A5050740875- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Monoclonal and Polyclonal Antibodies Research
- Genetics, Bioinformatics, and Biomedical Research
- Rheumatoid Arthritis Research and Therapies
- Machine Learning in Bioinformatics
- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Cytokine Signaling Pathways and Interactions
- Cell Image Analysis Techniques
- Protein Structure and Dynamics
- PI3K/AKT/mTOR signaling in cancer
- Data-Driven Disease Surveillance
- Protease and Inhibitor Mechanisms
- Systemic Lupus Erythematosus Research
- Immunotherapy and Immune Responses
- HER2/EGFR in Cancer Research
- Cancer, Hypoxia, and Metabolism
- Mast cells and histamine
- CAR-T cell therapy research
- Cellular transport and secretion
- Single-cell and spatial transcriptomics
- Supramolecular Self-Assembly in Materials
Inria Saclay - Île de France
2020-2024
Genopole (France)
2017-2024
Université Toulouse III - Paul Sabatier
2024
Université Paris-Saclay
2018-2024
Université d'Évry Val-d'Essonne
2018-2024
Centre National de la Recherche Scientifique
2013-2024
Institut national de recherche en informatique et en automatique
2020
University of Patras
2007-2019
Institut de Biologie de l'École Normale Supérieure
2012-2014
Inserm
2013-2014
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
We need to effectively combine the knowledge from surging literature with complex datasets propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets intervention. Here, we describe a large-scale community effort build an open access, interoperable computable repository COVID-19 molecular mechanisms. The Disease Map (C19DMap) is graphical, interactive representation disease-relevant mechanisms linking many sources. Notably, it computational...
Macrophages play an essential role in rheumatoid arthritis. Depending on their phenotype (M1 or M2), they can a the initiation resolution of inflammation. The M1/M2 ratio arthritis is higher than healthy controls. Despite this, no treatment targeting specifically macrophages currently used clinics. Thus, devising strategies to selectively deplete proinflammatory and promote anti-inflammatory could be promising therapeutic approach. State-of-the-art molecular interaction maps M1 M2 are...
Abstract Motivation Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour described system under different conditions. Computational modelling means study dynamic properties through silico simulations perturbations. We aim bridge gap between representations systems with CaSQ, software tool that infers Boolean rules based on...
Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid fibroblast-like synoviocytes (RA-FLS) play significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become...
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 The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. generation novel, relevant hypotheses from this enormous quantity remains challenging. Logical models have long been used to answer a variety questions regarding the dynamical behaviours regulatory networks. As number published logical increases, there is pressing need model annotation, referencing curation in community-supported standardised formats....
Abstract Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These provide a means to analyze dynamics systems they describe, and interrogate their properties, insights about emerging behavior system presence single or combined perturbations. Aimed at those who are new modeling, we present here practical hands-on protocol breaking down process mechanistic modeling succession precise steps. The provides framework that includes...
Abstract Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With rise number computational models, finding ways improve reusability these and their ability reproduce virtual experiments becomes critical. Correct effective model annotation community-supported standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework annotated, accessible, reproducible interoperable biology,...
Rheumatoid Arthritis (RA) is an autoimmune disease characterized by a highly invasive pannus formation consisting mainly of Synovial Fibroblasts (RASFs). This leads to cartilage, bone, and soft tissue destruction in the affected joint. RASFs' activation associated with metabolic alterations resulting from dysregulation extracellular signals' transduction gene regulation. Deciphering intricate mechanisms at origin this reprogramming may provide significant insight into involvement RA's...
The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification drug repurposing.
In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA). We are constructing detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts’ advice. The RA will be web-published in the coming months form an interactive map, using MINERVA platform, allowing for easy access, navigation search all pathways implicated...
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical networks can be to predict biological and cellular behaviors by system perturbations silico simulations. Today, broad sets causal are available a variety knowledge resources. However, different visions, based on distinct interests, have led development multiple ways describe annotate interactions. It therefore challenging efficiently...
Rheumatoid Arthritis (RA) is an autoimmune disease of unknown aetiology involving complex interactions between environmental and genetic factors. Its pathogenesis suspected to arise from intricate interplays signalling, gene regulation metabolism, leading synovial inflammation, bone erosion cartilage destruction in the patients’ joints. In addition, resident synoviocytes macrophage fibroblast types can interact with innate adaptive immune cells contribute disease’s debilitating symptoms....
As a conceptual model of disease mechanisms, map integrates available knowledge and is applied for data interpretation, predictions hypothesis generation. It possible to mechanisms on different levels granularity adjust the approach goals particular project. This rich environment together with requirements high-quality network reconstruction makes it challenging new curators groups be quickly introduced development methods. In this review, we offer step-by-step guide developing within its...
Abstract Molecular interaction maps (MIMs) are static graphical representations depicting complex biochemical networks that can be formalized using one of the Systems Biology Graphical Notation languages. Regardless their extensive coverage various biological processes, they limited in terms dynamic insights. However, MIMs serve as templates for developing computational models. We present MetaLo, an open-source Python package enables coupling Boolean models inferred from process description...