Transcription in living cells: molecular mechanisms of bursting

J Rodriguez, DR Larson - Annual review of biochemistry, 2020 - annualreviews.org
gene regulation at the single-cell level. … or how gene activity or expression is modulated
in response to stimuli, we can obtain a unique and dynamic perspective of gene regulation. …

Multiplex transcriptional characterizations across diverse bacterial species using cellfree systems

SS Yim, NI Johns, J Park, ALC Gomes… - Molecular Systems …, 2019 - embopress.org
… approaches to new areas of bacterial physiology. … cellfree expression systems derived
from eukaryotic organisms to study and engineer increasingly complex layers of gene regulation

Predictive biology: modelling, understanding and harnessing microbial complexity

AJ Lopatkin, JJ Collins - Nature Reviews Microbiology, 2020 - nature.com
… value in a wide range of physiological settings. These … metabolism in addition to
transcriptional control to achieve … As enumerated in the above sections, predictive modelling has …

A dynamical paradigm for molecular cell biology

JJ Tyson, B Novak - Trends in cell biology, 2020 - cell.com
… important in understanding some aspect of cell physiology. The model may be relatively simple,
… To connect this abstract mathematical notion to cell physiology we must recognize that a …

In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller

DK Agrawal, R Marshall, V Noireaux… - Nature …, 2019 - nature.com
… , a phenomenon in which physiological variables are … In addition, the cell-free reaction
platform makes the design … to the limitations of quantitative predictive models for the latter …

A genetic mammalian proportional–integral feedback control circuit for robust and precise gene regulation

T Frei, CH Chang, M Filo… - Proceedings of the …, 2022 - National Acad Sciences
… universal gene regulatory motif that produces robust perfect adaptation for mammalian cells,
… The importance of homeostasis is clearly exemplified in physiology and medicine, where a …

Transcription factor dynamics

F Lu, T Lionnet - Cold Spring Harbor Perspectives in …, 2021 - cshperspectives.cshlp.org
… key roles in transcription regulation that are not yet fully understood. The emerging model is
that … Furthermore, in situ studies are necessary to recapitulate physiological chromatin states …

Eukaryotic transcription factors can track and control their target genes using DNA antennas

M Castellanos, N Mothi, V Muñoz - Nature Communications, 2020 - nature.com
… regions of genes under its transcriptional control. We utilize biophysical methods to dissect
the binding process, statistical mechanical modeling to integrate and rationalize the results, …

Transcription factors and DNA play hide and seek

DM Suter - Trends in cell biology, 2020 - cell.com
Gene expression is central to all living systems and subject to a complex regulation all the
way from RNA synthesis to … Transcriptional initiation is the most important point of control in the …

Figure 1 theory meets figure 2 experiments in the study of gene expression

R Phillips, NM Belliveau, G Chure… - Annual review of …, 2019 - annualreviews.org
… these same kinds of predictive models can describe induction of transcription. Furthermore,
… our results entail for future efforts in understanding gene regulation. We argue that we have …