A5031779274- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Plant Molecular Biology Research
- Marine and coastal plant biology
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Hidradenitis Suppurativa and Treatments
- Rabies epidemiology and control
- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- Colorectal and Anal Carcinomas
- Cancer-related gene regulation
- Algorithms and Data Compression
- Hereditary Neurological Disorders
- Chromosomal and Genetic Variations
Université Paris-Saclay
2019-2024
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2016-2024
CEA Paris-Saclay
2019-2024
Centre National de Recherche en Génomique Humaine
2018-2024
Institut Mérieux (France)
2020-2021
Sanofi (France)
2020-2021
Institut Curie
2012-2018
Direction de la Recherche Fondamentale
2017-2018
Inserm
2013-2017
Université Paris Sciences et Lettres
2016-2017
The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and extreme record of pesticide resistance. Here we present the completely sequenced annotated genome, representing first complete chelicerate genome. At 90 megabases T. has smallest arthropod Compared other arthropods, genome shows unique changes in hormonal environment organization Hox complex, also reveals evolutionary innovation silk production. We find strong signatures polyphagy...
The genome of Ectocarpus, a model organism for brown algae, has been sequenced. Brown algae are complex photosynthetic organisms that have adapted to life in rocky coastal environments. Genome analysis sheds light on this adaptation and reveals an extended set light-harvesting pigment biosynthesis genes novel metabolic processes such as halide metabolism. Comparative genomic analyses highlight the likely importance family receptor kinases related molecules evolution multicellularity plants,...
Different methods of data analysis (e.g. clustering and ordination) are based on distance matrices. In some cases, researchers may wish to compare several matrices with one another in order test a hypothesis concerning possible relationship between these However, this is not always self-evident. Usually, values are, way, correlated therefore the usual assumption independence objects violated classical tests approach. Furthermore, often, spurious correlations can be observed when comparing...
Abstract Motivation: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the folding energy of RNA sequences, such as microRNA precursors, transfer ribosomal in several eukaryotic taxa. Statistical biases assessed randomization test, which predicted minimum free is compared with values obtained for structures inferred from randomly shuffling original sequences. Results: In contrast RNAs, majority sequences...
MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression target genes by means complementary base pair interactions. Although first miRNAs were discovered in Caenorhabditis elegans , >300 recently documented animals and plants, both cloning methods computational predictions. We present a genome-wide approach to detect miRNA Arabidopsis thaliana genome. Our method is based on conservation short sequences between genomes rice ( Oryza sativa ) properties...
Abstract Summary: We present a new web server called TAPIR, designed for the prediction of plant microRNA targets. The offers possibility to search miRNA targets using fast and precise algorithm. option is much slower but guarantees find less perfectly paired miRNA-target duplexes. Furthermore, allows target mimics, which are characterized by duplex having large loop, making them undetectable traditional tools. Availability: TAPIR can be accessed at:...
Defining protein complexes is critical to virtually all aspects of cell biology because many cellular processes are regulated by stable complexes, and their identification often provides insights into function. We describe the development application a high throughput tandem affinity purification/mass spectrometry platform for suspension cultures analyze cycle-related in Arabidopsis thaliana. Elucidation this protein-protein interaction network essential fully understand functional...
Despite many recent efforts, in silico identification of promoter regions is still its infancy. However, the accurate and delineation important for several reasons, such as improving genome annotation devising experiments to study understand transcriptional regulation. Current methods identify core region promoters require large amounts high-quality training data often behave like black box models that output predictions are difficult interpret. Here, we present a novel approach predicting...
Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application bioinformatics systems biology methods for analysis high-throughput data in cancer research heavily depends on availability global detailed reconstructions signalling networks amenable computational analysis. We present here Atlas Cancer Signalling Network (ACSN), an interactive...
Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points a dynamic process. We have developed Lemon-Tree, open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module inference....
Abstract Huntington’s disease is a fatal neurodegenerative characterized by striatal neurodegeneration, aggregation of mutant Huntingtin and the presence reactive astrocytes. Astrocytes are important partners for neurons engage in specific response that involves morphological, molecular functional changes. How astrocytes contribute to still an open question, especially because their state poorly reproduced experimental mouse models. Here, we show JAK2-STAT3 pathway, central cascade...
Abstract Background Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many that facilitate the analysis high-throughput experimental work formulation new hypotheses to be tested, a fundamental principle systems biology approach. However, large-scale molecular maps are not always easy mine interpret. Results We developed BiNoM (Biological Network Manager), Cytoscape plugin, which provides functions for import-export some...
In many analyses of high-throughput data in systems biology, there is a need to quantify the activity set genes individual samples. A typical example case where it necessary estimate transcription factor (which often not directly measurable) from expression its target genes. We present here ROMA (Representation and quantification Of Module Activities) Java software, designed for fast robust computation gene sets (or modules) with coordinated expression. based on simplest uni-factor linear...
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses now in clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues still one most abundant source cancer specimen, unfortunately this method preparation is known degrade therefore compromise subsequent analysis. Some have reported that variant can be performed on FFPE samples sequenced...
Background MicroRNAs (miRNAs) are small RNAs that recognize and regulate mRNA target genes. Multiple lines of evidence indicate they key regulators numerous critical functions in development disease, including cancer. However, defining the place function miRNAs complex regulatory networks is not straightforward. Systems approaches, like inference a module network from expression data, can help to achieve this goal. Methodology/Principal Findings During last decade, much progress has been...
Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism aetiopathogenesis, progress and chronicity the involves genetic, epigenetic environmental factors. To understand molecular mechanisms underlying phenotypes, one has to place implicated factors in their functional context. However, integration organization such data systematic manner remains challenging task. Molecular maps are widely used biology provide useful intuitive...
Abstract Peripheral blood mononuclear cells (PBMCs) are that a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs commonly study global response disease outbreak and progression, pathogen infections, for vaccine development multitude other clinical applications. Over past few years, revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification gene expression thousands...
In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene data. Despite the demonstrated success of such algorithms in uncovering biologically relevant relations, further developments area are hampered by a lack tools compare performance alternative module network learning strategies. Here, we demonstrate use synthetic data generator SynTReN for purpose testing comparing algorithms. We introduce software...
Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms health disease. NaviCell Web Service a tool network-based 'omics' data which implements several visual representation methods utilities combining them together. uses Google Maps semantic zooming to browse large network maps, represented in various formats, together with different types the molecular mapped top them. For achieving this, provides...
Abstract Targeted therapies interfering with specifically one protein activity are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins signaling networks involved disease is often necessary. Thus, important problem biomedical research design and prioritization optimal combinations interventions to repress a pathological behavior, while minimizing side-effects. OCSANA (optimal from network...
Abstract High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell tissue transcriptomes. It also being increasingly a number of clinical applications, including profiling diagnostics alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging some situations, instance cases low input amounts or degraded samples. Several protocols...
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats computational systems biology related fields. This report summarizes topics activities fourth edition annual COMBINE meeting, held Paris during September 16-20 2013, attended by a total 96 people. pioneered first day devoted modeling approaches biology, which attracted broad audience scientists thanks panel renowned speakers. During subsequent days,...
Abstract Motivation: Cancer is a complex disease, triggered by mutations in multiple genes and pathways. There growing interest the application of systems biology approaches to analyze various types cancer-related data understand overwhelming complexity changes induced disease. Results: We reconstructed regulatory module network using gene expression, microRNA expression clinical parameter, all measured lymphoblastoid cell lines derived from patients having aggressive or non-aggressive forms...