A5102780086- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Semantic Web and Ontologies
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Parkinson's Disease Mechanisms and Treatments
- Neuroscience and Neuropharmacology Research
- Neuroinflammation and Neurodegeneration Mechanisms
- Multiple Sclerosis Research Studies
- Nerve injury and regeneration
- Anesthesia and Neurotoxicity Research
- Neonatal and fetal brain pathology
- Dementia and Cognitive Impairment Research
- Traumatic Brain Injury and Neurovascular Disturbances
- Gene expression and cancer classification
- Blood Coagulation and Thrombosis Mechanisms
- Genomics and Phylogenetic Studies
- Anesthesia and Sedative Agents
- Scientific Computing and Data Management
- Embedded Systems Design Techniques
- Epilepsy research and treatment
- Molecular Sensors and Ion Detection
- Neurological disorders and treatments
- Competitive and Knowledge Intelligence
Sorbonne Université
2020-2023
Institut national de recherche en informatique et en automatique
2018-2022
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2015-2021
Institut du Cerveau
2018-2020
Centre National de la Recherche Scientifique
2017-2020
Université Paris-Saclay
2017-2020
Inserm
2007-2020
Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers
2017-2019
Allen Institute for Brain Science
2018-2019
Laboratoire de Recherche en Informatique
2017
Recent advances in 'omic' technologies have created unprecedented opportunities for biological research, but current software and database resources are extremely fragmented. OMICtools is a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics metabolomics. All been classified by omic (next-generation sequencing, microarray, mass spectrometry nuclear magnetic resonance) associated with published...
Abstract Parkinson's disease (PD) is characterized by the bilateral degeneration of midbrain dopamine‐containing neurons with most severe lesion in posterolateral part substantia nigra pars compacta (SNpc). In humans, such lesions lead to specific motor abnormalities (i.e., akinesia, rigidity, and tremor) that are greatly improved levodopa treatment. After a few years, beneficial effect treatment frequently offset development dyskinesias. To improve strategies, an animal model showing...
In both Parkinson disease and in animal models of disease, there is a microglial reaction addition to the loss dopaminergic neurons ventral midbrain. To determine pathological role this reaction, we analyzed kinetics activation cell death induced rats with neurotoxin 6-hydroxydopamine. As early as Day 1 after injection, was decline motor performance 6-hydroxydopamine-lesioned that correlated reduction innervation contralateral striatum. Loss midbrain developed few days later seemed follow...
During cortex development, fine interactions between pyramidal cells and migrating GABA neurons are required to orchestrate correct positioning of interneurons, but cellular molecular mechanisms not yet clearly understood. Functional age-specific expression NMDA receptors by neonate endothelial suggests a vascular contribution the trophic role glutamate during cortical development. Associating functional loss-of-function approaches, we found that stimulates activity proteases MMP-9 t-PA...
Two potential disease-modifying approaches for dementia are being vigorously tested: the early targeting of neuropathology Alzheimer’s disease (AD) and multi-domain lifestyle interventions to promote resilience neuropathology. We apply “web information” model clinical translation both argue firstly that tests treatments aiming achieve clinically meaningful outcomes should remain simple, secondly, building clinically-meaningful be kept separate from public health policy which means promoting...
Ketamine is a NMDA receptor (NMDAR) antagonist used in pediatric anesthesia. Given the role of glutamatergic signaling during brain maturation, we studied effects single ketamine injection (40 mg/kg s.c) mouse neonates depending on postnatal age at (P2, P5, or P10) cortical NMDAR subunits expression and association with Membrane-Associated Guanylate Kinases PSD95 SAP102. The P2, P10 motor activity were compared adulthood. increased GluN2A GluN2B mRNA levels P2-treated mice without change...
Hypoxia-ischemia (HI) and excitotoxicity are validated causes of neonatal brain injuries tissue plasminogen activator (t-PA) participates in the processes through proteolytic receptor-mediated pathways. Brain microvascular endothelial cells from neonates culture, contain release more t-PA gelatinases upon glutamate challenge than adult cells. We have studied to gelatinase (MMP-2 MMP-9) activity links HI lesion models 5 day–old pups wild type or its inhibitor (PAI-1) genes inactivated mice....
Glutamate transporters (excitatory amino-acid (EAATs)) are essential for brain homeostasis. While previous studies indicate that the vascular endothelium contributes to glutamate efflux in adult brain, little information is available regarding uptake immature brain. The present study shows a differential expression pattern of EAATs between cortical microvessels adults and newborns. In addition, endothelial cells take up more efficiently than neonatal cells. Our findings age-specific changes...
High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these together with knowledge is a critical issue in biology and requires integrative tools methods such as bio-ontologies to extract share valuable information. In parallel, the development recent whole-cell models using systemic cell description opened alternatives for integration. Integrating within bio-ontology would help progress integration modeling synergistically. We...
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge locating and comparing an exponentially growing number programs websites dedicated to computational biology, in order maximize potential their data. OMICtools is designed meet this need its open-access search engine offering easy means right tools corresponding each researcher specific biological data analyses. The website (https://OMICtools.com) centralizes more than...
Abstract Background Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such challenge at whole-cell scale. In representations, cell is considered as system composed interlocked subsystems. The need now define relevant formalization description cellular processes. Results We introduce BiPOm ( B iological i nterlocked P rocess O ntology for m etabolism) an ontology...
Identifying the nodes able to drive state of a network is crucial understand, and eventually control, biological systems. Despite recent advances, such identification remains difficult because huge number equivalent controllable configurations, even in relatively simple networks. Based on evidence that many applications it essential test ability individual control specific target subset, we develop fast principled method identify driver-target configurations sparse directed We demonstrate...
Omics technologies offer great promises for improving our understanding of diseases.The integration and interpretation such data pose major challenges, calling adequate knowledge models.Disease maps provide curated about disorders' pathophysiology at the molecular level adapted to omics measurements.However, expressiveness disease could be increased help avoiding ambiguities misinterpretations reinforce their interoperability with other resources.Ontologies are an framework overcome this...
Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different formalisms, for which simulation could remain tractable. Here, we introduce BiPSim, open-source stochastic simulator template-based polymerization processes, such as replication, transcription and translation. BiPSim combines efficient abstract representation reactions a constant-time implementation the Gillespie's Stochastic Simulation Algorithm (SSA) with respect to reactions, makes it...
Alzheimer s disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding generating new hypotheses. However, integration interpretation of such data pose major challenges, calling adequate knowledge models. AlzPathway a map that gives detailed broad account AD pathophysiology. lacks formalism, which can lead ambiguity misinterpretation. Ontologies are an framework...