Quantitative Biology
We investigate the adaptive Ambush strategy in cyclic models following the rules of the spatial rock-paper-scissors game. In our model, individuals of one species possess cognitive abilities to perceive environmental cues and assess the…
Cardiovascular disease (CVD) risk stratification remains a major challenge due to its multifactorial nature and limited availability of high-quality labeled datasets. While genomic and electrophysiological data such as SNP variants and ECG…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
Cancer exhibits diverse and complex phenotypes driven by multifaceted molecular interactions. Recent biomedical research has emphasized the comprehensive study of such diseases by integrating multi-omics datasets (genome, proteome,…
Emergency departments worldwide face rising patient volumes, workforce shortages, and variability in triage decisions that threaten the delivery of timely and accurate care. Current triage methods rely primarily on vital signs, routine…
Normative modelling is an increasingly common statistical technique in neuroimaging that estimates population-level benchmarks in brain structure. It enables the quantification of individual deviations from expected distributions whilst…
Sequence matching algorithms such as BLAST and FASTA have been widely used in searching for evolutionary origin and biological functions of newly discovered nucleic acid and protein sequences. As parts of these search tools, alignment…
Generating large ensembles of candidate conformations is standard for improving biomolecular structure prediction. Yet aimless sampling is inefficient and costly, producing many redundant conformations with limited diversity, so additional…
This chapter focuses on variable maturation delay or, more precisely, on the mathematical description of a size-structured population consuming an unstructured resource. When the resource concentration is a known function of time, we can…
This chapter reviews some aspects of the theory of age-structured models of populations with finite maximum age. We formulate both the renewal equation for the birth rate and the partial differential equation for the age density, and show…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
Understanding how cortex, subcortex and cerebellum integrate is a major challenge for neuroscience, however, studies of the brain's structural connectivity have mostly focused on cortico-cortical links. Here, we used diffusion imaging to…
Genomic studies face a vast hypothesis space, while interventions such as gene perturbations remain costly and time-consuming. To accelerate such experiments, gene perturbation models predict the transcriptional outcome of interventions.…
This study proposes a deep learning framework and annotation methodology for the automatic detection of periodontal bone loss landmarks, associated conditions, and staging. 192 periapical radiographs were collected and annotated with a…
Controlling the stochastic dynamics of biological populations is a challenge that arises across various biological contexts. However, these dynamics are inherently nonlinear and involve a discrete state space, i.e., the number of molecules,…
The vision of personalized medicine is to identify interventions that maintain or restore a person's health based on their individual biology. Medical digital twins, computational models that integrate a wide range of health-related data…
Axes of polarity (and primary morphogenetic gradients) are established in the oocyte - early embryo through active transport and localization of maternal factors. It is the oocyte - syncytial embryo of Drosophila (D. melanogaster) that is a…
Chikungunya virus is a mosquito-borne arbovirus with the potential to establish sustained transmission in subtropical regions like Florida, where climatic and ecological conditions support vector proliferation. In this study, we develop a…
The Paradox of Enrichment (PoE) predicts that increasing resources, such as nutrient inputs like fertilizers or food availability, should destabilize ecological systems, such as crop-pest dynamics, leading to population cycles that can…
Cardiovascular disease and chronic kidney disease are major complications of diabetes, leading to high morbidity and mortality. Early detection of these conditions is critical, yet traditional diagnostic markers often lack sensitivity in…