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<h4>Motivation</h4>The rapid expansion of three-dimensional (3D) biomolecular structure information, driven by breakthroughs in artificial intelligence/deep learning (AI/DL)-based structure predictions, has created an urgent need for scalable and efficient structure similarity search methods. Traditional alignment-based approaches, …
Read PDF<h4>Motivation</h4>Dendritic spines, postsynaptic structures characterized by their complex shapes, provide the essential structural foundation for synaptic function. Their shape is dynamic, undergoing alterations in various conditions, notably during neurodegenerative disorders like Alzheimer's disease. The dramatically …
Read PDF<h4>Summary</h4>Spherical harmonics have emerged as a powerful framework for molecular shape and electrostatic comparison in ligand-based virtual screening. Here, we present LiraSearch, a high-performance implementation and web server that uses spherical harmonics expansions to encode …
Read PDFRestoring CD8⁺T cell infiltration and potentiating anti-tumor immune responses in the tumor microenvironment (TME) is critical for developing effective immunotherapies against triple-negative breast cancer(TNBC), while the regulatory role of N⁶-methyladenosine (m⁶A)-modified circular RNAs (circRNAs) in …
Read PDF<h4>Motivation</h4>De novo molecular design remains a fundamental challenge in drug discovery, requiring simultaneous optimization of multiple conflicting objectives such as drug-likeness, synthetic accessibility, and novelty while maintaining chemical validity. We present HybridMolGen, a novel unified …
Read PDFGlobal biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes of nucleic acid sequencing. Concurrently, epidemiological studies and clinical records are generating enormous amounts of data …
Read PDF<h4>Background</h4>Inflammatory signaling and oxidative stress machinery are interconnected and play roles in apoptosis, proliferation, redox state control, and the progression of many diseases, including cancer. The marine environment harbors a wealth of organisms that produce …
Read PDF<h4>Motivation</h4>High-fidelity scoring of RNA three-dimensional structures remains a major challenge in RNA structure prediction and conformational sampling. While single-model methods for scoring RNA structures can capture individual structural features, they fail to capture the broader …
Read PDF<h4>Motivation</h4>Advances in live-cell fluorescence microscopy have enabled us to visualize single molecules (such as mRNAs and nascent proteins) in real time with high spatiotemporal resolution. However, these experiments generate large datasets that require complex computational …
Read PDFComputational antibody design has seen many recent advances pioneered via the use of language models and advanced structure prediction tools. Developing a de novo antibody against a specific antigen requires structural awareness that most language …
Read PDF<h4>Motivation</h4>We introduce a statistical approach for pattern recognition in multivariate spatial transcriptomics data.<h4>Results</h4>Our algorithm constructs a projection of the data onto a low-dimensional feature space which is optimal in maximizing Moran's I, a measure of …
Read PDFThe increasing incidence of diabetic foot ulcer (DFU) and growing recognition of environmental pollutants have highlighted polyethylene terephthalate microplastics (PET-MP) as a potential metabolic disease trigger. However, the molecular mechanisms linking PET-MP to DFU remain …
Read PDF<h4>Summary</h4>Genome-wide association studies have revealed that many disease-associated genetic variants lie in non-coding regions of the genome. To prioritize these variants and clarify their functional roles, accurate classification of <i>cis</i>-regulatory elements is essential. Early approaches …
Read PDF<h4>Motivation</h4>Protein sequence variation analysis is a topic of broad interest in drug discovery and protein engineering to support modulation of protein function for diverse biotechnological and therapeutic applications. To assist in the analysis of multiple …
Read PDFThis study is aimed at systematically identifying key genes associated with EGFR mutations and developing a molecular classification model in lung adenocarcinoma (LUAD) using integrative bioinformatics approaches. Multi-omics datasets derived from cBioPortal and The Cancer …
Read PDF<h4>Motivation</h4>Molecular dynamics (MD) simulations model the physical movements of atoms in biomolecular systems over time, providing atomic-resolution insight into conformational changes, binding events, and dynamic behaviors that cannot be captured by static structures alone. As …
Read PDFBioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this mostly human-centric design limits machine readability for large language models (LLMs) …
Read PDF<h4>Motivation</h4>Genome-wide association study (GWAS) meta-analysis tools are essential for integrating summary statistics across multiple cohorts, thereby increasing statistical power and validating genetic associations. Widely cited tools, such as METAL, PLINK, and GWAMA, have facilitated numerous …
Read PDF<h4>Motivation</h4>Understanding pan-cancer level mutational landscape offers critical insights into the molecular mechanisms underlying tumorigenesis. While patient-level machine learning techniques have been widely employed to identify tumor subtypes, cohort-level clustering-where entire cancer types are grouped based …
Read PDF<h4>Summary</h4>The accurate development, assessment, interpretation, and benchmarking of bioinformatics frameworks for analyzing transcriptional regulatory grammars rely on controlled simulations to validate the underlying methods. However, existing simulators often lack end-to-end flexibility or ease of integration, …
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