Related papers: Epigenetic Tracking: a model for all biology
A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Cell detection and tracking are paramount for bio-analysis. Recent approaches rely on the tracking-by-model evolution paradigm, which usually consists of training end-to-end deep learning models to detect and track the cells on the frames…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
A new model is suggested and used to mimic various spatial or temporal designs in biological or non biological formations where the focus is on the normal or irregular electrical signals coming from human heart (ECG) or brain (EEG). The…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
Living biological tissue is a complex system, constantly growing and changing in response to external and internal stimuli. These processes lead to remarkable and intricate changes in shape. Modeling and understanding both natural and…
Ecology studies biodiversity in its variety and complexity. It describes how species distribute and perform in response to environmental changes. Ecological processes and structures are highly complex and adaptive. In order to quantify…