Quantitative Biology
Real ecosystems are characterized by sparse and asymmetric interactions, posing a major challenge to theoretical analysis. We introduce a new method to study the generalized Lotka-Volterra model with stochastic dynamics on sparse graphs. By…
Understanding disease relationships through blood biomarkers offers a pathway toward data-driven taxonomy and precision medicine. In this study, we constructed a digital blood twin, a computational model derived from 103 disease signatures…
Blood reference intervals (RIs) underpin diagnostic interpretation and therapeutic monitoring worldwide. However, many widely used RI systems originate from limited historical cohorts and have been propagated across health systems without…
Cardiac muscle tissue exhibits highly non-linear hyperelastic and orthotropic material behavior during passive deformation. Traditional constitutive identification protocols therefore combine multiple loading modes and typically require…
Single-cell RNA sequencing (scRNA-seq) frameworks lack explainable approaches for identifying cell subpopulations harboring strong pairwise monotonic gene-module relationships between a gene of interest (GOI) and its co-expressed genes.…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Understanding and predicting evolutionary accumulation pathways is a key objective in many fields of research, ranging from classical evolutionary biology to diverse applications in medicine. In this context, we are often confronted with…
Explaining individual differences in cognitive abilities requires both identifying brain parameters that vary across individuals and understanding how brain networks are recruited for specific tasks. Typically, task performance relies on…
Study Objectives: We investigate a Mamba-based deep learning approach for sleep staging on signals from ANNE One (Sibel Health, Evanston, IL), a non-intrusive dual-module wireless wearable system measuring chest electrocardiography (ECG),…
Consciousness science faces the challenge of bridging first-person experience with third-person empirical measurements. Neurophenomenology aims to build such `generative passages' connecting the content of experience with behavioural and…
Forecasting disease spread is a critical tool to help public health officials design and plan public health interventions. However, the expected future state of an epidemic is not necessarily well defined as disease spread is inherently…
Robust and efficient interpretation of QSAR methods is quite useful to validate AI prediction rationales with subjective opinion (chemist or biologist expertise), understand sophisticated chemical or biological process mechanisms, and…
AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream…
Reliable control in motor imagery brain-computer interfaces (MI-BCIs) requires the precise decoding of user-specific neural rhythms, which vary significantly across individuals. The Common Spatial Pattern (CSP) algorithm is a cornerstone of…
The stochastic simulation algorithm (SSA) is widely used to perform exact forward simulation of discrete stochastic processes in biology. However, the computational cost, driven by sequential event-by-event sampling across large ensembles,…
Anxiety includes behavioural, physiological, and subjective components that do not always align, and it remains unclear whether these dimensions are supported by distinct intrinsic brain networks. Guided by the two-system framework, we…
We introduce LNODE, a mechanism-based phenomenological model for amyloid beta (A$\beta$) dynamics, calibrated using positron emission tomography (PET) imaging. A$\beta$ is a key biomarker of Alzheimer's disease. LNODE is designed to support…
Percolation theory from statistical physics has been applied to several aspects of tumor progression. Tumor growth on percolation clusters has been used to model spatial expansion, vascular percolation to describe nutrient supply and…
DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent…
We present EPITIME (EPidemic Integral models TIMe profile Explorer), a computational framework for the simulation of two classes of integral epidemic models: an age of infection model and an information dependent behavioural model. The…