定量生物学

Mental rotation -- the ability to compare objects seen from different viewpoints -- is a fundamental example of mental simulation and spatial world modeling in humans. Here we propose a mechanistic model of human mental rotation, leveraging…

Projection neurons in the dorsal horn relay nociceptive input to supraspinal centers. During central sensitization, a subset of them switches from tonic firing to plateau potentials with sustained afterdischarges, a change that requires…

Backpropagation is the core learning mechanism underlying deep learning. However, whether and how this algorithm is implemented in the brain remains highly debated. In particular, while forward activations of pretrained models reliably map…

From molecular, cellular, to ecological systems, the modeling of biological processes often stands on the assumption that fast components immediately reach the equilibrium at each moment (quasi-steady state) and only slow components govern…

PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…

Active sensing links behavior and learning through an action-perception loop: actions determine the observations used to update internal predictive models of perception, which subsequently guide the next actions. Predictive-coding…

Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes…

Whisking is a rhythmic and adaptive behavior that rodents use to probe and interact with their environment, and the frequency of movement reflects both sensorimotor processing and internal brain states. A robust and traditional method of…

Simulation of post-prandial pharmacokinetics, such as muscle protein synthesis (MPS) through mTORC1 and insulin-induced glucose uptake, is often challenging due to the computational intensity of the multi-compartmental approach. In this…

Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…

Digital twins of sensory cortex serve as powerful response oracles. Although prediction accuracy is the central metric by which these models are evaluated, it provides limited insight into the latent representations that support those…

Speech neuroprosthesis systems decode intended speech from neural activity in the absence of audible output, offering a path to restoring communication for individuals with speech-impairing conditions. Current approaches decode…

Species sharing a habitat will co-evolve to make use of the available resources, as consumption is modulated by competition and negative feedback loops between consumers and resources. The dietary range of a given species determines the…

Motivation: Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin…

Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data.…

Chronic Wasting Disease (CWD) is a neurological disease impacting deer, elk, moose, and other cervid populations and is caused by a misfolded protein known as a prion. CWD is difficult to control due to the persistence of prions in the…

Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

We study an ecology-inspired model for a population of bounded size, whose dynamics is governed by random birth, death, and immigration events. Stochastic fluctuations in the number of individuals give rise to a succession of alternating…

Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas…