Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

DJ Warne, RE Baker… - Journal of the Royal …, 2019‏ - royalsocietypublishing.org
Stochasticity is a key characteristic of intracellular processes such as gene regulation and
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …

Digital models in biotechnology: Towards multi-scale integration and implementation

FSF Hartmann, IA Udugama, GM Seibold… - Biotechnology …, 2022‏ - Elsevier
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary
research activities. With the recent megatrend of digitalization swee** across all …

Central dogma rates and the trade-off between precision and economy in gene expression

J Hausser, A Mayo, L Keren, U Alon - Nature communications, 2019‏ - nature.com
Steady-state protein abundance is set by four rates: transcription, translation, mRNA decay
and protein decay. A given protein abundance can be obtained from infinitely many …

The strength and pattern of natural selection on gene expression in rice

SC Groen, I Ćalić, Z Joly-Lopez, AE Platts, JY Choi… - Nature, 2020‏ - nature.com
Levels of gene expression underpin organismal phenotypes,, but the nature of selection that
acts on gene expression and its role in adaptive evolution remain unknown,. Here we …

Massively parallel interrogation of the effects of gene expression levels on fitness

L Keren, J Hausser, M Lotan-Pompan, IV Slutskin… - Cell, 2016‏ - cell.com
Data of gene expression levels across individuals, cell types, and disease states is
expanding, yet our understanding of how expression levels impact phenotype is limited …

Diverse spatial expression patterns emerge from unified kinetics of transcriptional bursting

B Zoller, SC Little, T Gregor - Cell, 2018‏ - cell.com
How transcriptional bursting relates to gene regulation is a central question that has
persisted for more than a decade. Here, we measure nascent transcriptional activity in early …

Effective bet-hedging through growth rate dependent stability

DH de Groot, AJ Tjalma, FJ Bruggeman… - Proceedings of the …, 2023‏ - pnas.org
Microbes in the wild face highly variable and unpredictable environments and are naturally
selected for their average growth rate across environments. Apart from using sensory …

Intercellular variability in protein levels from stochastic expression and noisy cell cycle processes

M Soltani, CA Vargas-Garcia, D Antunes… - PLoS computational …, 2016‏ - journals.plos.org
Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-
cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable …

Why haploinsufficiency persists

SA Morrill, A Amon - Proceedings of the National Academy of Sciences, 2019‏ - pnas.org
Haploinsufficiency describes the decrease in organismal fitness observed when a single
copy of a gene is deleted in diploids. We investigated the origin of haploinsufficiency by …

Topology-dependent interference of synthetic gene circuit function by growth feedback

R Zhang, J Li, J Melendez-Alvarez, X Chen… - Nature chemical …, 2020‏ - nature.com
Growth-mediated feedback between synthetic gene circuits and host organisms leads to
diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity …