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Examining Sources of Error in PCR by Single-Molecule Sequencing
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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The fidelity of Taq polymerase catalyzing PCR is improved by an N-terminal deletion
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An optimized protocol for forensic application of the PreCR™ Repair Mix to multiplex STR amplification of UV-damaged DNA
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Reducing chimera formation during PCR amplification to ensure accurate genotyping
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Recognition of the Pro-mutagenic Base Uracil by Family B DNA Polymerases from Archaea
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Polymerase specific error rates and profiles identified by single molecule sequencing
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8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions.
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The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I.
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Principles and challenges of genome-wide DNA methylation analysis
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Structural basis for uracil recognition by archaeal family B DNA polymerases
inferredcites →https://doi.org/10.1046/j.1462-2920.2002.00326.xopenalex-snapshot
Factors affecting PCR‐mediated recombination
inferredcites →https://doi.org/10.1073/pnas.1105422108openalex-snapshot
Detection and quantification of rare mutations with massively parallel sequencing
inferredcites →https://doi.org/10.1073/pnas.1208715109openalex-snapshot
Detection of ultra-rare mutations by next-generation sequencing
inferredcites →https://doi.org/10.1073/pnas.1210309109openalex-snapshot
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
inferredcites →https://doi.org/10.1073/pnas.1607794113openalex-snapshot
Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing
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A constant rate of spontaneous mutation in DNA-based microbes.
inferredcites →https://doi.org/10.1093/nar/18.13.3739openalex-snapshot
High fidelity DNA synthesis by theThermus aquaticusDNA polymerase
inferredcites →https://doi.org/10.1093/nar/19.15.4193openalex-snapshot
Fidelity of Thermococcus litoralis DNA polymerase (Vent TM ) in PCR determined by denaturing gradient gel electrophoresis
inferredcites →https://doi.org/10.1093/nar/23.11.2049openalex-snapshot
Template-switching during DNA synthesis byThermus aquaticusDNA polymerase I
inferredcites →https://doi.org/10.1093/nar/24.14.2774openalex-snapshot
Analysis and Suppression of DNA Polymerase Pauses Associated with a Trinucleotide Consensus
inferredcites →https://doi.org/10.1093/nar/24.18.3546openalex-snapshot
PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases
inferredcites →https://doi.org/10.1093/nar/gkv717openalex-snapshot
Sources of PCR-induced distortions in high-throughput sequencing data sets
inferredcites →https://doi.org/10.1093/nar/gkw436openalex-snapshot
Mapping DNA polymerase errors by single-molecule sequencing
inferredcites →https://doi.org/10.1101/gr.1.1.17openalex-snapshot
DNA polymerase fidelity and the polymerase chain reaction.
inferredcites →https://doi.org/10.1101/gr.1.1.63openalex-snapshot
Optimization of the polymerase chain reaction with regard to fidelity: modified T7, Taq, and vent DNA polymerases.
inferredcites →https://doi.org/10.1111/tan.12269openalex-snapshot
Next‐generation sequencing can reveal in vitro‐generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT / HLA database
inferredcites →https://doi.org/10.1126/science.aab4082openalex-snapshot
Somatic mutation in cancer and normal cells
inferredcites →https://doi.org/10.1126/science.aaf5409openalex-snapshot
Synthetic evolutionary origin of a proofreading reverse transcriptase
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Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes
inferredcites →https://doi.org/10.1155/2014/287430openalex-snapshot
Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase
inferredcites →https://doi.org/10.1186/s12864-016-2669-3openalex-snapshot
High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
inferredcites →https://doi.org/10.1371/journal.pone.0027310openalex-snapshot
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
inferredcites →https://doi.org/10.1371/journal.pone.0146638openalex-snapshot
Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations
inferredcites →https://doi.org/10.2144/000113219openalex-snapshot
Reducing the Impact of PCR-Mediated Recombination in Molecular Evolution and Environmental Studies Using a New-Generation High-Fidelity DNA Polymerase
