Quantitative Biology
Acute stress alters cognitive performance, yet competing models make divergent predictions regarding the mechanisms, scope, and temporal dynamics of these effects. This large-scale randomized controlled trial tested predications from three…
We present a mathematical model that describes the synergistic mechanism of combined Vesicular Stomatitis Virus (VSV) and Vaccinia Virus (VV). The model captures the dynamic interplay between tumor cells, viral replication, and the…
Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for…
Although most theories posit that natural behavior can be explained as maximizing some form of extrinsic reward, often called utility, some behaviors appear to be reward independent. For instance, spontaneous motor babbling in human…
Atrial fibrillation (AF) is a common cardiac arrhythmia that significantly increases the risk of stroke and heart failure, necessitating reliable and generalizable detection methods from electrocardiogram (ECG) recordings. Although deep…
The presence of correlated noise, arising from a mixture of independent fluctuations and a common noisy input shared across the neural population, is a ubiquitous feature of neural circuits, yet its impact on collective network dynamics…
Neuropixels probes, initially developed for use in small animal models, have transformed basic neuroscience by enabling high-density, single-cell resolution recordings across multiple brain regions simultaneously. The recent development of…
The Moran process is a foundational model of genetic drift and mutation in finite populations. In its standard two-allele form with population size $n$, allele counts, and hence allele frequencies, change through stochastic replacement and…
Tuberculosis (TB) is an airborne disease caused by the pathogen Mycobacterium tuberculosis. In 2023, it returned to being the leading cause of death from an infectious agent globally, replacing COVID-19; in the nineteenth century, one in…
Batch effects represent a major confounder in genomic diagnostics. In copy number variant (CNV) detection from NGS, many algorithms compare read depth between test samples and a reference sample, assuming they are process-matched. When this…
Estimating population-level prevalence and transmission dynamics of wildlife pathogens can be challenging, partly because surveillance data is sparse, detection-driven, and unevenly sequenced. Using highly pathogenic avian influenza A/H5…
In this paper, we study the absorption and fixation times for evolutionary processes on graphs, under different updating rules. While in Moran process a single neighbour is randomly chosen to be replaced, in proliferation processes other…
Bacteria seem masters of chemotaxis, yet recent work suggests otherwise. Henry Mattingly and colleagues (Nature Physics, 2026) argue that Escherichia coli uses only a small fraction of the sensory information available at its surface,…
The outbreak of mutant strains and vaccination behaviors have been the focus of recent epidemiological research, but most existing epidemic models failed to simultaneously capture viral mutation and consider the complexity and behavioral…
Gene regulatory networks are typically modeled using ordinary differential equations (ODEs) with phenomenological Hill functions to represent transcriptional regulation. While computationally efficient, Hill functions lack mechanistic…
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…
Scientists and engineers alike target modeling of complex, high dimensional, and nonlinear dynamical systems as a central goal. Machine learning breakthroughs alongside mounting computation and data advance the efficacy of learning from…
While there are many different methods for peak detection, no automatic methods for marking peak boundaries to calculate area under the curve (AUC) and signal-to-noise ratio (SNR) estimation exist. An algorithm for the automation of liquid…
This article seeks to address the prevailing issue of how to measure specific process components of psychobiological stress responses. Particularly the change of cortisol secretion due to stress exposure has been discussed as an…
Epithelial cells regulate ion concentrations and volume through coordinated membrane pumps, ion channels, and paracellular pathways which can be modeled by classical single-compartment pump-leak equations (PLEs). Many epithelial functions,…