Quantitative Biology
We analyzed the body structure of the Blackstripe Cichlid Vieja fenestrata (G\"unther, 1860), a species with highly phenotypic variability, by the Systemics Morphometrics Methodology, previously proposed by one of the authors. From this…
Biological engineering, the convergence between engineering and biology, is at the forefront of significant advances in healthcare, agriculture, and environmental sustainability, making it highly relevant to current scientific and societal…
Autism spectrum disorder (ASD) is associated with atypical large-scale brain organization, yet the functional principles underlying these alterations remain incompletely understood. We examined whether coevolutionary balance, a…
Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell…
This study investigates the influence of aneurysm evolution on hemodynamic characteristics within the sac region. Using computational fluid dynamics (CFD), blood flow through the parent vessel and aneurysm sac was analyzed to assess the…
Type 2 diabetes progresses slowly and may be reversed through lifestyle changes, but quantifying the long-term impact of regular physical activity remains challenging due to sparse longitudinal data. Mechanistic models offer a powerful tool…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Dryland vegetation can survive water stress by forming spatial patterns but is often subjected to herbivory as an additional stress that puts it at risk of desertification. Understanding the mutual relationships between vegetation…
Determining the three-dimensional structure of a protein from its amino-acid sequence remains a fundamental problem in biophysics. The discrete Frenet geometry of the C$_\alpha$ backbone can be mapped, via a Hasimoto-type transform, onto a…
Summary: A bioinformatics tool is presented for estimating recent effective population size by using a neural network to automatically compute linkage disequilibrium-related features as a function of genomic distance between polymorphisms.…
Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods…
Life over the past four billion years has been shaped by proteins and their capacity to assemble into three dimensional conformations. Protein sequence alignments have been the enabling technology for exploring the evolution and functional…
Developmental amnesia, featured with severely impaired episodic memory and almost normal semantic memory, has been discovered to occur in children with hippocampal atrophy. This unique combination of characteristics seems to challenge the…
Medical image foundation models (MIFMs) have demonstrated remarkable potential for a wide range of clinical tasks, yet their development is constrained by the scarcity, heterogeneity, and high cost of large-scale annotated datasets. Here,…
In this paper, we present ChemRecon, a meta-database and Python interface for integrating and exploring biochemical data across multiple heterogeneous resources by consolidating compounds, reactions, enzymes, molecular structures, and…
The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most…
Elucidating the language-brain relationship requires bridging the methodological gap between the abstract theoretical frameworks of linguistics and the empirical neural data of neuroscience. Serving as an interdisciplinary cornerstone,…
From ant-acacia mutualism to performative conflict resolution among Inuit, dedicated punishments between distinct subsets of a population are widespread and can reshape the evolutionary trajectory of cooperation. Existing studies have…
Aortic valve (AV) biomechanics play a critical role in maintaining normal cardiac function. Pathological variations, particularly in bicuspid aortic valves, alter leaflet loading, increase strain, and accelerate disease progression.…
Functional MRI is a neuroimaging technique that analyzes the functional activity of the brain by measuring blood-oxygen-level-dependent signals throughout the brain. The derived functional features can be used for investigating brain…