定量生物学
Genome-wide association studies (GWAS) are widely used to discover genetic variants associated with diseases. To control false positives, all findings from GWAS need to be verified with additional evidences, even for associations discovered…
Protein function is executed at the molecular surface, where shape and chemistry act together to govern interaction. Yet most comparison methods treat these aspects separately, privileging either global fold or local descriptors and missing…
We present a mathematical model of the curvature blindness illusion in which sinusoids appear as angular zigzags when drawn with alternating contrast polarity against a gray background. The model identifies two complementary mechanisms,…
Animal brains exhibit remarkable efficiency in perception and action, while being robust to both external and internal perturbations. The means by which brains accomplish this remains, for now, poorly understood, hindering our understanding…
Biological learning achieves temporal credit assignment despite sparse and imprecise feedback, often relying on neuromodulatory signals acting over space and time. Here, we introduce a learning mechanism in which error information diffuses…
Homeostasis is widely observed in biological systems and refers to their ability to maintain an output quantity approximately constant despite variations in external disturbances. Mathematically, homeostasis can be formulated through an…
Classical reaction-diffusion models of the 14th-century Black Death fail to explain the rapid genetic radiation of \textit{Yersinia pestis} and the anomalous emergence of vast, untouched geographic safe zones, such as Central Europe. In…
Phase-amplitude coupling (PAC), a form of cross-frequency interaction, has been implicated in various cognitive functions and, by extension, in neural communication and information integration. Accurately detecting and characterising PAC is…
Mass-action networks are special cases of chemical reaction networks. For these systems, we argue that conserved quantities are dual to internal cycles. We introduce maximal invariant polyhedral supports, and we conjecture that there is a…
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves. We review deterministic models in which temperature…
Krotov and Hopfield (2021) proposed a biologically plausible two-layer associative memory network with memory storage capacity exponential in the number of visible neurons. However, the capacity was only linear in the number of hidden…
Vertical federated learning (VFL) enables multi-laboratory collaboration on distributed multi-omics datasets without sharing raw data, but exhibits severe instability under extreme data scarcity (P >> N) when applied generically. Here, we…
Virtually every biological rate depends on temperature, yet the resulting rate-temperature relationships often deviate strongly from simple Arrhenius behavior. In this first part of a two-part review, we survey phenomenological models used…
Subjective cognitive decline (SCD) doubles dementia risk. This study investigates how self-perceived cognitive worsening manifests in neural dynamics during naturalistic speech perception. EEG was collected from 60 cognitively normal older…
Chimeric antigen receptor (CAR) T cell therapy has shown remarkable success in hematological malignancies, yet patient responses remain highly variable and the roles of CD4+ and CD8+ subsets are not fully understood. We present an extended…
Agent-based models (ABMs) are widely used in biology to understand how individual actions scale into emergent population behavior. Modelers employ sensitivity analysis (SA) algorithms to quantify input parameters' impact on model outputs,…
Understanding peptide properties is often assumed to require modeling long-range molecular interactions, motivating the use of complex graph neural networks and pretrained transformers. Yet, whether such long-range dependencies are…
Oncolytic viral therapy (OVT) is an emerging precision therapy for aggressive and recurrent cancers. However, its clinical efficacy is hindered by the complexity of tumor-virus-immune interactions and the lack of predictive models for…
Collective migration is an important component of many biological processes, including wound healing, tumorigenesis, and embryo development. Spatial agent-based models (ABMs) are often used to model collective migration, but it is…
How does the brain optimize sensory information for decision-making in new tasks? One hypothesis suggests learning reduces redundancy in neural representations to improve efficiency, while another, based on Bayesian inference, predicts…