Quantitative Biology
Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic…
Respiratory syncytial virus (RSV) is a leading cause of bronchiolitis and other lower respiratory tract infections in infants. Increased viral circulation in the post-COVID era and heterogeneous prevention strategies across regions have…
We propose a phenomenological model of the Global Neuronal Workspace (GNW) in which early sensory processing generates an effective complex-valued landscape governing the dynamics of high-level stimulus representations. This landscape…
Disturbance regimes and nutrient inputs are changing worldwide, with consequences for the structure and functioning of plant communities. Classical life-history theory predicts that disturbance should shift communities from long-lived…
Perfusion imaging guides clinical evaluation of stroke and brain tumors by characterizing tissue-level hemodynamics. Routine quantification relies on manual arterial input function (AIF) selection followed by deconvolution, producing…
Designing protein sequences that bind specific ligands benefits from an inverse-folding model conditioned on full ligand geometry. We present UMA-Inverse, which replaces the sparse graph backbone of LigandMPNN with a dense…
Ramkrishna, Kompala, and Tsao proposed the cybernetic model of microbial growth, in which cells allocate enzyme synthesis resources according to a matching rule that mimics rational decision-making. The matching rule was later shown to be…
Large language models (LLMs) demonstrate remarkable reasoning capabilities, yet their stateless architecture fundamentally limits deployment in long-horizon research workflows requiring multi-session continuity and quantitative rigor. Here…
Many biological processes are governed by complex dynamical mechanisms that remain incompletely understood despite increasing volumes of experimental data. Biologically-informed neural networks (BINNs) seek to address this challenge by…
Root-mean-square deviation (RMSD) is the standard metric of structural comparison in molecular dynamics (MD) simulations. In its conventional form, RMSD assigns equal weight to all atoms regardless of mobility. Hence, flexible loops and…
Magnesium ions are essential for RNA structure but difficult to model due to slow binding kinetics and experimental limitations. We present an enhanced-sampling strategy that accelerates Mg$^{2+}$ inner-shell binding by orders of magnitude,…
The Moran process with selection and recurrent mutation is a classical model in population genetics, yet how the placement of selection within the update rule shapes the stationary distribution has received little attention. We study a…
Information Processing Pathway Maps (IPPMs) offer a scalable framework for formalizing the complex sequence of mathematical transformations applied to sensory stimuli. These maps chart the latency and cortical expression of computational…
We extend the standard susceptible-infected-recovered framework to incorporate natural immune boosting during a short-scale outbreak. By deriving closed-form final size relations, we analytically link total attack rates to boosting dynamics…
Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with a high recurrence rate. The molecular profiling of DLBCL tumors culminated in several immunohistochemistry algorithms for prognostic stratification.…
Statistical learning is essential for individuals to discover structure in the sensory environment, especially during communication via speech or music. Individual differences in statistical learning abilities have been proposed to account…
\textbf{Background:} In Costa Rica, dengue is reported and controlled at the canton level, and outbreaks in one canton are often followed by outbreaks in others. Climate models describe where conditions favor transmission but not how dengue…
Phylogenetic trees are rooted trees with branch lengths that record genetic divergence or elapsed time, and quantifying differences between them is central to a wide range of evolutionary and epidemiological analyses. Graph-polynomial…
With the enormous advances in cerebral imaging techniques, a large amount of data is available for studying the aging and demented brain. In this contribution, we apply the OASIS-3 dataset for identifying small areas of the human gray…
ssys is a Python package for exact algebraic recasting of supported ODE models into S-system or Generalized Mass Action form. It reads Antimony and SBML models, introduces auxiliary variables through symbolic lifting, and validates…