Quantitative Biology
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
The need for effective biomonitoring in wastewater has become clear due to the impracticality of continuously tracking all chemicals and emerging contaminants in the aquatic exposome. Effect-based biomonitoring provides a cost-effective…
Large language models (LLMs) increasingly mediate human decision-making and behaviour. Ensuring LLM processing of moral meaning therefore has become a critical challenge. Current approaches rely predominantly on bottom-up methods such as…
The Adaptive Exponential Integrate-and-Fire (AdEx) model is a simplified framework that effectively characterizes neuronal electrical activity. The aim of this paper is to employ phase plane analysis to systematically investigate diverse…
This tutorial covers the emerging field of coarse-grained cellular growth modeling, and aims to bridge the gap between theoretical foundations and practical application. By adopting an original "cookbook" approach, it is designed to offer a…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
The linear noise approximation (LNA) describes the random fluctuations from the mean-field concentrations of a chemical reaction network due to intrinsic noise. It is also used as a test probe to determine the accuracy of reduced…
Traumatic Brain Injury (TBI) results from an impact or concussion to the head with the injury being specifically characterized through pathological degradation at various biological length scales. Following injury, various mechanical…
Biological information processing often arises from mesoscopic molecular systems operating far from equilibrium, yet their complexity can make the underlying principles difficult to visualize. In this study, we introduce a macroscopic…
Clemmesen's hook refers to a commonly observed slowdown and rebound in breast cancer incidence around the age at menopause. It suggests a shift in the underlying carcinogenic dynamics, but the mechanistic basis remains poorly understood.…
In recent years there has been a paradigm shift from the study of local task-related activation to the organization and functioning of large-scale functional and structural brain networks. However, a long-standing challenge in this…
Identifying key driver genes governing biological processes such as development and disease progression remains a challenge. While existing methods can reconstruct cellular trajectories or infer static gene regulatory networks (GRNs), they…
Blini is a tool for quick lookup of nucleotide sequences in databases, and for quick dereplication of sequence collections. It is meant to help clean and characterize large collections of assembled contigs or long sequences that would…
We look at the interaction of dispersal and environmental stochasticity in $n$-patch models. We are able to prove persistence and extinction results even in the setting when the dispersal rates are stochastic. As applications we look at…
Biomarkers are critical tools in the diagnosis and monitoring of neurodegenerative diseases. Reliable quantification depends on assay validity, especially the demonstration of parallelism between diluted biological samples and the assay's…
Accurate diagnosis of spitzoid tumors (ST) is critical to ensure a favorable prognosis and to avoid both under- and over-treatment. Epigenetic data, particularly DNA methylation, provide a valuable source of information for this task.…
Cell populations invade through a combination of proliferation and motility. Proliferation depends on the internal timing of cell division: how long cells take to complete the cell cycle. This timing varies substantially within (and across)…
In this work, the effects of dopamine neurotransmitter within the Cortico-Striatal-Thalamo-Cortical (CSTC) loop have been investigated. Simulations confirmed dopamine facilitates movement via thalamic disinhibition. Analysis of its impact…
Seagrass meadows contribute to the conservation of marine ecosystems, reduction in global warming impacts and pathogen controls. However, the decline in seagrass habitats due to environmental loads has become an urgent global issue. One way…
We developed an explainable deep learning framework integrating protein-protein interaction (PPI) network centrality metrics with node embeddings for cancer therapeutic target prioritization. A high-confidence PPI network was constructed…