A5069731113- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Genetic Associations and Epidemiology
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- DNA Repair Mechanisms
- Bayesian Modeling and Causal Inference
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Genetic Mapping and Diversity in Plants and Animals
- DNA and Nucleic Acid Chemistry
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Spine and Intervertebral Disc Pathology
- Medical Imaging and Analysis
- Data Mining Algorithms and Applications
- Advanced biosensing and bioanalysis techniques
- Musculoskeletal pain and rehabilitation
- CRISPR and Genetic Engineering
- Genetic and phenotypic traits in livestock
- RNA modifications and cancer
- Radiomics and Machine Learning in Medical Imaging
- Microbial Metabolic Engineering and Bioproduction
- ECG Monitoring and Analysis
Université Toulouse III - Paul Sabatier
2015-2024
Université de Toulouse
2017-2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2022-2024
Département Mathématiques et Informatique Appliquées
2024
Mathématiques et Informatique Appliquées
2024
Université de Rennes
2024
Inserm
2024
Centre National de la Recherche Scientifique
2011-2023
Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération
2018-2023
Centre de Biologie du Développement
2021
Abstract The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in repair has been investigated 1,2 , chromosome folding these processes remains unclear 3 . Here we report that, after production double-stranded breaks (DSBs) mammalian cells, ATM drives formation a new compartment (D compartment) through clustering damaged topologically associating domains, decorated with γH2AX and 53BP1. This forms by mechanism that consistent...
In data analysis, latent variables play a central role because they help provide powerful insights into wide variety of phenomena, ranging from biological to human sciences. The tree model, particular type probabilistic graphical models, deserves attention. Its simple structure - allows and efficient inference, while its capture complex relationships. the past decade, model has been subject significant theoretical methodological developments. this review, we propose comprehensive study...
Abstract Common variants at many loci have been robustly associated with asthma but explain little of the overall genetic risk. Here we investigate role rare (<1%) and low-frequency (1–5%) using Illumina HumanExome BeadChip array in 4,794 cases, 4,707 non-asthmatic controls 590 case–parent trios representing European Americans, African Americans/African Caribbeans Latinos. Our study reveals one missense mutation GRASP gene that is Latino sample ( P =4.31 × 10 −6 ; OR=1.25; MAF=1.21%) two...
In the cell nucleus, each chromosome is confined to a territory. This spatial organization of chromosomes plays crucial role in gene regulation and genome stability. An additional level has been discovered at scale: segregation into open closed chromatins form two genome-wide compartments. Although considerable progress made our knowledge chromatin organization, fundamental issue remains understanding its dynamics, especially cancer. To address this issue, we performed mapping interactions...
Discovering the genetic basis of common diseases in human genome represents a public health issue. However, dimensionality data (up to 1 million markers) and its complexity make statistical analysis challenging task. We present an accurate modeling dependences between markers, based on forest hierarchical latent class models which is particular probabilistic graphical models. This model offers adapted framework deal with fuzzy nature linkage disequilibrium blocks. In addition, can be reduced...
Abstract Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in genes handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), entails R-loop accumulation dissolution. Here, we uncover function for the Bloom RecQ helicase (BLM) TC-DSBR human cells. BLM is recruited transcription dependent-manner at DSBs where it fosters resection, RAD51 binding accurate Homologous Recombination repair....
Antiretroviral-naive HIV-positive individuals contribute to the transmission of drug-resistant viruses, compromising first-line therapy. Using phylogenetic inference, we quantified proportion transmitted drug-resistance originating from a treatment-naive source.Using novel phylotype-based approach, 24 550 HIV-1 subtype B partial pol gene sequences UK HIV Drug Resistance database were analysed. Ongoing drug resistance amongst was identified as phylotypes at least three with one shared...
Recent advances in long-range Hi-C contact mapping have revealed the importance of 3D structure chromosomes gene expression. A current challenge is to identify key molecular drivers this structure. Several genomic features, such as architectural proteins and functional elements, were shown be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression those features that positively or negatively influence border establishment...
DNA is a complex molecule carrying the instructions an organism needs to develop, live and reproduce. In 1953, Watson Crick discovered that composed of two chains forming double-helix. Later on, other structures were shown play important roles in cell, particular G-quadruplex (G4). Following genome sequencing, several bioinformatic algorithms developed map G4s vitro based on canonical sequence motif, G-richness G-skewness or alternatively features including k-mers, more recently machine/deep...
Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause abnormal chromosomal rearrangements associated with cancer. Recent techniques allow genome-wide mapping at high resolution, enabling comprehensive study their origins. However, these are costly challenging. Hence, we devise a computational approach to predict using epigenomic chromatin context, for which public data readily available ENCODE project. We...
Abstract Motivation Genome-wide association studies have systematically identified thousands of single nucleotide polymorphisms (SNPs) associated with complex genetic diseases. However, the majority those SNPs were found in non-coding genomic regions, preventing understanding underlying causal mechanism. Predicting molecular processes based on DNA sequence represents a promising approach to understand role SNPs. Over past years, deep learning was successfully applied regulatory prediction...
Abstract Purpose Lumbar spinal stenosis (LSS) is a condition affecting several hundreds of thousands adults in the United States each year and associated with significant economic burden. The current decision-making practice to determine surgical candidacy for LSS often subjective clinician specific. In this study, we hypothesize that performance artificial intelligence (AI) methods could prove comparable terms prediction accuracy panel spine experts. Methods We propose novel hybrid AI model...
Abstract Objectives To develop a three-stage convolutional neural network (CNN) approach to segment anatomical structures, classify the presence of lumbar spinal stenosis (LSS) for all 3 types: central, lateral recess and foraminal assess its severity on spine MRI demonstrate efficacy as an accurate consistent diagnostic tool. Methods The model was trained 1635 annotated studies consisting T2-weighted sagittal axial planes at each vertebral level. Accuracy evaluated external validation set...
Abstract The recent development of deep learning methods have undoubtedly led to great improvement in various machine tasks, especially prediction tasks. This type also been adapted answer problems bioinformatics, including automatic genome annotation, artificial generation or phenotype prediction. In particular, a specific method, called graph neural network (GNN) has repeatedly reported as good candidate predict phenotypes from gene expression because its ability embed information on...
Abstract Despite their central role in transcription, it has been difficult to define universal sequences associated eukaryotic promoters. Within chromatin context, recruitment of the transcriptional machinery requires opening promoter but how DNA elements could contribute this process remained elusive. Here, we show that G-quadruplex (G4) secondary structures are highly enriched mammalian core elements. G4s located at deepest point nucleosome exclusion promoters and correlate with maximum...
The three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression and DNA replication regulations. mechanisms by which molecular drivers functionally organize 3D genome, such as topologically associating domains (TADs), remain be explored. Current approaches consist in assessing enrichments or influences proteins at TAD borders. Here, we propose a TAD-free model directly estimate blocking effects architectural proteins,...
Study Design Medical vignettes. Objectives Lumbar spinal stenosis (LSS) is a degenerative condition with high prevalence in the elderly population, that associated significant economic burden and often requires surgery. Prior authorization of surgical candidates required before patients can be covered by health plan must approved medical directors (MDs), which subjective clinician specific. In this study, we hypothesized prediction accuracy machine learning (ML) methods regarding comparable...
Abstract Background Typical analysis of time-series gene expression data such as clustering or graphical models cannot distinguish between early and later drug responsive targets in cancer cells. However, these genes would represent good candidate biomarkers. Results We propose a new model - the dynamic time order network to connect targets. This is constructed based on an integrated differential equation. Spline regression applied for accurate modeling variation expressions. Then likelihood...
Abstract Background/Aim In higher eukaryotes, the three-dimensional (3D) organization of genome is intimately related to numerous key biological functions including gene expression, DNA repair and replication regulations. Alteration 3D organization, in particular topologically associating domains (TADs), detrimental organism can give rise a broad range diseases such as cancers. Methods Here, we propose versatile regression framework which not only identifies TADs fast accurate manner, but...
We describe a novel probabilistic graphical model customized to represent the statistical dependencies between genetic markers, in Human genome. Our proposal relies on forest of hierarchical latent class models. The motivation is reduce dimension data be further submitted association tests with respect diseased/non diseased status. A generic algorithm, CFHLC, has been designed tackle learning both structure and probability distributions. first implementation shown tractable benchmarks...