates algorithms from UMD-Predictor® and HSF® in order to allow a rapid selection of variations of interest from large-scale sequencing experiment.

Locus Specific Databases (LSDBs). Since 1994, our team developed the Universal Mutation Database system (UMD®) an international reference system for the creation of Locus Specific Databases (LSDBs).

Patient registries. We also developed through years, patient registries for neuromuscular rare diseases and others.

Our Tools

Our Team develops several tools, databases and registries:

UMD databases

Locus-specific databases (LSDBs) to collect annotated mutations from several genes

Human Splicing Finder

The reference tool for splicing analysis and pathogenicity prediction

UMD-Predictor

The most accurate pathogenicity prediction system for cDNA substitutions

VarAFT

Desktop Application for annotation and filtration of variants from NGS data

BANCCO

The french databases of Copy Number Variations

RDVD

The french Rare Disease Variant Database

Skip-e

System to select AON to induce exon skipping or gene silencing

CrawFish

Innovative system to design trans-splicing gene therapy for genetic diseases

Registries

Patients registries for genetic diseases

Publications

Hardware

Si stante, hoc natura videlicet vult, salvam esse se, quod concedimus ses haec dicturum fuisse

International

Erdo lide, nora porodo filece, salvam esse se, quod concedimus ses haec dicturum fuisse

RD-Connect

FP7 EU-funded project
We are leading the clinical bioinformatics workpackage. With our partners, we developed several tools to help researchers analyse omics data and identify targets for potential therapies. These include variant analysis and annotation tools as well as therapeutic prediction tools and gene-drug interaction resources.
Our team is labelled as an IFB platform (French Bioinformatics Institute) and a French Elixir Node. We provide to the community data, tools, trainings and expertises in human genetics and bioinformatics to foster data collection and sharing, to speed up gene discovery and disease-causing mutations identification as well as new therapeutic developments to cure rare genetics diseases.

An IFB French Elixir Node

EU bioinformatics network

TREAT-NMD Alliance

International Project
With national curators from more than 50 countries, we have been able to create the TREAT-NMD global registries for DMD and SMN1 mutations responsible for Duchenne/Becker Muscular Dystrophy and Spinal Muscular Atrophy. Those international registries are regularly used for feasibility studies and patients recruitment for clinical trials.
The International Consortium for Personalised Medicine (ICPerMed) brings together over 30 European and international partners representing ministries, funding agencies and the European Commission (EC). Together, we work on coordinating and fostering research to develop and evaluate personalised medicine approaches.

International Consortium for Personalised Medicine

Our Team

Pr. Christophe Béroud

Team Leader

Dr. Gwenaelle Collod-Béroud

Researcher

Dr. David Salgado

Research Engineer Bioinformatic

Jean-Pierre Desvignes

Engineer Bioinformatic

Céline Guien

Engineer Bioinformatic

Marc Garibal

Engineer Bioinformatic

Coralie Grattepanche

PhD student

Mélanie Corcuff

PhD student

Contact US