The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

M Ebadi, Q Bafort, E Mizrachi… - Proceedings of the …, 2023 - National Acad Sciences
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas
some view WGD mainly as detrimental and an evolutionary dead end, there is growing …

High-resolution studies of lysis–lysogeny decision-making in bacteriophage lambda

Q Shao, JT Trinh, L Zeng - Journal of Biological Chemistry, 2019 - ASBMB
Cellular decision-making guides complex development such as cell differentiation and
disease progression. Much of our knowledge about decision-making is derived from simple …

The systems biology of single-cell aging

R Song, EA Sarnoski, M Acar - Iscience, 2018 - cell.com
Aging is a leading cause of human morbidity and mortality, but efforts to slow or reverse its
effects are hampered by an incomplete understanding of its multi-faceted origins. Systems …

A synthetic circuit for buffering gene dosage variation between individual mammalian cells

J Yang, J Lee, MA Land, S Lai, OA Igoshin… - Nature …, 2021 - nature.com
Precise control of gene expression is critical for biological research and biotechnology.
However, transient plasmid transfections in mammalian cells produce a wide distribution of …

Noise reduction facilitated by dosage compensation in gene networks

W Peng, R Song, M Acar - Nature communications, 2016 - nature.com
Genetic noise together with genome duplication and volume changes during cell cycle are
significant contributors to cell-to-cell heterogeneity. How can cells buffer the effects of these …

Noise reduction as an emergent property of single-cell aging

P Liu, R Song, GL Elison, W Peng, M Acar - Nature communications, 2017 - nature.com
Noise-induced heterogeneity in gene expression is an inherent reality for cells. However, it
is not well understood how noise strength changes for a single gene while the host cell is …

Coupling of DNA replication and negative feedback controls gene expression for cell-fate decisions

Q Shao, MG Cortes, JT Trinh, J Guan, G Balázsi… - Iscience, 2018 - cell.com
Cellular decision-making arises from the expression of genes along a regulatory cascade,
which leads to a choice between distinct phenotypic states. DNA dosage variations, often …

Impact of the cell division cycle on gene circuits

V Bierbaum, S Klumpp - Physical biology, 2015 - iopscience.iop.org
In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus,
protein concentrations vary over the cell division cycle. We have developed a theoretical …

A cell size-and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells

R Song, W Peng, P Liu, M Acar - BMC systems biology, 2015 - Springer
Background Despite the development of various modeling approaches to predict gene
network activity, a time dynamic stochastic model taking into account real-time changes in …

Modeling aging and its impact on cellular function and organismal behavior

E Santiago, DF Moreno, M Acar - Experimental Gerontology, 2021 - Elsevier
Aging is a complex phenomenon of functional decay in a biological organism. Although the
effects of aging are readily recognizable in a wide range of organisms, the cause (s) of aging …