Quantitative Biology
Background: Large foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidney's complex…
Motor adaptation is a learning process that enables humans to regain proficiency when sensorimotor conditions are sustainably altered. Many studies have documented the properties of motor adaptation, yet the underlying mechanisms of motor…
Event cameras are bio-inspired vision sensor that encode visual information with high dynamic range, high temporal resolution, and low latency.Current state-of-the-art event stream processing methods rely on end-to-end deep learning…
Application of electroencephalography (EEG) in educational research has grown substantially, yet a comprehensive integration of methodological frameworks, educational constructs, computational methods, and research gaps remains limited.…
Decoding the heterogeneity of biological neural systems is key to understanding the nervous system's complex dynamical behaviors. This study analyzes the comprehensive Drosophila brain connectome, which is the most recent data set,…
The brain-body-environment framework studies adaptive behavior through embodied and situated agents, emphasizing interactions between brains, biomechanics, and environmental dynamics. However, many models often treat the brain as a network…
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver…
Chronic critical illness (CCI) is a disease state in which, following an initial insult, a patient neither recovers nor dies but instead remains in a state of critical illness. CCI is characterized by prolonged organ dysfunction, weight…
Single-cell and single-nucleus RNA sequencing (scRNA-seq /snRNA-seq) are widely used to reveal heterogeneity in cells, showing a growing potential for precision and personalized medicine. Nonetheless, sustainable drug discovery must be…
This study develops and analyzes an extended Susceptible, Infected, Hospitalized and Recovered (SIHR) model incorporating time dependent control functions to capture preventive measures (e.g., distancing, mask use) and resource limited…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
Machine learning has markedly advanced de novo peptide sequencing (DNS) for mass spectrometry-based proteomics. DNS tools offer a reliable way to identify peptides without relying on reference databases, extending proteomic analysis and…
In metapopulations, genetic variation of local populations is influenced by the genetic content of the founders, and of migrants following establishment. We analyse the effect of multiple paternity on genetic diversity using a model in…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
We suggest a simple deterministic approximation for the growth of the favoured-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitch-hiking. Only when Ns < 10 (N is the…
Selective interleukin-23 receptor antagonists (IL-23RA) show promise for treating moderate to severe ulcerative colitis (UC) but their efficacy and safety are not fully understood. We performed a systematic review and meta-analysis of…
In recent decades, European forests have faced an increased incidence of fire disturbances. This phenomenon is likely to persist, given the rising frequency of extreme events expected in the future. Estimating canopy recovery time after…
Recordings of brain activity, such as functional MRI (fMRI), provide low-dimensional, indirect observations of neural dynamics evolving in high-dimensional, unobservable spaces. Embedding observed brain dynamics into a higher-dimensional…