定量方法
Background: Both between- and within-subject variations in circadian timing matter for health. If lifestyle changes could be used to regulate circadian timing, they would offer accessible and scalable routes to chronotherapy, but this link…
Parameter inference and state estimation in stochastic and partially observed biological systems remain major problems in mathematical biology. In this work, we introduce a two-dimensional lattice graph model for the spread of infectious…
In transcriptomics, gene-set-aware factorization methods such as the Pathway Level Information Extractor (PLIER) are most effective when trained on large, heterogeneous expression compendia. Yet, many clinically relevant cohorts cannot be…
A novel two-phase molecule inference framework, mol-infer, has recently been developed to infer chemical graphs with prescribed abstract structures and desired property values through mixed integer linear programming (MILP) under the…
Antibodies play a central role in the immune response by specifically recognizing and neutralizing antigens, and therapeutic antibodies have become major drugs for cancer and autoimmune diseases. However, their discovery still relies on…
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…
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…
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.…
Graph Neural Networks (GNNs) have emerged as a structurally natural approach for molecular toxicity prediction, operating directly on atomic connectivity without the information loss inherent to fixed-length fingerprints. However, the…
Isotopically non-stationary metabolic flux analysis (INST $^{13}$C-MFA) provides unique insights into cellular physiology but is typically limited by low throughput and high experimental costs. Here, we present a miniaturized and automated…
Accurate quantification of intracellular metabolic fluxes is central to systems biology and biotechnology. Flux estimation relies on biochemical network models, with $^{13}$C metabolic flux analysis (MFA) being the state-of-the-art…
Animal behavior unfolds across many timescales, from fast movement patterns to slow changes in internal states such as hunger, arousal, and circadian phase. These slow variables are rarely measured directly and must instead be inferred from…
Cells in multicellular organisms coordinate to form structural and functional niches. With spatial transcriptomics (ST) enabling gene expression profiling in spatial contexts, it has been revealed that spatial niches serve as cohesive and…
The Chemical Reaction Networks (CRN) interpreted through the differential semantics, even when restricted to elementary reactions with mass action law kinetics, form a Turing-complete language. This means that any computable real function…
Large language models are moving scientific research from text assistance toward agentic workflows, yet biological research requires strong object validation, methodological suitability, reproducibility, and auditability. Prompt…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
Machine learning methods provide a methodological innovation that can help screen for cardiovascular disease through noninvasive and readily available measurement modalities. Recent investments in using electrocardiogram (ECG) data to…
Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We…
Understanding the environmental drivers of forest transpiration is critical for improving global predictions of water availability and ecosystem health. Due to many competing controls on plant water stress and ecosystem transpiration,…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…