A5087487293- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Shoulder Injury and Treatment
- Sports injuries and prevention
- Molecular Biology Techniques and Applications
- Traumatic Brain Injury Research
- Cancer-related molecular mechanisms research
- Biofuel production and bioconversion
- Protein Structure and Dynamics
- Cardiac Arrest and Resuscitation
- Algorithms and Data Compression
- Genomics and Chromatin Dynamics
- Cardiovascular Effects of Exercise
- Data Visualization and Analytics
- Sports Performance and Training
- CRISPR and Genetic Engineering
- Genetics, Bioinformatics, and Biomedical Research
- Insect symbiosis and bacterial influences
Laboratoire de Biométrie et Biologie Evolutive
2014-2024
Université Claude Bernard Lyon 1
2013-2023
Centre National de la Recherche Scientifique
2013-2023
Institut national de recherche en informatique et en automatique
2007-2022
Montreal General Hospital
2022
McGill University
1998-2022
Centre Inria de l'Université Grenoble Alpes
2008-2020
Université Grenoble Alpes
2015-2020
Centre Paul Albert-Février
2018
Laboratório Nacional de Computação Científica
2013
Objective A study to examine the incidence and characteristics of concussions among Canadian university athletes during 1 full year football soccer participation. Design Retrospective survey. Participants Three hundred eighty 240 players reporting 1999 fall training camp. Of these, 328 201 returned a completed questionnaire. Main Outcome Measures Based on self-reported symptoms, calculations were made determine number experienced previous or participation, duration time for return play, any...
High-throughput sequencing of cDNA libraries constructed from cellular RNA complements (RNA-Seq) naturally provides a digital quantitative measurement for every expressed molecule. Nature, impact and mutual interference biases in different experimental setups are, however, still poorly understood—mostly due to the lack data intermediate protocol steps. We analysed multiple RNA-Seq experiments, involving sample preparation protocols platforms: we broke them down into their common—and...
The classic organization of a gene structure has followed the Jacob and Monod bacterial model proposed more than 50 years ago. Since then, empirical determinations complexity transcriptomes found in yeast to human blurred definition physical boundaries genes. Using multiple analysis approaches we have characterized individual mapping on chromosomes 21 22. Analyses locations 5′ 3′ transcriptional termini 492 protein coding genes revealed that for 85% these extend beyond current annotated...
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of effect. Recently, alignment-free based on k-mer composition proven their ability explore the accessory genome. However, they lead redundant descriptions and which are sometimes hard interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable variants associated with distinct phenotypes. Relying...
Abstract Myotonic dystrophy (DM) is caused by the expression of mutant RNAs containing expanded CUG repeats that sequester muscleblind-like (MBNL) proteins, leading to alternative splicing changes. Cardiac alterations, characterized conduction delays and arrhythmia, are second most common cause death in DM. Using RNA sequencing, here we identify novel alterations DM heart samples, including a switch from adult exon 6B towards fetal 6A cardiac sodium channel, SCN5A . We find MBNL1 regulates...
The classic view of metabolism as a collection metabolic pathways is being questioned with the currently available possibility studying whole networks. Novel ways decomposing network into modules and motifs that could be considered building blocks are suggested. In this work, we introduce new definition motif in context Unlike previous works on (other) biochemical networks, not based only topological features. We propose instead to use an alternative functional nature components form motif,...
Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts been identified among ESTs isolated several organisms using high throughput RNA sequencing. The few corresponding protein products characterized mostly result chromosomal translocations are associated with cancer. Here, we systematically establish some of genuinely expressed in human cells. Using...
Abstract Background In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling full transcripts. Based on fundamental idea that each polymorphism corresponds to a recognisable pattern De Bruijn graph constructed from reads, propose general model for all such graphs. We then introduce an exact algorithm, called K IS S PLICE , extract alternative splicing events. Results show enables identify more...
Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use reference genome. As non-model organisms are increasingly investigated, the need for reference-free has been amplified. Most of existing have fundamental limitations: they can only call SNPs exactly two datasets, and/or require prohibitive amount computational resources. The method we propose, discoSnp, detects both heterozygous and...
Abstract Our vision of DNA transcription and splicing has changed dramatically with the introduction short-read sequencing. These high-throughput sequencing technologies promised to unravel complexity any transcriptome. Generally gene expression levels are well-captured using these technologies, but there still remaining caveats due limited read length fact that RNA molecules had be reverse transcribed before Oxford Nanopore Technologies recently launched a portable sequencer which offers...
To examine the incidence and characteristics of concussions for one season in Canadian Football League (CFL).Retrospective survey.289 players reporting to CFL training camp. Of these, 154 had played during 1997 season.Based on self-reported symptoms, calculations were made determine number experienced previous season, duration time return play after concussion, any associated risk factors concussions.Of all athletes who 44.8% symptoms a concussion. Only 18.8% these concussed recognized they...
SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them currently well developed model species, but rely on the availability of (good) reference genome, and therefore cannot be applied non-model species. They also mostly tailored whole genome (re-)sequencing experiments, whereas in many cases, transcriptome sequencing can used as cheaper alternative which already enables located transcribed...
Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from organisms; they might represent functional proteins produce disease phenotypes. The ChiTaRS database of Transcripts RNA-Sequencing data (http://chitars.bioinfo.cnio.es/) collects than 16 000 chimeric humans, mice fruit flies, 233 chimeras confirmed by RNA-seq reads ∼2000 cancer breakpoints. indicates expression tissue specificity these...
Objective A pilot study to examine the incidence and characteristics of concussions for one season university football soccer. Design Retrospective survey. Participants 60 70 soccer players reporting 1998 fall training camp. Of these, 44 52 returned a completed questionnaire. Main Outcome Measures Based on self-reported symptoms, calculations were made determine number experienced during previous season, duration time return play any associated risk factors concussions. Results all athletes...
Objective: This is a retrospective study of 98 hockey players who underwent 107 surgical explorations for refractory lower abdominal and groin pain that prevented them from playing at an elite level. Design: Retrospective chart review combined with complete follow-up examination questionnaire. Setting: The were treated in ambulatory care university tertiary centre. Patients: A total intractable preventing their play. Follow-up was 100%. Intervention: Each player had repair tear the external...
Abstract Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most start by mapping the reads an annotated reference genome, but some a de novo assembly reads. In this paper, we present systematic comparison mapping-first approach (F RL ine ) and assembly-first (K is S plice ). We applied these independent datasets found...
Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations RNU4ATAC , transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi–Linder (TALS/MOPD1), Roifman (RFMN), Lowry–Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on few RFMN patient cells, none performed...
Folding and intermingling of chromosomes has the potential bringing close to each other loci that are very distant genomically or even on different chromosomes. On hand, genomic rearrangements also play a major role in reorganisation proximities. Whether same involved both mechanisms been studied case somatic rearrangements, but never from an evolutionary standpoint. In this paper, we analysed correlation between two datasets: (i) whole-genome chromatin contact data obtained human cells...
Groin injuries are a major diagnostic and therapeutic challenge in sports medicine. The aim of this review is to describe the clinical surgical findings associated with an atypical lower abdominal pain syndrome occurring elite ice hockey players.Eleven professional players from various National Hockey League teams were referred Montreal General Hospital between 1989 1996, suffering refractory paraesthesia abdomen. Despite use conventional investigative procedures such as physical...