Quantitative Biology
We present a miniature brain transformer architecture that extends the attention-coupled latent memory framework with four additional brain-region analogues: a thalamic relay, an amygdaloid salience module, a prefrontal working-memory (PFC)…
DNA foundation models have become transformative tools in bioinformatics and healthcare applications. Trained on vast genomic datasets, these models can be used to generate sequence embeddings, dense vector representations that capture…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…
Motivation: GWAS (genome-wide association study) summary statistic files are essential inputs for polygenic risk score (PRS) calculation. However, identifying suitable files across thousands of catalog entries typically requires downloading…
The mitotic cell cycle governs DNA replication and cell division. The effectiveness of radiotherapy and chemotherapy depends on cell-cycle position, with increased resistance during DNA replication and mitosis. Thus, accurate mathematical…
Frogeye Leaf Spot (FLS), caused by Cercospora sojina, poses a significant threat to soybean production, with yield losses of 30-60%. Traditional mass-action models assume homogeneous mixing, which rarely holds in real fields and limits…
This study simulated the introduction of Foot-and-mouth disease (FMD) into Mato Grosso do Sul, Brazil, to evaluate the effectiveness of outbreak control strategies. Our susceptible-exposed-infected-recovered model generated a range of…
Aging interventions frequently improve function and healthspan without arresting long-term deterioration, indicating that existing frameworks do not fully specify the control conditions required for bounded organismal aging. A compact…
Multiple Sclerosis is a chronic autoimmune disorder characterized by the degradation of the myelin sheath in the central nervous system, leading to neurological impairments. In this work, we analyze a reaction-diffusion model derived from…
We study a multitype SIR epidemic model where individuals are categorized into different types, and where infection spread is characterized by a next-generation matrix $M=\{m_{ij}\}$ with community fractions $\{\pi_j\}$ for the different…
High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta…
Millions of users turn to consumer AI chatbots to discuss mental health and behavioral concerns. While this presents unprecedented opportunities to deliver population-level support, it also highlights an urgent need for rigorous and…
Summary: Modern omics experiments now involve multiple conditions and complex designs, producing an increasingly large set of differential expression and functional enrichment analysis results. However, no standardized data structure exists…
Protein inverse folding, the design of an amino acid sequence based on a target protein structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external…
Accurate cell type annotation across datasets is a key challenge in single-cell analysis. snRNA-seq enables profiling of frozen or difficult-to-dissociate tissues, complementing scRNA-seq by capturing fragile or rare cell types. However,…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Identifying causal interactions in complex dynamical systems is a fundamental challenge across the computational sciences. Existing functional connectivity methods capture correlations but not causation. While addressing directionality,…
Human cognitive responses, behavioral responses, and disease dynamics co-evolve over the course of any disease outbreak, and can result in complex feedbacks. We present a dynamic agent-based model that explicitly couples the spread of…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…