ArticleMolecular therapy. Nucleic acids2024
AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.
Article in Molecular therapy. Nucleic acids, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Quantifying PD1 Saturation by PDL1 in Tumor Tissue Using a Novel RNA Aptamer-Based Assay.International journal of molecular sciences · 2026Article
- Article
- Interpretable prediction and generation of ASC-speck aptamers using multiscale deep biological learning models.Bioinformatics advances · 2026Article
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Targeting Neutrophil/Eosinophil Extracellular Traps by Aptamer-Functionalized Nanosheets to Overcome Recalcitrant Inflammatory Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Sorting high-affinity aptamers in a single selection round.Nature chemical biology · 2025Article
- A new program for SELEX sorting and visualization of aptamers.Molecular therapy. Nucleic acids · 2025Article
- Identification of In Vivo Internalizing Cardiac-Specific RNA Aptamers.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative systematic evolution of ligands by exponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Here we present AptamerRunner, an aptamer sequence and/or structure clustering algorithm that synergistically integrates computational analysis with visualization and expertise-directed decision making. The visual integration of networked aptamers with ranking data, such as fold enrichment or scoring algorithm results, represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner have broad-reaching implications for aptamer researchers across a wide range of disciplines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.