A5085105326- Ionosphere and magnetosphere dynamics
- Solar and Space Plasma Dynamics
- Geophysics and Gravity Measurements
- Gene Regulatory Network Analysis
- Mathematical Biology Tumor Growth
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- Microtubule and mitosis dynamics
- Radioactive element chemistry and processing
- Simulation Techniques and Applications
- Image and Object Detection Techniques
- Cellular Mechanics and Interactions
- Receptor Mechanisms and Signaling
- Fibroblast Growth Factor Research
- Advanced Measurement and Detection Methods
- Melanoma and MAPK Pathways
- Analytical Chemistry and Sensors
- Endoplasmic Reticulum Stress and Disease
- Cancer, Hypoxia, and Metabolism
- 3D Printing in Biomedical Research
- Remote Sensing and LiDAR Applications
- Psoriasis: Treatment and Pathogenesis
- Radioactive contamination and transfer
Institut Curie
2019-2025
Inserm
2019-2024
Université Paris Sciences et Lettres
2019-2024
ParisTech
2019-2024
École Nationale Supérieure des Mines de Paris
2019-2024
Stanford Synchrotron Radiation Lightsource
2020-2023
SLAC National Accelerator Laboratory
2020-2023
University of Nebraska–Lincoln
2022-2023
Lawrence Berkeley National Laboratory
2023
Los Alamos National Laboratory
2023
Abstract In systems biology, mathematical models and simulations play a crucial role in understanding complex biological systems. Different modelling frameworks are employed depending on the nature scales of system under study. For instance, signalling regulatory networks can be simulated using Boolean modelling, whereas multicellular studied agent-based modelling. Herein, we present PhysiBoSS 2.0, hybrid framework that allows simulating within individual cell agents. 2.0 is redesign...
Biochemical networks are used in computational biology, to model mechanistic details of systems involved cell signaling, metabolism, and regulation gene expression. Parametric structural uncertainty, as well combinatorial explosion strong obstacles against analyzing the dynamics large models this type. Multiscaleness, an important property these networks, can be get past some obstacles. Networks with many separated time scales, reduced simpler models, a way that depends only on orders...
Mathematical models of biological processes altered in cancer are built using the knowledge complex networks signaling pathways, detailing molecular regulations inside different cell types, such as tumor cells, immune and other stromal cells. If these mainly focus on intracellular information, they often omit a description spatial organization among cells their interactions, with tumoral microenvironment.
The study of response to cancer treatments has benefited greatly from the contribution different omics data but their interpretation is sometimes difficult. Some mathematical models based on prior biological knowledge signaling pathways facilitate this often require fitting parameters using perturbation data. We propose a more qualitative mechanistic approach, logical formalism and sole mapping data, able recover differences in sensitivity gene inhibition without model training. This...
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.
We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. apply this method a cell cycle oscillator model. The reduced hybridized model can be used as hybrid for cycle. also propose practical recipe detecting quasi-equilibrium QE reactions quasi-steady state QSS species in models with rational rate functions reduction. Interestingly, QE/QSS invariant manifold smooth dynamics along put into tropical variety hybridization sliding modes...
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 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,...
This tutorial provides stepwise instructions to install the 20 tools integrated in CoLoMoTo software suite, develop reproducible dynamical analyses of logical models complex biological molecular networks. The specifically focuses on analysis a previously published model regulatory network controlling mammalian cell proliferation. It includes chunks python code reproduce several results and figures original article further extend these with help selection included suite. notebook covers...
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a classical metabolic enzyme involved in energy production and plays role additional nuclear functions, including transcriptional control, recognition of misincorporated nucleotides DNA maintenance telomere structure. Here, we show that the recombinant protein T. cruzi GAPDH (rTcGAPDH) binds single-stranded telomeric DNA. We demonstrate binding to correlates with balance between oxidized reduced forms nicotinamide adenine dinucleotides...
Defining a multicellular model can be challenging. There may hundreds of parameters that specify the attributes and behaviors objects. In best case, will defined using some format specification – markup language provide easy sharing (and minimal step toward reproducibility). PhysiCell is an open-source, physics-based simulation framework with active growing user community. It uses XML to define and, traditionally, users needed manually edit modify model. Studio tool make this task easier....
The extracellular matrix, composed of macromolecules like collagen fibres, provides structural support to cells and acts as a barrier that metastatic degrade spread beyond the primary tumour. While agent-based frameworks, such PhysiCell, can simulate spatial dynamics tumour evolution, they only implement circles (2D) or spheres (3D). To model matrix network we require new type agent represented by line segments cylinders Here, present PhysiMeSS, an addon introducing describe fibres their...
In malignant transformation, cellular stress‐response pathways are dynamically mobilized to counterbalance oncogenic activity, keeping cancer cells viable. Therapeutic disruption of this vulnerable homeostasis might change the outcome many human cancers, particularly those for which no effective therapy is available. Here, we report use fibroblast growth factor 2 ( FGF 2) demonstrate that further mitogenic activation disrupts and strongly sensitizes stress‐targeted therapeutic inhibitors. We...
An outbreak of influenza A occurred in a prison system New South Wales, Australia January 2003 during the southern hemisphere summer. This report documents only third confirmed environment. The investigation included case ascertainment, state-wide surveillance, case-control study and interventions to limit such as infection control, quarantine, cohorting cases, use antiviral medication for prophylaxis. total 37 clinical cases were identified. Influenza virus was detected 11 22 respiratory...
As opposed to the standard tolerogenic apoptosis, immunogenic cell death (ICD) constitutes a type of cellular demise that elicits an adaptive immune response. ICD has been characterized in4malignant cells following cytotoxic interventions, such as chemotherapy or radiotherapy. Briefly, cancer releases some stress/danger signals attract and activate dendritic (DCs). The latter can then engulf cross-present tumor antigens T lymphocytes, thus priming cancer-specific immunity. This series...
Psoriasis arises from complex interactions between keratinocytes and immune cells, leading to uncontrolled inflammation, hyperactivation, a perturbed keratinocyte life cycle. Despite the availability of drugs for psoriasis management, disease remains incurable. Treatment response variability calls new tools approaches comprehend mechanisms underlying development. We present Boolean multiscale population model that captures dynamics cell-specific phenotypes in psoriasis, integrating discrete...
Abstract Background Computational models in systems biology are becoming more important with the advancement of experimental techniques to query mechanistic details responsible for leading phenotypes interest. In particular, Boolean well fit describe complexity signaling networks while being simple enough scale a very large number components. With advance model inference techniques, field is transforming from an artisanal way building moderate size automatized one, models. this context,...
Abstract Multiscale models provide a unique tool for analyzing complex processes that study events occurring at different scales across space and time. In the context of biological systems, such can simulate mechanisms happening intracellular level as signaling, extracellular where cells communicate coordinate with other cells. These aim to understand impact genetic or environmental deregulation observed in diseases, describe interplay between pathological tissue immune system, suggest...