Exploiting information and control theory for directing gene expression in cell populations

L Henrion, M Delvenne, F Bajoul Kakahi… - Frontiers in …, 2022 - frontiersin.org
Microbial populations can adapt to adverse environmental conditions either by appropriately
sensing and responding to the changes in their surroundings or by stochastically switching …

Phage infection and lysis

JJ Dennehy, ST Abedon - Bacteriophages: biology, technology, therapy, 2021 - Springer
Viruses are differentiated from other mobile genetic elements by the encapsidation of their
genomes during some stage of their life cycles. It is during their infection of bacteria that …

Noise suppression in stochastic genetic circuits using pid controllers

S Modi, S Dey, A Singh - PLoS Computational Biology, 2021 - journals.plos.org
Inside individual cells, protein population counts are subject to molecular noise due to low
copy numbers and the inherent probabilistic nature of biochemical processes. We …

Bacterial replication initiation as precision control by protein counting

H Fu, F Xiao, S Jun - PRX life, 2023 - APS
Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations
of stable proteins remain steady. However, this poses a conceptual challenge to modeling …

Exact distribution of threshold crossing times for protein concentrations: Implication for biological timekeeping

K Rijal, A Prasad, A Singh, D Das - Physical Review Letters, 2022 - APS
Stochastic protein accumulation up to some concentration threshold sets the timing of many
cellular physiological processes. Here we obtain the exact distribution of first threshold …

Infection by bacteriophage lambda: an evolving paradigm for cellular individuality

I Golding - Current Opinion in Microbiology, 2018 - Elsevier
Highlights•E. coli infection by bacteriophage lambda is a paradigm for cellular
individuality.•Early studies attributed cell–cell differences to random biochemical …

Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder

C Nieto, CA Vargas-García, JM Pedraza… - npj Systems Biology and …, 2024 - nature.com
Under ideal conditions, Escherichia coli cells divide after adding a fixed cell size, a strategy
known as the adder. This concept applies to various microbes and is often explained as the …

An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time

K Abley, P Formosa-Jordan, H Tavares, EYT Chan… - Elife, 2021 - elifesciences.org
Genetically identical plants growing in the same conditions can display heterogeneous
phenotypes. Here we use Arabidopsis seed germination time as a model system to examine …

Relating cellular signaling timescales to single-molecule kinetics: A first-passage time analysis of Ras activation by SOS

WYC Huang, S Alvarez, Y Kondo… - Proceedings of the …, 2021 - National Acad Sciences
Son of Sevenless (SOS) is a Ras guanine nucleotide exchange factor (GEF) that plays a
central role in numerous cellular signaling pathways. Like many other signaling molecules …

The linear framework II: using graph theory to analyse the transient regime of Markov processes

KM Nam, J Gunawardena - Frontiers in Cell and Developmental …, 2023 - frontiersin.org
The linear framework uses finite, directed graphs with labelled edges to model biomolecular
systems. Graph vertices represent chemical species or molecular states, edges represent …