定量生物学
Any mass action network gives rise to a parameterised family of polynomial equations whose positive solutions are the positive equilibria of the network. Here, we consider alternative systems of equations, whose solutions are in smooth,…
In biological systems, neural circuits compute through directed, short-latency interactions whose effects unfold across multiple time scales and behavioral contexts. We address the problem of inferring these local, lag-specific interactions…
Gene programs co-activate within cells, but existing single-cell methods either treat programs independently or require experimental perturbation data to model their interactions. We introduce ORBIT, a self-supervised transformer that…
Quantitative susceptibility mapping (QSM) has been increasingly applied in longitudinal studies of neurodegenerative diseases and aging to assess temporal alterations in brain iron and myelin. The accuracy of such investigations depends on…
Regeneration of the nervous system after injury remains an important therapeutic objective, especially in the central nervous system (CNS), in which regeneration is restricted by both neuronal limitations as well as adverse extracellular…
Human cognition emerges from coordinated spiking dynamics in distributed neural circuits, where information is encoded via both firing rates and precise spike timing determined by brain rhythms. Inspired by this notion, we propose a…
How do we measure genuine understanding in artificial cognitive systems? Current approaches face a measurement gap: probabilistic systems refine confidence gradually, practice-based systems compile knowledge through repeated execution, and…
Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases…
Indoor lighting affects cognition, affect, and behavioural regulation, but these effects are often treated as isolated findings rather than as parts of a unified process. This paper proposes an active inference account of shared indoor…
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are a promising therapy for regenerating myocardium after infarction, but their use is limited by graft-related arrhythmias that frequently occur shortly after transplantation.…
Hill functions, the standard tool for modelling gene regulatory networks, carry three structural flaws when the cooperativity exponent is non-integer: loss of global smoothness, silent complex-valued arithmetic corruption of ODE…
De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applications in biotechnology and medicine. Existing approaches…
In this work, we introduce CellxPert, a scalable multimodal foundation model that unifies single-cell and spatial multi-omics within a common representation space. CellxPert jointly encodes transcriptomic (scRNA-seq),…
Agentic AI scientists equipped with domain-specific tools are rapidly entering scientific workflows across disciplines, with especially strong uptake in the life sciences where they can be used for literature synthesis, sequence analysis,…
Neuroscience and Artificial Intelligence (AI) have made impressive progress in recent years but remain only loosely interconnected. Based on a workshop convened by the National Science Foundation in August 2025, we identify three…
The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold…
This work introduces a statistical procedure to infer the interaction graph of neuronal networks modeled by Galves-L\"ocherbach dynamics. The methodology performs bivariate inference, identifying synaptic links from the spike trains of…
We present a compact dynamical mean-field theory (DMFT) for large networks of coupled phase oscillators whose phases live on the circle $S^1$ and interact with both coherent mean-field coupling and quenched randomness. Starting from wrapped…
Genotype-to-phenotype prediction is a central goal of statistical genetics, yet practical comparisons of prediction workflows remain limited in small, heterogeneous, participant-shared genomic datasets. Here, we benchmarked end-to-end…
Affinity-based biosensors have become indispensable in modern diagnostics and health monitoring. While considerable research has focused on optimizing analyte transport and binding kinetics, a fundamental parameter - sample volume - remains…