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Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art
Stochasticity is a key characteristic of intracellular processes such as gene regulation and
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
Digital models in biotechnology: Towards multi-scale integration and implementation
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary
research activities. With the recent megatrend of digitalization swee** across all …
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
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 …
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
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 …
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
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 …
expanding, yet our understanding of how expression levels impact phenotype is limited …
Diverse spatial expression patterns emerge from unified kinetics of transcriptional bursting
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 …
persisted for more than a decade. Here, we measure nascent transcriptional activity in early …
Effective bet-hedging through growth rate dependent stability
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 …
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
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 …
cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable …
Why haploinsufficiency persists
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 …
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
Growth-mediated feedback between synthetic gene circuits and host organisms leads to
diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity …
diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity …