Studying stochastic systems biology of the cell with single-cell genomics data
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …
promise for systems biology. However, rigorously probing the biology of living cells requires …
Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions
Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers
measured using smFISH (single molecule fluorescence in situ hybridization) with the …
measured using smFISH (single molecule fluorescence in situ hybridization) with the …
Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis
Intracellular reaction rates depend on concentrations and hence their levels are often
regulated. However classical models of stochastic gene expression lack a cell size …
regulated. However classical models of stochastic gene expression lack a cell size …
Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations
P Thomas, V Shahrezaei - Journal of the Royal Society …, 2021 - royalsocietypublishing.org
The chemical master equation and the Gillespie algorithm are widely used to model the
reaction kinetics inside living cells. It is thereby assumed that cell growth and division can be …
reaction kinetics inside living cells. It is thereby assumed that cell growth and division can be …
Approximating solutions of the chemical master equation using neural networks
Summary The Chemical Master Equation (CME) provides an accurate description of
stochastic biochemical reaction networks in well-mixed conditions, but it cannot be solved …
stochastic biochemical reaction networks in well-mixed conditions, but it cannot be solved …
Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …
telegraph model which includes synthesis and degradation of mRNA, and switching of the …
Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation
The stochasticity of gene expression is manifested in the fluctuations of messenger
ribonucleic acid and protein copy numbers within a cell lineage over time. While data of this …
ribonucleic acid and protein copy numbers within a cell lineage over time. While data of this …
Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number
Identifying the sources of cell-to-cell variability in signaling dynamics is essential to
understand drug response variability and develop effective therapeutics. However, it is …
understand drug response variability and develop effective therapeutics. However, it is …
Cell size distribution of lineage data: analytic results and parameter inference
Recent advances in single-cell technologies have enabled time-resolved measurements of
the cell size over several cell cycles. These data encode information on how cells correct …
the cell size over several cell cycles. These data encode information on how cells correct …
Quantifying and correcting bias in transcriptional parameter inference from single-cell data
R Grima, PM Esmenjaud - Biophysical Journal, 2024 - cell.com
The snapshot distribution of mRNA counts per cell can be measured using single-molecule
fluorescence in situ hybridization or single-cell RNA sequencing. These distributions are …
fluorescence in situ hybridization or single-cell RNA sequencing. These distributions are …