Challenges in measuring and understanding biological noise

N Eling, MD Morgan, JC Marioni - Nature Reviews Genetics, 2019 - nature.com
Biochemical reactions are intrinsically stochastic, leading to variation in the production of
mRNAs and proteins within cells. In the scientific literature, this source of variation is typically …

Bacterial growth: a statistical physicist's guide

RJ Allen, B Waclaw - Reports on Progress in Physics, 2018 - iopscience.iop.org
Bacterial growth presents many beautiful phenomena that pose new theoretical challenges
to statistical physicists, and are also amenable to laboratory experimentation. This review …

Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments

DA Van Valen, T Kudo, KM Lane… - PLoS computational …, 2016 - journals.plos.org
Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays
in dynamic, living systems. A major critical challenge for this class of experiments is the …

Bacterial persisters are a stochastically formed subpopulation of low-energy cells

S Manuse, Y Shan, SJ Canas-Duarte, S Bakshi… - PLoS …, 2021 - journals.plos.org
Persisters represent a small subpopulation of non-or slow-growing bacterial cells that are
tolerant to killing by antibiotics. Despite their prominent role in the recalcitrance of chronic …

Mechanistic origin of cell-size control and homeostasis in bacteria

F Si, G Le Treut, JT Sauls, S Vadia, PA Levin, S Jun - Current Biology, 2019 - cell.com
Evolutionarily divergent bacteria share a common phenomenological strategy for cell-size
homeostasis under steady-state conditions. In the presence of inherent physiological …

Gateways to the FANTOM5 promoter level mammalian expression atlas

M Lizio, J Harshbarger, H Shimoji, J Severin… - Genome biology, 2015 - Springer
The FANTOM5 project investigates transcription initiation activities in more than 1,000
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …

Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

Y Xiao, CH Bowen, D Liu, F Zhang - Nature chemical biology, 2016 - nature.com
Biosynthesis enables renewable production of manifold compounds, yet often biosynthetic
performance must be improved for it to be economically feasible. Nongenetic, cell-to-cell …

A fast chemical reprogramming system promotes cell identity transition through a diapause-like state

X Chen, Y Lu, L Wang, X Ma, J Pu, L Lin, Q Deng… - Nature Cell …, 2023 - nature.com
Cellular reprogramming by only small molecules holds enormous potentials for regenerative
medicine. However, chemical reprogramming remains a slow process and labour intensive …

Rapid cell-free forward engineering of novel genetic ring oscillators

H Niederholtmeyer, ZZ Sun, Y Hori, E Yeung… - elife, 2015 - elifesciences.org
While complex dynamic biological networks control gene expression in all living organisms,
the forward engineering of comparable synthetic networks remains challenging. The current …

Size control in mammalian cells involves modulation of both growth rate and cell cycle duration

C Cadart, S Monnier, J Grilli, PJ Sáez… - Nature …, 2018 - nature.com
Despite decades of research, how mammalian cell size is controlled remains unclear
because of the difficulty of directly measuring growth at the single-cell level. Here we report …