Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics

M Mofatteh, F Echegaray-Iturra, A Alamban… - Elife, 2021 - elifesciences.org
How do cells perceive time? Do cells use temporal information to regulate the production/
degradation of their enzymes, membranes, and organelles? Does controlling biological time …

[HTML][HTML] Metabolic dynamics during the cell cycle

A Zylstra, M Heinemann - Current Opinion in Systems Biology, 2022 - Elsevier
While we have a solid understanding of the cell biological and biochemical control aspects
of the eukaryotic cell growth and division process, much less is known about the metabolic …

Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast

M Barberis - NPJ systems biology and applications, 2021 - nature.com
Networks of interacting molecules organize topology, amount, and timing of biological
functions. Systems biology concepts required to pin down 'network motifs' or 'design …

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis

T Fan, Y Huang - Scientific Reports, 2021 - nature.com
This study was conducted to investigate epigenetic landscape across multiple species and
identify transcription factors (TFs) and their roles in controlling cell fate decision events …

Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae

CM Kelliher, MW Foster, FC Motta… - Molecular biology of …, 2018 - Am Soc Cell Biol
In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the
periodic expression of many genes during the cell cycle, including gene products required …

Influence of cell volume on the gene transcription rate

JE Pérez-Ortín, MJ García-Marcelo… - … et Biophysica Acta (BBA …, 2024 - Elsevier
Cells vary in volume throughout their life cycle and in many other circumstances, while their
genome remains identical. Hence, the RNA production factory must adapt to changing …

A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets

J Fox, B Cummins, RC Moseley, M Gameiro… - Mathematical …, 2024 - Elsevier
Modeling biological systems holds great promise for speeding up the rate of discovery in
systems biology by predicting experimental outcomes and suggesting targeted …

Interactions, structural aspects and evolutionary perspectives of the yeast 'START'-regulatory network

OOH Stephan - FEMS Yeast Research, 2022 - academic.oup.com
Molecular signal transduction networks, which conduct transcription at the G1 to S phase
transition of the eukaryotic cell division cycle have been identified in diverse taxa from …

Using extremal events to characterize noisy time series

E Berry, B Cummins, RR Nerem, LM Smith… - Journal of mathematical …, 2020 - Springer
Experimental time series provide an informative window into the underlying dynamical
system, and the timing of the extrema of a time series (or its derivative) contains information …

Experimental guidance for discovering genetic networks through hypothesis reduction on time series

B Cummins, FC Motta, RC Moseley… - PLoS computational …, 2022 - journals.plos.org
Large programs of dynamic gene expression, like cell cyles and circadian rhythms, are
controlled by a relatively small “core” network of transcription factors and post-translational …