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Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress,…

Molecular Networks · Quantitative Biology 2015-05-11 I. Tavassoly , J. Parmar , A. N. Shajahan-Haq , R. Clarke , W. T. Baumann , J. J. Tyson

A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and…

Cell Behavior · Quantitative Biology 2009-09-29 B. Szabo , Zs. Kornyei , J. Zach , D. Selmeczi , G. Csucs , A. Czirok , T. Vicsek

Autophagy is an intracellular degradation process that employs complex membrane dynamics to isolate and break down cellular components. However, many unanswered questions remain concerning remodeling of autophagic membranes. Here, we focus…

Subcellular Processes · Quantitative Biology 2019-03-25 Jaime Agudo-Canalejo , Roland L. Knorr

Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…

Biological Physics · Physics 2013-05-29 L. Bruno , V. Levi , M. Brunstein , M. A. Despósito

Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on…

Biological Physics · Physics 2025-08-26 Tianxiang Ma , Valeriia Grudtsyna , Robin V. Bölsterli , Amin Doostmohammadi

Autophagy is an intracellular degradation process that is mediated by de novo formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a disk-shaped membrane cisterna grows, bends to become a cup-shaped…

Biological Physics · Physics 2020-09-04 Yuji Sakai , Ikuko Koyama-Honda , Masashi Tachikawa , Roland L. Knorr , Noboru Mizushima

Axon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely- Duane Retraction Syndrome (DRS) , Horizontal Gaze Palsy with Progressive Scoliosis…

Other Quantitative Biology · Quantitative Biology 2018-05-04 Ishtiaque Ahammad

Early endolysosomal and autophagic defects are among the earliest cellular alterations observed in Alzheimers disease (AD), yet the molecular drivers linking amyloid precursor protein (APP) metabolism to vesicle trafficking dysfunction…

Neurons and Cognition · Quantitative Biology 2026-04-28 Hao Huang , Kaijing Xu , Michael Lardelli

Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…

Biological Physics · Physics 2015-02-10 Jingwei Li , Yunxin Zhang

The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…

Statistical Mechanics · Physics 2020-03-11 Annwesha Dutta , Gunter M Schütz , Debashish Chowdhury

Atherosclerotic plaques are fatty growths in artery walls that cause heart attacks and strokes. Plaque formation is orchestrated by macrophages that are recruited to the artery wall to consume and remove blood-derived lipids, such as…

Cell Behavior · Quantitative Biology 2022-05-12 M. G. Watson , K. L. Chambers , M. R. Myerscough

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…

Statistical Mechanics · Physics 2009-02-18 Michael Bachmann , Wolfhard Janke

Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…

Biological Physics · Physics 2026-04-10 Le Qiao , Peter Gispert , Lukas S. Stelzl , Friederike Schmid

Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene translation includes several steps. During the elongation step,…

Genomics · Quantitative Biology 2014-07-02 Yoram Zarai , Michael Margaliot , Tamir Tuller

Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…

Molecular Networks · Quantitative Biology 2015-09-25 Denis Michel

Atherosclerosis is an inflammatory disease characterised by the formation of plaques, which are deposits of lipids and cholesterol-laden macrophages that form in the artery wall. The inflammation is often non-resolving, due in large part to…

Cell Behavior · Quantitative Biology 2024-01-19 Ishraq U. Ahmed , Helen M. Byrne , Mary R. Myerscough

Pediatric high grade gliomas are lethal evolutionary disorders with stalled developmental trajectories and disrupted differentiation hierarchies. We integrate transcriptional and algorithmic network complexity based perturbation analysis to…

Quantitative Methods · Quantitative Biology 2025-09-24 Abicumaran Uthamacumaran , Hector Zenil

Influenza viruses enter a cell via endocytosis after binding to the surface. During the endosomal journey, acidification triggers a conformational change of the virus spike protein hemagglutinin (HA) that results in escape of the viral…

Subcellular Processes · Quantitative Biology 2015-10-22 Thibault Lagache , Christian Sieben , Tim Meyer , Andreas Herrmann , David Holcman

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are…

Molecular Networks · Quantitative Biology 2017-08-23 Yan Fu , Trevor Glaros , Meng Zhu , Ping Wang , Zhanghan Wu , John J Tyson , Liwu Li , Jianhua Xing

Collective cell migration underlies important biological processes, such as embryonic development, wound healing and cancer invasion. While many aspects of single cell movements are now well established, the mechanisms leading to…

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