Quantitative Biology
Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models…
Biological intelligence is inherently adaptive -- animals continually adjust their actions based on environmental feedback. However, creating adaptive artificial intelligence (AI) remains a major challenge. The next frontier is to go beyond…
Mediation analysis aims to identify and estimate the effect of an exposure on an outcome that is mediated through one or more intermediate variables. In the presence of multiple intermediate variables, two pertinent methodological questions…
A number of recent articles have employed the Lorentz ansatz to reduce a network of Izhikevich neurons to a tractable mean-field description. In this letter, we construct an equivalent phase model for the Izhikevich model and apply the…
Predicting the docking between proteins and ligands is a crucial and challenging task for drug discovery. However, traditional docking methods mainly rely on scoring functions, and deep learning-based docking approaches usually neglect the…
Gene regulatory networks are powerful tools for modeling interactions among genes to regulate their expression for homeostasis and differentiation. Single-cell sequencing offers a unique opportunity to build these networks with…
Serine hydroxymethyltransferase is an essential enzyme in the Escherichia coli folate pathway, yet it has not been adopted as an antibacterial target, unlike DHFR, DHPS, or thymidylate synthase. To investigate this discrepancy, we applied a…
Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations.…
We have previously shown that Good-Turing statistics can be applied to molecular dynamics trajectories to estimate the probability of observing completely new (thus far unobserved) biomolecular structures, and showed that the method is…
Background: Accurate week-ahead forecasts of continuous glucose monitoring (CGM) derived metrics could enable proactive diabetes management, but relative performance of modern tabular learning approaches is incompletely defined. Methods: We…
Aim/background: Continuous glucose monitoring (CGM) generates dense time-series data, posing challenges for efficient storage, transmission, and analysis. This study evaluates novel encoding strategies that reduce CGM profiles to a compact…
Many of the most consequential dynamics in human cognition occur \emph{before} events become explicit: before decisions are finalized, emotions are labeled, or meanings stabilize into narrative form. These pre-event states are characterized…
Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure…
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stable yet dynamic epigenetic modification,…
Bioprinting technology has advanced significantly in the fabrication of tissue-like constructs with complex geometries for regenerative medicine. However, maintaining the structural integrity of bioprinted materials remains a major…
Biological Petri Nets (Bio-PNs) require extensions beyond classical formalism to capture biochemical reality: multiple reactions simultaneously affect shared metabolites through convergent production or regulatory coupling, while signal…
The increasing use of 3D imaging technologies in biological sciences is generating vast repositories of anatomical data, yet significant barriers prevent this data from reaching its full potential in educational and collaborative contexts.…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
The survival of populations hinges on their ability to offset local extinctions through new colonizations. The dispersal area ($A$) plays a crucial role in this process, as it determines the probability of finding colonizable vacant sites.…
Biological systems organize into hierarchies to manage complexity, yet the mechanisms governing hierarchical control remain incompletely understood. Using information theory and the Lambda phage lysis-lysogeny decision as a model system, we…