Systems biology primer: the basic methods and approaches

I Tavassoly, J Goldfarb, R Iyengar - Essays in biochemistry, 2018 - portlandpress.com
Systems biology is an integrative discipline connecting the molecular components within a
single biological scale and also among different scales (eg cells, tissues and organ systems) …

Steps in mechanotransduction pathways that control cell morphology

H Wolfenson, B Yang, MP Sheetz - Annual review of physiology, 2019 - annualreviews.org
It is increasingly clear that mechanotransduction pathways play important roles in regulating
fundamental cellular functions. Of the basic mechanical functions, the determination of …

A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes

KE Scott, SI Fraley, P Rangamani - … of the National Academy of Sciences, 2021 - pnas.org
YAP/TAZ is a master regulator of mechanotransduction whose functions rely on
translocation from the cytoplasm to the nucleus in response to diverse physical cues …

Machine-learning-based approach to decode the influence of nanomaterial properties on their interaction with cells

AV Singh, RS Maharjan, A Kanase… - … Applied Materials & …, 2020 - ACS Publications
In an in vitro nanotoxicity system, cell–nanoparticle (NP) interaction leads to the surface
adsorption, uptake, and changes into nuclei/cell phenotype and chemistry, as an indicator of …

Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome

K Venkatraman, CT Lee, GC Garcia… - The EMBO …, 2023 - embopress.org
Cristae are high‐curvature structures in the inner mitochondrial membrane (IMM) that are
crucial for ATP production. While cristae‐sha** proteins have been defined, analogous …

Automated brightfield morphometry of 3D organoid populations by OrganoSeg

MA Borten, SS Bajikar, N Sasaki, H Clevers… - Scientific reports, 2018 - nature.com
Spheroid and organoid cultures are powerful in vitro models for biology, but size and shape
diversity within the culture is largely ignored. To streamline morphometric profiling, we …

Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo

GW Bassel, P Stamm, G Mosca… - Proceedings of the …, 2014 - pnas.org
Morphogenesis occurs in 3D space over time and is guided by coordinated gene expression
programs. Here we use postembryonic development in Arabidopsis plants to investigate the …

Robust and automated detection of subcellular morphological motifs in 3D microscopy images

MK Driscoll, ES Welf, AR Jamieson, KM Dean… - Nature …, 2019 - nature.com
Rapid developments in live-cell three-dimensional (3D) microscopy enable imaging of cell
morphology and signaling with unprecedented detail. However, tools to systematically …

Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction

H Jafarinia, A Khalilimeybodi, J Barrasa-Fano… - NPJ systems biology …, 2024 - nature.com
YAP/TAZ signaling pathway is regulated by a multiplicity of feedback loops, crosstalk with
other pathways, and both mechanical and biochemical stimuli. Computational modeling …

Cell shape and the microenvironment regulate nuclear translocation of NF‐κB in breast epithelial and tumor cells

JE Sero, HZ Sailem, RC Ardy, H Almuttaqi… - Molecular systems …, 2015 - embopress.org
Although a great deal is known about the signaling events that promote nuclear
translocation of NF‐κB, how cellular biophysics and the microenvironment might regulate …