The causes of evolvability and their evolution

JL Payne, A Wagner - Nature Reviews Genetics, 2019 - nature.com
Evolvability is the ability of a biological system to produce phenotypic variation that is both
heritable and adaptive. It has long been the subject of anecdotal observations and …

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 …

Single-cell measurement of plasmid copy number and promoter activity

B Shao, J Rammohan, DA Anderson… - Nature …, 2021 - nature.com
Accurate measurements of promoter activities are crucial for predictably building genetic
systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts …

Homeostasis of protein and mRNA concentrations in growing cells

J Lin, A Amir - Nature communications, 2018 - nature.com
Many experiments show that the numbers of mRNA and protein are proportional to the cell
volume in growing cells. However, models of stochastic gene expression often assume …

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 …

What's luck got to do with it: single cells, multiple fates, and biological nondeterminism

O Symmons, A Raj - Molecular cell, 2016 - cell.com
The field of single-cell biology has morphed from a philosophical digression at its inception,
to a playground for quantitative biologists, to a major area of biomedical research. The last …

Single-cell analysis of transcription kinetics across the cell cycle

SO Skinner, H Xu, S Nagarkar-Jaiswal, PR Freire… - Elife, 2016 - elifesciences.org
Transcription is a highly stochastic process. To infer transcription kinetics for a gene-of-
interest, researchers commonly compare the distribution of mRNA copy-number to the …

BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells

M Douaihy, R Topno, M Lagha, E Bertrand… - Nucleic Acids …, 2023 - academic.oup.com
Monitoring transcription in living cells gives access to the dynamics of this complex
fundamental process. It reveals that transcription is discontinuous, whereby active periods …

Sequence specificity in DNA binding is mainly governed by association

E Marklund, G Mao, J Yuan, S Zikrin… - Science, 2022 - science.org
Sequence-specific binding of proteins to DNA is essential for accessing genetic information.
We derive a model that predicts an anticorrelation between the macroscopic association and …

Measurement of gene regulation in individual cells reveals rapid switching between promoter states

LA Sepúlveda, H Xu, J Zhang, M Wang, I Golding - Science, 2016 - science.org
In vivo mapping of transcription-factor binding to the transcriptional output of the regulated
gene is hindered by probabilistic promoter occupancy, the presence of multiple gene copies …