Quantitative Biology
Objectives: The role of advanced diffusion-weighted imaging (DWI) in chronic liver disease (CLD) has not been fully studied. Chronic liver disease (CLD) is a progressive deterioration of liver functions, caused by one or more etiology. This…
This study explores how the selection of neuron models and learning rules impacts the classification performance of Spiking Neural Networks (SNNs), with a focus on applications in bio-signal processing. We compare biologically inspired…
Physical activity is a modifiable lifestyle factor with potential to support cognitive resilience. However, the association of moderate-to-vigorous physical activity (MVPA) intensity, and timing, with cognitive function and region-specific…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
Dynamical systems theory describes how interacting quantities change over time and space, from molecular oscillators to large-scale biological patterns. Such systems often involve nonlinear feedbacks, delays, and interactions across scales.…
The majority of therapeutic monoclonal antibodies (mAbs) on the market are produced using Chinese Hamster Ovary (CHO) cells cultured at scale in chemically defined cell culture medium. Because of the high costs associated with mammalian…
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…
As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithmic framework for the Minimum-Cost Synthetic Genome Planning…
We develop a mother machine-like microfluidic device specifically designed to track the proliferation of T-cells via live-cell microscopy. Although numerous microfluidic setups have been developed to study cell proliferation at the…
Accurate epidemic forecasting is critical for effective public health interventions. This study compares Bayesian and Frequentist estimation frameworks within deterministic compartmental epidemic models, focusing on nonlinear least squares…
We propose a multi-patch model of cholera transmission integrating environmental contamination, human mobility, and nutritional vulnerability. The population is stratified by food security status, and transmission occurs via human contact,…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
Cryo-electron microscopy can now routinely deliver atomic resolution structures for a variety of biological systems. The relevance and value of these structures is directly related to their ability to help rationalize experimental…
Improved hygiene and infant vaccinations have led to age specific variations in hepatitis A antibody prevalence in Korea, with lower rates among individuals in their 20s to 40s. Given that the fatality rate of hepatitis A increases for…
Brain morphology is shaped by genetic and mechanical factors and is linked to biological development and diseases. Its fractal-like features, regional anisotropy, and complex curvature distributions hinder quantitative insights in medical…
Molecular docking is a cornerstone of drug discovery, relying on high-resolution ligand-bound structures to achieve accurate predictions. However, obtaining these structures is often costly and time-intensive, limiting their availability.…
The functional brain network emerges from the complex, coordinated activity of distinct yet connected regions, which underlie the diverse repertoire of human cognitive functions. Structural Balance Theory (SBT) has been successfully applied…
Finding interesting phenomena is the core of scientific discovery, but it is a manual, ill-defined concept. We present an integrative pipeline for automating the discovery of interesting simple hypotheses (feature-target relations with…