Related papers: Quantifying yeast colony morphologies with feature…
Clustering artworks is difficult for several reasons. On the one hand, recognizing meaningful patterns in accordance with domain knowledge and visual perception is extremely difficult. On the other hand, applying traditional clustering and…
Structured populations are ubiquitous across the biological sciences. Mathematical models of these populations allow us to understand how individual physiological traits drive the overall dynamics in aggregate. For example, linear age- or…
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is…
Tumor cells acquire different genetic alterations during the course of evolution in cancer patients. As a result of competition and selection, only a few subgroups of cells with distinct genotypes survive. These subgroups of cells are often…
We study the spatial evolutionary dynamics of solid tumors as they obtain additional driver mutations. We start with a cancer clone that expands uniformly in three dimensions giving rise to a spherical shape. We assume that cell division…
Clustering analysis identifies samples as groups based on either their mutual closeness or homogeneity. In order to detect clusters in arbitrary shapes, a novel and generic solution based on boundary erosion is proposed. The clusters are…
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…
This article introduces novel and practicable Bayesian factor analysis frameworks that are computationally feasible for moderate to large spatiotemporal data. Previous Bayesian analysis of spatiotemporal data has utilized a Bayesian factor…
Superficial (two dimensional) crack patterns appear when a thin layer of material elastically attached to a substrate contracts. We study numerically the maturation process undergone by these crack patterns when they are allowed to adapt in…
Functional concurrent, or varying-coefficient, regression models are commonly used in biomedical and clinical settings to investigate how the relation between an outcome and observed covariate varies as a function of another covariate. In…
We introduce a new neural architecture and an unsupervised algorithm for learning invariant representations from temporal sequence of images. The system uses two groups of complex cells whose outputs are combined multiplicatively: one that…
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…
Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Segmenting overlapping cytoplasm of cells in cervical smear images is a clinically essential task, for quantitatively measuring cell-level features in order to diagnose cervical cancer. This task, however, remains rather challenging, mainly…
In this paper, we propose a new texture descriptor, scale selective extended local binary pattern (SSELBP), to characterize texture images with scale variations. We first utilize multi-scale extended local binary patterns (ELBP) with…
Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues, and organs, coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach…
Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and \textit{in vitro} drug testing. In the present paper, a…
Discrete mixture models provide a well-known basis for effective clustering algorithms, although technical challenges have limited their scope. In the context of gene-expression data analysis, a model is presented that mixes over a finite…
The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of…