ArticleNucleic acids research2015
Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Selection of aptamers against triple negative breast cancer cells using high throughput sequencing.Scientific reports · 2021Trial
- DeepPNI: a language- and graph-based model for mutation-driven protein-nucleic acid binding energetics.Nucleic acids research · 2026Article
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer.Nucleic acids research · 2026Article
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Therapeutic Oligonucleotides for Neurodegenerative Diseases: Aptamer Strategies and Clay Nanoparticle-Based Delivery.Chemical record (New York, N.Y.) · 2025Review
- Landscape of small nucleic acid therapeutics: moving from the bench to the clinic as next-generation medicines.Signal transduction and targeted therapy · 2025Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.Molecular therapy. Nucleic acids · 2024Article
- AptaDiff: de novo design and optimization of aptamers based on diffusion models.Briefings in bioinformatics · 2024Article
- Selection of DNA aptamers that prevent the fibrillization of α-synuclein protein in cellular and mouse models.Molecular therapy. Nucleic acids · 2024Article
- Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review.ACS omega · 2024Review
- Aptamers as an approach to targeted cancer therapy.Cancer cell international · 2024Review
- Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development.Molecules (Basel, Switzerland) · 2024Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.bioRxiv : the preprint server for biology · 2023Article
- Aptasensor for the Detection ofBioengineering (Basel, Switzerland) · 2023Article
- Aptamer-Based Tumor-Targeted Diagnosis and Drug Delivery.Advances in experimental medicine and biology · 2023Review
- Parallel screening and cheminformatics modeling of flavonoid activated aptasensors.Synthetic and systems biotechnology · 2022Article
- SELEX: Critical factors and optimization strategies for successful aptamer selection.Biotechnology and applied biochemistry · 2022Review
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut-a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the 'parent' sequence and AptaCluster-an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.
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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.