Related papers: Screening by changes in stereotypical behavior dur…
Animal behavior spans many timescales, from short, seconds-scale actions to circadian rhythms over many hours to life-long changes during aging. Most quantitative behavior studies have focused on short-timescale behaviors such as locomotion…
Non-genetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong…
Feature or variable selection is a problem inherent to large data sets. While many methods have been proposed to deal with this problem, some can scale poorly with the number of predictors in a data set. Screening methods scale linearly…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Animals often exhibit changes in their behavior during migration. Telemetry data provide a way to observe geographic position of animals over time, but not necessarily changes in the dynamics of the movement process. Continuous-time models…
The classification of microscopy videos capturing complex cellular behaviors is crucial for understanding and quantifying the dynamics of biological processes over time. However, it remains a frontier in computer vision, requiring…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
Many applications of machine learning methods involve an iterative protocol in which data are collected, a model is trained, and then outputs of that model are used to choose what data to consider next. For example, one data-driven approach…
Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for…
Metastasis is a process of cell migration that can be collective and guided by chemical cues. Viewing metastasis in this way, as a physical phenomenon, allows one to draw upon insights from other studies of collective sensing and migration…
Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…
High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…
For the past few years, deep generative models have increasingly been used in biological research for a variety of tasks. Recently, they have proven to be valuable for uncovering subtle cell phenotypic differences that are not directly…
Single-cell omics enable the profiles of cells, which contain large numbers of biological features, to be quantified. Cluster analysis, a dimensionality reduction process, is used to reduce the dimensions of the data to make it…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion.…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…