A5028521086- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Genomics and Chromatin Dynamics
- Developmental Biology and Gene Regulation
- RNA modifications and cancer
- Metabolomics and Mass Spectrometry Studies
- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Single-cell and spatial transcriptomics
- Liver Disease Diagnosis and Treatment
- Diabetes and associated disorders
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Advanced Glycation End Products research
- Mycobacterium research and diagnosis
- Hepatitis C virus research
- Protein Structure and Dynamics
- Cancer Genomics and Diagnostics
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
Institut de Biologie Intégrative de la Cellule
2020-2023
Centre National de la Recherche Scientifique
2015-2022
CEA Paris-Saclay
2020-2022
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2020-2022
Université Paris-Saclay
2020-2022
Inserm
1998-2021
École Normale Supérieure - PSL
2015-2021
Institut de Biologie de l'École Normale Supérieure
2016-2021
Université Paris Sciences et Lettres
2016-2021
Université Paris-Sud
2020
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases software tools in different areas life sciences. Scientists can henceforth access seamlessly a wide range domains, such proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual (databases, web-based...
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cisregulatory elements in genome sequences.Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding (quality assessment, comparisons and clustering), (iii) comparative genomics (iv) regulatory variations.Nine new programs have been added 43 described 2011 NAR Web Software Issue, including tool extract sequences from list...
Abstract High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality Reduction (jDR) methods among the most efficient approaches. However, several jDR available, urging need for a comprehensive benchmark with practical guidelines. We perform systematic evaluation nine representative using three complementary benchmarks. First, we evaluate their...
Abstract Motivation: The study of genetic regulatory networks has received a major impetus from the recent development experimental techniques allowing measurement patterns gene expression in massively parallel way. This progress calls for appropriate computer tools modeling and simulation regulation processes. Results: We present Genetic Network Analyzer (GNA), tool networks. is based on qualitative method that employs coarse-grained models use GNA illustrated by case network genes...
The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction bound genomic regions. To identify sequences responsible for recruitment this transcription factor (TF) individual loci, we turned high-resolution ChIP-exo approach. We exploited signal by determining footprint profiles TF binding single-base-pair resolution using ExoProfiler, computational pipeline based on motifs. When applied our GR and few available public data sets, find...
The logical formalism is well adapted to model large cellular networks, in particular when kinetic data are scarce. This tutorial focuses on this well-established qualitative framework. Relying GINsim (release 3.0), a software implementing formalism, we guide the reader step by towards definition, analysis and simulation of four-node mammalian p53-Mdm2 network.
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times additional manual steps. The accessibility and reproducibility such is challenging, as publications often overlook analysis details, because some these may be difficult to install, and/or have a steep learning curve. CoLoMoTo Interactive Notebook provides unified environment edit, execute, share, reproduce analyses qualitative...
CD4+ T cells recognize antigens through their cell receptors (TCRs); however, additional signals involving costimulatory receptors, for example, CD28, are required proper activation. Alternative have been proposed, including members of the Toll-like receptor (TLR) family, such as TLR5 and TLR2. To understand molecular mechanism underlying a potential role TLR5, we generated detailed maps logical models TCR signaling pathways merged model cross-interactions between two pathways. Furthermore,...
The N6-methyladenosine (m6A) modification of HIV-1 RNAs plays an essential role in regulating viral infection. This has been widely studied but the number and precise positions m6A sites remain unclear due to lack precision detection methods. We used latest Nanopore chemistry direct base-calling option identify 18 m6As, 14 which were located at 3′ end genome, other four being central regions. Our data reveal differential methylation these between splicing isoforms. Eleven are clustered two...
The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins broad variety functions termed clients, Hsp90 maintains key essential oncogenic signalling pathways. Consequently, inhibitors are being tested as anti-cancer drugs. Using an integrated systematic approach analyse the effects inhibition in T-cells, we quantified differential changes proteome, interactome, selection transcriptome....
Standard proteomics methods allow the relative quantitation of levels thousands proteins in two or more samples. While such are invaluable for defining variations protein concentrations which follow perturbation a biological system, they do not offer information on mechanisms underlying changes. Expanding previous work [1], we developed pulse-chase (pc) variant SILAC (stable isotope labeling by amino acids cell culture). pcSILAC can quantitate one experiment and conditions newly synthesized...
Cellular differentiation is accompanied by dramatic changes in chromatin structure which direct the activation of lineage-specific transcriptional programs. Structure-specific recognition protein-1 (SSRP1) a histone chaperone important for chromatin-associated processes such as transcription, DNA replication and repair. Since function SSRP1 during cell remains unclear, we investigated its potential role controlling lineage determination. Depletion human mesenchymal stem cells elicited...
The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for antiviral intervention but also key player in persistence pathogenesis HCV. It cleaves thereby inactivates two crucial adaptor proteins RNA sensing innate immunity, mitochondrial signaling protein (MAVS) TRIF, phosphatase involved growth factor signaling, T-cell tyrosine (TC-PTP), E3 ubiquitin ligase UV-damaged DNA-binding 1 (DDB1). Here we explored...
Hox genes encode transcription factors that specify segmental identities along the anteroposterior body axis. These are organized in clusters, where their order corresponds to activity axis, a feature known as collinearity. In Drosophila, BX-C cluster contains three most posterior genes, collinear activation incorporates progressive changes histone modifications, chromatin architecture, and use of boundary elements cis-regulatory regions. To dissect functional hierarchies, we compare...
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in infected cell, leading to production of new virions. The virus modulates host cellular machinery order support its life while counteracting intracellular defense mechanisms. We investigated dynamic response infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes uninfected SupT1 CD4+ T cells at five time points viral process. By means a Gaussian...
In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it clearly best enzyme available, sole use trypsin rarely leads to complete sequence coverage, even for abundant proteins. It commonly assumed that this because many tryptic peptides are either too short or long be identified by RPLC−MS/MS. We show through in silico analysis 20−30% total three proteomes (Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Homo...
At the crossroad between biology and mathematical modelling, computational systems can contribute to a mechanistic understanding of high-level biological phenomenon. But as our knowledge accumulates, size complexity models increase, calling for development efficient dynamical analysis methods. Here, we take advantage generic techniques enable study complex cellular network models. A first approach, called "model verification" inspired by unitary testing in software development, enables...
Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably vertebrates. The mouse gene Krox20 encodes a transcription factor required for specification of two segments (rhombomeres) developing hindbrain. In rhombomere 3, is subject direct positive feedback governed by an...