定量方法
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…
Stride-to-stride fluctuations in human walking carry a fractal correlation structure that reverses sign under external cueing: self-paced gait is persistent, whereas metronomic or visually cued gait is anti-persistent. Three decades of…
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of…
Brain stroke remains one of the principal causes of death and disability worldwide, yet most tabular-data prediction models still hover below the 95% accuracy threshold, limiting real-world utility. Addressing this gap, the present work…
We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed…
Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present…
Soft X-ray tomography provides detailed structural insight into whole cells but is hindered by experimental artifacts such as the missing wedge and by limited availability of annotated datasets. We present SimAQ, a simulation pipeline that…
Alcohol Use Disorder (AUD) is a prevalent addictive disorder affecting an estimated 29.5 million Americans. It is characterized by impaired control over alcohol consumption despite negative consequences. The number of diagnostic criteria…
Proteolysis-targeting chimeras (PROTACs) represent a promising therapeutic modality that induces targeted protein degradation by hijacking the ubiquitin-proteasome system. However, rational PROTAC design remains challenging due to the…