BiPSim: a flexible and generic stochastic simulator for polymerization processes

Autor: Stephan Fischer, Marc Dinh, Vincent Henry, Philippe Robert, Anne Goelzer, Vincent Fromion

Publikováno v: Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)

Abstract Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator

Externí odkaz: https://doaj.org/article/ac317034f0994e66bdcdba31c8db31dd

Models of protein production along the cell cycle: An investigation of possible sources of noise.

Autor: Renaud Dessalles, Vincent Fromion, Philippe Robert

Publikováno v: PLoS ONE, Vol 15, Iss 1, p e0226016 (2020)

In this article, we quantitatively study, through stochastic models, the effects of several intracellular phenomena, such as cell volume growth, cell division, gene replication as well as fluctuations of available RNA polymerases and ribosomes. These

Externí odkaz: https://doaj.org/article/d81b0e0fbafb4694b20895bc576a8e19

Contrasting mechanisms of growth in two model rod-shaped bacteria

Autor: Cyrille Billaudeau, Arnaud Chastanet, Zhizhong Yao, Charlène Cornilleau, Nicolas Mirouze, Vincent Fromion, Rut Carballido-López

Publikováno v: Nature Communications, Vol 8, Iss 1, Pp 1-11 (2017)

Protein MreB participates in elongation of sidewalls during growth of most rod-shaped bacteria. Here, the authors use fluorescence microscopy and single-particle tracking to visualize MreB, showing thatBacillus subtilis and Escherichia coliappear to

Externí odkaz: https://doaj.org/article/7f305f31f56e4a188b662d8f1685c72b

An Ontology to Structure Biological Data: The Contribution of Mathematical Models

Autor: Olivier Inizan, Anne Goelzer, Fatiha SAIS, Danai Symeonidou, Vincent Fromion

Publikováno v: Metadata and Semantic Research ISBN: 9783030988753
METADATA AND SEMANTIC RESEARCH, MTSR 2021
15th International Conference on Metadata and Semantics Research
15th International Conference on Metadata and Semantics Research, Nov 2021, Madrid & Virtual, Spain. pp.57-64, ⟨10.1007/978-3-030-98876-0_5⟩

International audience; The biology is a research field well known for its huge quantity and diversity of data. Today, these data are still recognized as heterogeneous and fragmented. Despite the fact that several initiatives of biological knowledge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::78d47864b96320ca37d983682cb13ff9
https://doi.org/10.1007/978-3-030-98876-0_5

Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application to

Autor: Ibrahim, Sultan, Vincent, Fromion, Sophie, Schbath, Pierre, Nicolas

Publikováno v: J R Soc Interface

Automatic de novo identification of the main regulons of a bacterium from genome and transcriptome data remains a challenge. To address this task, we propose a statistical model that can use information on exact positions of the transcription start s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::0ccaf9c83500f56f7ec79680cb0805d1
https://pubmed.ncbi.nlm.nih.gov/33023397