ArticleBioinformatics (Oxford, England)2018
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Unique molecular identifiers don't need to be unique: a collision-aware estimator for RNA-seq quantification.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide screening reveals producer-cell modifications that improve virus-like particle production and delivery potency.Nature communications · 2026Article
- Diversity-generating retroelements for programmable targeted hypermutagenesis.Nature biotechnology · 2026Article
- An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines.Nature communications · 2026Article
- Genome-wide screening reveals producer-cell modifications that improve virus-like particle production and delivery potency.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking UMI clustering tools for accurate detection of low-frequency variants from deep sequencing.Scientific reports · 2025Article
- Linking Genotype to Clinical Features inGenes · 2025Review
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- Deep Learning Based Models for CRISPR/Cas Off-Target Prediction.Small methods · 2025Review
- Next-generation sequencing: A powerful multi-purpose tool in cell line development for biologics production.Computational and structural biotechnology journal · 2025Review
- Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing.Nature biomedical engineering · 2025Article
- Continuous evolution of compact protein degradation tags regulated by selective molecular glues.Science (New York, N.Y.) · 2024Article
- Article
- High-throughput library transgenesis ineLife · 2023Article
- Benefits of applying molecular barcoding systems are not uniform across different genomic applications.Journal of translational medicine · 2023Article
- DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA.Cell reports methods · 2023Article
- Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements.Journal of cardiovascular development and disease · 2023Review
- Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2023Article
- Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene.Scientific reports · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Motivation: Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments. Results: Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. Availability and implementation: AmpUMI is open-source and freely available at http://github.com/pinellolab/AmpUMI.
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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.