Related papers: Quantifying yeast colony morphologies with feature…
It is widely accepted that population genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution.…
Bacteria are prolific at colonizing diverse surfaces under a widerange of environmental conditions, and exhibit fascinating examples of self-organization across scales. Though it has recently attracted considerable interest, the role of…
The phenotypic plasticity of cancer cells has received special attention in recent years. Even though related models have been widely studied in terms of mathematical properties, a thorough statistical analysis on parameter estimation and…
Recent advances in multiplex imaging have enabled researchers to locate different types of cells within a tissue sample. This is especially relevant for tumor immunology, as clinical regimes corresponding to different stages of disease or…
The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for…
We study the clustering of a model cyanobacterium \textit{Synechocystis} into microcolonies. The bacteria are allowed to diffuse onto surfaces of different hardness, and interact with the others by aggregation and detachment. We find that…
The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a…
Fungi undergo dynamic morphological transformations throughout their lifecycle, forming intricate networks as they transition from spores to mature mycelium structures. To support the study of these time-dependent processes, we present a…
The evolutionary success of bacteria lies in their ability to form complex surface-associated communities in diverse biophysical settings. However, it remains poorly understood how compliance of soft surfaces, measured in terms of their…
High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…
The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells…
Exemplar-based texture synthesis is the process of generating, from an input sample, new texture images of arbitrary size and which are perceptually equivalent to the sample. The two main approaches are statistics-based methods and patch…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
An extension of coupled maps is given which allows for the growth of the number of elements, and is inspired by the cell differentiation problem. The growth of elements is made possible first by clustering the phases, and then by…
In this paper we present a methodology that uses convolutional neural networks (CNNs) for segmentation by iteratively growing predicted mask regions in each coordinate direction. The CNN is used to predict class probability scores in a…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
We use a semisupervised learning algorithm based on a topological data analysis approach to assign functional categories to yeast proteins using similarity graphs. This new approach to analyzing biological networks yields results that are…
Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during…
A time- and space-discrete model for the growth of a rapidly saturating local biological population $N(x,t)$ is derived from a hierarchical random deposition process previously studied in statistical physics. Two biologically relevant…
Spatial domain identification requires jointly modeling molecular signatures and physical coordinates, yet current tools frequently over-smooth biological boundaries, require user-specified cluster numbers, and lack principled multimodal…