Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

[HTML][HTML] Participation of microbiota in the development of gastric cancer

LL Wang, XJ Yu, SH Zhan, SJ Jia, ZB Tian… - World journal of …, 2014 - ncbi.nlm.nih.gov
There are a large number of bacteria inhabiting the human body, which provide benefits for
the health. Alterations of microbiota participate in the pathogenesis of diseases. The gastric …

First-passage time approach to controlling noise in the timing of intracellular events

KR Ghusinga, JJ Dennehy… - Proceedings of the …, 2017 - National Acad Sciences
In the noisy cellular environment, gene products are subject to inherent random fluctuations
in copy numbers over time. How cells ensure precision in the timing of key intracellular …

Stochastic timing in gene expression for simple regulatory strategies

AD Co, MC Lagomarsino, M Caselle… - Nucleic acids …, 2017 - academic.oup.com
Timing is essential for many cellular processes, from cellular responses to external stimuli to
the cell cycle and circadian clocks. Many of these processes are based on gene expression …

Optimum threshold minimizes noise in timing of intracellular events

S Kannoly, T Gao, S Dey, N Wang, A Singh… - Iscience, 2020 - cell.com
How the noisy expression of regulatory proteins affects timing of intracellular events is an
intriguing fundamental problem that influences diverse cellular processes. Here we use the …

A stochastic vs deterministic perspective on the timing of cellular events

L Ham, MA Coomer, K Öcal, R Grima… - Nature …, 2024 - nature.com
Cells are the fundamental units of life, and like all life forms, they change over time. Changes
in cell state are driven by molecular processes; of these many are initiated when molecule …

Comparing feedback strategies for minimizing noise in gene expression event timing

Z Vahdat, KR Ghusinga, A Singh - 2021 29th Mediterranean …, 2021 - ieeexplore.ieee.org
Many cellular events occur when their corresponding regulatory proteins attain critical
thresholds. Can cells schedule such events with precision by controlling the dynamics of the …

Temporal development of Drosophila embryos is highly robust across a wide temperature range

J Chong, C Amourda… - Journal of the Royal …, 2018 - royalsocietypublishing.org
Development is a process precisely coordinated in both space and time. Spatial precision
has been quantified in a number of developmental systems, and such data have contributed …

Temporal precision of regulated gene expression

S Gupta, J Varennes, HC Korswagen… - PLoS computational …, 2018 - journals.plos.org
Important cellular processes such as migration, differentiation, and development often rely
on precise timing. Yet, the molecular machinery that regulates timing is inherently noisy …

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 …