定量生物学

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…

There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…

Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks…

The United States Food and Drug Administration (FDA) conducted a benefit-risk assessment for Moderna's COVID vaccine mRNA-1273 prior to its full approval, announced 1/31/2022. The FDA's assessment focused on males of ages 18-64 years…

The Collaborative Research Center for Everyday Activity Science & Engineering (CRC EASE) aims to enable robots to perform environmental interaction tasks with close to human capacity. It therefore employs a shared ontology to model the…

The brain interprets visual information through learned regularities, a computation formalized as probabilistic inference under a prior. The visual cortex establishes priors for this inference, some delivered through established top-down…