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Active nematic models explain the topological defects and flow patterns observed in epithelial tissues, but the nature of active stress-whether it is extensile or contractile, a key parameter of the theory-is not well established…
The behavior of a colloidal suspension of rod-like {\it fd} viruses in the nematic phase, subjected to steady state and transient shear flows is studied. The monodisperse nature of these rods combined with relatively small textural…
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we…
Competition between parasitoids can reduce the success of pest control in biological programs using two species as bio-control agents or when multiple species exploit the same host crop. Parasitoid foraging behavior and the ability to…
The amount of power in different frequency bands of the electroencephalogram (EEG) carries information about the behavioral state of a subject. Hence, neurologists treating epileptic patients monitor the temporal evolution of the different…
We study the evolution of a pathogen with two allelic types infecting a population of hosts, where within-host type frequencies evolve in discrete time. Our framework is built on a two-parameter family of transition kernels on [0,1], which…
Early initiation of alcohol, nicotine, cannabis, and other substances predicts later substance use disorders and related psychopathology. We integrate time-varying environmental factors with polygenic risk scores (PRS) in a longitudinal…
During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated…
Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…
Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly…
Background: Psoriasis is a multifactorial chronic inflammatory disorder of the skin with significant morbidity, characterized by hyper proliferation of the epidermis. Even though psoriasis etiology is not fully understood, it is believed to…
Background: Trypanosoma brucei is the causative agent of human African sleeping sickness and Nagana in cattle. In addition to being an important pathogen T. brucei has developed into a model system in cell biology. Results: Using Stable…
An accurate method for enumerating pathogen indicators, such as Escherichia coli (E. coli), and Salmonella spp. is important for assessing the safety of compost samples. This study aimed to determine the occurrence of pathogen indicators in…
Gene expression depends on thousands of factors and we usually only have access to tens or hundreds of observations of gene expression levels meaning we are in a high-dimensional setting. Additionally we don't always observe or care about…
Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Network ecology is a rising field of quantitative biology representing ecosystems as complex networks. A suitable example is parasite spreading: several parasites may be transmitted among their hosts through different mechanisms, each one…
The transcription factors, such as activators and repressors, can interact with the promoter of gene either in a competitive or non-competitive way. In this paper, we construct a stochastic model with non-competitive transcriptional…