François Bertaux

François Bertaux
Imperial College London | Imperial · Department of Mathematics

PhD

About

22
Publications
2,333
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338
Citations
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April 2010 - present

Publications

Publications (22)
Article
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Small-scale, low-cost bioreactors provide exquisite control of environmental parameters of microbial cultures over long durations. Their use is gaining popularity in quantitative systems and synthetic biology. However, existing setups are limited in their measurement capabilities. Here, we present ReacSight, a strategy to enhance bioreactor arrays...
Article
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Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Here, we determined the importance of the growth rate in explaining relative changes in protein and mRNA levels in the simple eukaryote Schizosaccharomyces pombe grown on non-limit...
Article
Full-text available
Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods and improved computational resources. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Applications in which r...
Article
Full-text available
Significance At the single-cell level, biochemical processes are inherently stochastic. For many natural systems, the resulting cell-to-cell variability is exploited by microbial populations. In synthetic biology, however, the interplay of cell-to-cell variability and population processes such as selection or growth often leads to circuits not func...
Article
When engineering microbes for bioproduction, one is necessarily confronted to the existing tradeoff between efficient bioproduction, and maintenance of the cell physiology and growth. Moreover, because cellular processes at the single-cell level are coupled with population dynamics via selection mechanisms, this question should be investigated at t...
Preprint
Full-text available
Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple...
Article
Full-text available
Universal observations in Biology are sometimes described as "laws". In E. coli, experimental studies performed over the past six decades have revealed major growth laws relating ribosomal mass fraction and cell size to the growth rate. Because they formalize complex emerging principles in biology, growth laws have been instrumental in shaping our...
Preprint
Full-text available
Universal observations in Biology are sometimes described as “laws”. In E. coli , experimental studies performed over the past six decades have revealed major growth laws relating ribosomal mass fraction and cell size to the growth rate. Because they formalize complex emerging principles in biology, growth laws have been instrumental in shaping our...
Article
Full-text available
Cell size varies during the cell cycle and in response to external stimuli. This requires the tight coordination, or "scaling," of mRNA and protein quantities with the cell volume in order to maintain biomolecule concentrations and cell density. Evidence in cell populations and single cells indicates that scaling relies on the coordination of mRNA...
Article
Full-text available
Motivation: Normalisation of single cell RNA sequencing (scRNA-seq) data is a prerequisite to their interpretation. The marked technical variability, high amounts of missing observations and batch effect typical of scRNA-seq datasets make this task particularly challenging. There is a need for an efficient and unified approach for normalisation, i...
Preprint
Full-text available
Cell size varies during the cell cycle and in response to external stimuli. This requires the tight coordination, or 'scaling', of mRNA and protein quantities with the cell volume in order to maintain biomolecules concentrations and cell density. Evidence in cell populations and single cells indicates that scaling relies on the coordination of mRNA...
Article
Full-text available
Phenotypic cell-to-cell variability is a fundamental determinant of microbial fitness that contributes to stress adaptation and drug resistance. Gene expression heterogeneity underpins this variability but is challenging to study genome-wide. Here we examine the transcriptomes of >2,000 single fission yeast cells exposed to various environmental co...
Preprint
Full-text available
Normalisation of single cell RNA sequencing (scRNA-seq) data is a prerequisite to their interpretation. The marked technical variability and high amounts of missing observations typical of scRNA-seq datasets make this task particularly challenging. Here, we introduce bayNorm, a novel Bayesian approach for scaling and inference of scRNA-seq counts....
Article
Full-text available
Recently, hepatocyte–sinusoid alignment (HSA) has been identified as a mechanism that supports the coordination of hepatocytes during liver regeneration to reestablish a functional micro-architecture (Hoehme et al. in Proc Natl Acad Sci 107(23):10371–10376, 2010). HSA means that hepatocytes preferentially align along the closest micro-vessels. Here...
Article
Full-text available
The cell division rate, size and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cyc...
Preprint
Full-text available
The cell division rate, size, and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cy...
Chapter
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein–protein interactions and post-translational modifications. The response to death receptor stimulation varies significantly from one cell line to another and even from one cell to another within a given cell line. In this context, it is often difficult to...
Article
Full-text available
Motivation: Quantitative models are increasingly-used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting. Results: In this paper, we propose to construct abstractions...
Thesis
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Cell-intrinsic, non-environmental sources of cell-to-cell variability, such as stochastic gene expression, are increasingly recognized to play an important role in the dynamics of tissues, tumors, microbial communities... However, they are usually ignored or oversimplified in theoretical models of cell populations.In this thesis, we propose a cell-...
Article
Full-text available
Isogenic cells sensing identical external signals can take markedly different decisions. Such decisions often correlate with pre-existing cell-to-cell differences in protein levels. When not neglected in signal transduction models, these differences are accounted for in a static manner, by assuming randomly distributed initial protein levels. Howev...
Article
Full-text available
Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for ne...
Article
Full-text available
Extrinsic apoptosis is a programmed cell death triggered by external ligands, such as the TNF-related apoptosis inducing ligand (TRAIL). Depending on the cell line, the specific molecular mechanisms leading to cell death may significantly differ. Precise characterization of these differences is crucial for understanding and exploiting extrinsic apo...

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