定量生物学
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
Biomolecules exhibit a remarkable property of transforming signals from their environment. This paper presents a communication system design using a light-modulated protein channel: Synthetic Photoisomerizable Azobenzene-regulated K+…
We employ an n-player coordination game to model mutualism emergence and abandonment. We illustrate our findings in the context of the host--host interactions among plants in plant-mycorrhizal fungi (MF) mutualisms. The coordination game…
Positive selection drives the emergence of adaptive mutations in Mycobacterium tuberculosis, shaping drug resistance, transmissibility, and virulence. Phylogenetic trees capture evolutionary relationships among isolates and provide a…
We investigate predator-prey school interactions in aquatic environments using a stochastic differential equation (SDE)-based, particle-level model that incorporates attraction, repulsion, alignment, and environmental noise. Two predation…
Biological control strategies against mosquito-borne diseases--such as the sterile insect technique (SIT), RIDL, and Wolbachia-based releases--require reliable estimates of dispersal and survival of released males. We propose a…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Current gastric cancer (GCa) risk systems are prone to errors since they evaluate a visual estimation of intestinal metaplasia percentages in histopathology images of gastric mucosa to assign a risk. This study presents an automated method…
Distance Geometry plays a central role in determining protein structures from Nuclear Magnetic Resonance (NMR) data, a task known as the Molecular Distance Geometry Problem (MDGP). A subclass of this problem, the Discretizable Distance…
Decoding sensory experiences from neural activity to reconstruct human-perceived visual stimuli and semantic content remains a challenge in neuroscience and artificial intelligence. Despite notable progress in current brain decoding models,…
Musculoskeletal (MSK) models offer a non-invasive way to understand biomechanical loads on joints and tendons, which are difficult to measure directly. Variations in muscle strength, especially relative differences between muscles,…
Asymmetric partition of fate determinants during cell division is a hallmark of cell differentiation. Recent work suggested that such a mechanism is hijacked by cancer cells to increase both their phenotypic heterogeneity and plasticity and…
Emerging infectious diseases and climate change are two of the major challenges in 21st century. Although over the past decades, highly-resolved mathematical models have contributed in understanding dynamics of infectious diseases and are…
Stroke is a leading cause of long-term disability and the second most common cause of death worldwide. Although acute treatments have advanced, recovery remains challenging and limited. Brain-computer interfaces (BCIs) have emerged as a…
The objective of this paper is to review physiological and computational aspects of the responsiveness of the cerebral cortex to stimulation, and how responsiveness depends on the state of the system. This correspondence between brain state…
Why do human populations remain vulnerable to collapse, even when they are large? Classical demographic theory predicts that volatility in growth should decline rapidly with size due to the averaging effects of the law of large numbers. As…
The forces generated by action potentials in muscle cells shuttle blood, food and waste products throughout the luminal structures of the body. Although non-invasive electrophysiological techniques exist, most mechanosensors cannot access…
Understanding how the primate brain transforms complex visual scenes into coherent perceptual experiences remains a central challenge in neuroscience. Here, we present a comprehensive framework for interpreting monkey visual processing by…
Members of the Rumex genus possess allelochemical compounds that vary depending on the plant part and extract concentrations. Therefore, this study aimed to investigate the allelopathic effects of extracts from the roots, stems, and leaves…
Early recurrence (ER) prediction after curative-intent resection remains a critical challenge in the clinical management of hepatocellular carcinoma (HCC). Although contrast-enhanced computed tomography (CT) with full multi-phase…