Related papers: Epigenetic Tracking: a Model for Multicellular Bio…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
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…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
In this survey article, a variety of systems modeling tumor growth are discussed. In accordance with the hallmarks of cancer, the described models incorporate the primary characteristics of cancer evolution. Specifically, we focus on…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using…
Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
Epigenetics has captured the attention of scientists in the past decades, yet its scope has been continuously changing. In this paper, we give an overview on how and why its definition has evolved and suggest several clarification on 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…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
Human embryonic stem cells (ESC) are undifferentiated and are endowed with the capacities of self renewal and pluripotential differentiation. Adult stem cells renew their own tissue, but whether they can trans-differentiate to other tissues…