定量生物学
Biological neural networks (BNNs) are increasingly explored for their rich dynamics, parallelism, and adaptive behavior. Beyond understanding their function as a scientific endeavour, a key focus has been using these biological systems as a…
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods from Potts models to AlphaFold, which infer protein structure…
Epidemic and pandemic preparedness with rapid outbreak response rely on timely, trustworthy evidence. Mathematical models are crucial for supporting timely and reliable evidence generation for public health decision-making with models…
On exposure to 1,2-propanediol (1,2-PD), Salmonella enterica serovar Typhimurium LT2 produces 1,2-PD utilization (Pdu) microcompartments (MCPs), nanoscale protein-bound shells that encapsulate metabolic enzymes. MCPs serve as a…
Modeling peptide cyclization is critical for the virtual screening of candidate peptides with desirable physical and pharmaceutical properties. This task is challenging because a cyclic peptide often exhibits diverse, ring-shaped…
How do social animals make effective decisions in the absence of a leader? While coordination can improve accuracy, it also introduces delays as information propagates through the group. In changing environments, these delays can outweigh…
Fluid-structure interaction (FSI) simulation of biological systems presents significant computational challenges, particularly for applications involving large structural deformations and contact mechanics, such as heart valve dynamics.…
Synthetic molecular communication (MC) in the cardiovascular system is a key enabler for many envisioned medical applications inside the human body, such as targeted drug delivery, early disease detection, and continuous health monitoring.…
This study investigates how listeners perceive consonance and dissonance in dyads composed of simple (sine) tones, focusing on the effects of frequency ratio ($R$) and mean frequency ($F$). Seventy adult participants - categorized by…
Integration and analysis of multi-omics data provide valuable insights for improving cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality…
Foundation models are transforming neuroscience but are often prohibitively large, data-hungry, and difficult to deploy. Here, we introduce BrainSymphony, a lightweight and parameter-efficient foundation model with plug-and-play integration…
Chemical language models (CLMs) are increasingly used for molecular design and property prediction. Because these models learn from textual encodings of molecules, differences in how such encodings are generated may affect their behavior.…
We develop a neurogeometric model for the arm area of motor cortex, which encodes complex motor primitives, ranging from simple movement features like movement direction, to short hand trajectories, termed fragments, and ultimately to more…
Spoken language is often, if not always, understood in a context formed by the identity of the speaker. For example, we can easily make sense of an utterance such as "I'm going to have a manicure this weekend" or "The first time I got…
Multivariate oscillatory signals from complex systems often exhibit non-stationary dynamics and metastable regime structure, making dynamical interpretation challenging. We introduce a ``dynamical microscope'' framework that converts…
To be practical for real-life applications, models for brain-computer interfaces must be easily and quickly deployable on new subjects, effective on affordable scanning hardware, and small enough to run locally on accessible computing…
Agentic systems for drug discovery have demonstrated autonomous synthesis planning, literature mining, and molecular design. We ask how well they generalize. Evaluating six frameworks against 15 task classes drawn from peptide therapeutics,…
Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their…
Ancestral recombination graphs (ARGs) are an increasingly important component of population and statistical genetics. The tskit library has become key infrastructure for the field, providing an expressive and general representation of ARGs…
Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact,…