ArticleBioinformatics (Oxford, England)2012
Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 109 citations in OpenAlex.
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- Are we there yet with XNA aptamers?RSC advances · 2026Review
- A Data-Analysis Pipeline for High-Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX) in the Characterization of Telomeric Proteins.bioRxiv : the preprint server for biology · 2026Article
- Microenvironment-Guided Evolution of ssDNA-SWCNT Probes for Selective Recognition of Aggressive Prostate Cancer Phenotypes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- From randomness to recognition: modeling the evolution of DNA sequence information during enrichment for binding.Bioinformatics advances · 2026Article
- Aptamers Targeting Immune Checkpoints for Tumor Immunotherapy.Pharmaceutics · 2025Review
- New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers.International journal of molecular sciences · 2024Review
- Aptamers as an approach to targeted cancer therapy.Cancer cell international · 2024Review
- Aptamer-Based Imaging of Polyisoprenoids in the Malaria Parasite.Molecules (Basel, Switzerland) · 2023Article
- DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design.PLoS computational biology · 2023Article
- In Silico Approaches for the Identification of Aptamer Binding Interactions toTropical medicine and infectious disease · 2023Article
- A capacitive laser-induced graphene based aptasensor for SARS-CoV-2 detection in human saliva.PloS one · 2023Article
- Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?Nano today · 2022Article
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.PLoS computational biology · 2022Article
- Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases.The Journal of biological chemistry · 2022Review
- Aptamer Applications in Neuroscience.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Selection and Characterization of Vimentin-Binding Aptamer Motifs for Ovarian Cancer.Molecules (Basel, Switzerland) · 2021Article
- Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development.Angewandte Chemie (International ed. in English) · 2021Review
- Artificial Intelligence in Aptamer-Target Binding Prediction.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
motivationSystematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process.
resultsTo close this gap we developed, Aptamotif, a computational method for the identification of sequence-structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process.
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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.