inferredcites →https://doi.org/10.2144/05391rv01openalex-snapshot
Real-Time PCR for mRNA Quantitation
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inferred← citeshttps://doi.org/10.1038/s41598-025-05267-8openalex-snapshot
GENOMICON-Seq enables realistic simulation of amplicon and exome sequencing for low-frequency mutation detection
inferred← citeshttps://doi.org/10.1038/s41598-025-10211-xopenalex-snapshot
Engineering of novel DNA polymerase variants for single enzyme quantitative multiplex reverse transcription-PCR
inferred← citeshttps://doi.org/10.1038/s41598-025-14826-yopenalex-snapshot
Target sequence of single cells captured by a polymeric microfluidic device
inferred← citeshttps://doi.org/10.1038/s42003-024-05955-7openalex-snapshot
Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis
inferred← citeshttps://doi.org/10.1038/s44320-025-00172-8openalex-snapshot
Single cell transcriptional perturbome in pluripotent stem cell models
inferred← citeshttps://doi.org/10.1039/d6cc02623kopenalex-snapshot
Gene mutation screening using single-molecule force spectroscopy: a novel way of PCR-independent genetic testing
inferred← citeshttps://doi.org/10.1073/pnas.2013106118openalex-snapshot
Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands
inferred← citeshttps://doi.org/10.1080/21501203.2019.1708492openalex-snapshot
Cultivable marine fungi from the Arctic Archipelago of Svalbard and their antibacterial activity
inferred← citeshttps://doi.org/10.1080/23802359.2019.1697188openalex-snapshot
Fidelity of DNA polymerases in the detection of intraindividual variation of mitochondrial DNA
inferred← citeshttps://doi.org/10.1089/hgtb.2018.037openalex-snapshot
Accurate and Rapid Sequence Analysis of Adeno-Associated Virus Plasmids by Illumina Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1089/hum.2021.055openalex-snapshot
Isolating Natural Adeno-Associated Viruses from Primate Tissues with a High-Fidelity Polymerase
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad002openalex-snapshot
Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae532openalex-snapshot
SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty1004openalex-snapshot
In silico error correction improves cfDNA mutation calling
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty790openalex-snapshot
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers
inferred← citeshttps://doi.org/10.1093/clinchem/hvab040openalex-snapshot
An Automated Correction Algorithm (ALPACA) for ddPCR Data Using Adaptive Limit of Blank and Correction of False Positive Events Improves Specificity of Mutation Detection
inferred← citeshttps://doi.org/10.1093/g3journal/jkab099openalex-snapshot
A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1093/g3journal/jkag107openalex-snapshot
Syrah: a pipeline to maximize spatial transcriptomics data output
inferred← citeshttps://doi.org/10.1093/gigascience/giz092openalex-snapshot
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
inferred← citeshttps://doi.org/10.1093/gpbjnl/qzae024openalex-snapshot
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs
inferred← citeshttps://doi.org/10.1093/nar/gkaa521openalex-snapshot
High-throughput methods for measuring DNA thermodynamics
inferred← citeshttps://doi.org/10.1093/nar/gkaa600openalex-snapshot
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
inferred← citeshttps://doi.org/10.1093/nar/gkaa929openalex-snapshot
Construction of a highly error-prone DNA polymerase for developing organelle mutation systems
inferred← citeshttps://doi.org/10.1093/nar/gkab471openalex-snapshot
Dissecting and tuning primer editing by proofreading polymerases
inferred← citeshttps://doi.org/10.1093/nar/gkaf1143openalex-snapshot
The A, B, C, D’s of replicative DNA polymerase fidelity: utilizing high-throughput single-molecule sequencing to understand the molecular basis for DNA polymerase accuracy
inferred← citeshttps://doi.org/10.1093/nar/gkaf793openalex-snapshot
Optimal sequencing depth for measuring the concentrations of molecular barcodes
inferred← citeshttps://doi.org/10.1093/nar/gkx691openalex-snapshot
A systematic comparison of error correction enzymes by next-generation sequencing
inferred← citeshttps://doi.org/10.1093/nar/gky112openalex-snapshot
High-throughput construction of multiple cas9 gene variants via assembly of high-depth tiled and sequence-verified oligonucleotides
inferred← citeshttps://doi.org/10.1093/nar/gky303openalex-snapshot
A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining
inferred← citeshttps://doi.org/10.1093/nar/gky341openalex-snapshot
Base modifications affecting RNA polymerase and reverse transcriptase fidelity
inferred← citeshttps://doi.org/10.1093/nar/gkz1085openalex-snapshot
DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote
inferred← citeshttps://doi.org/10.1093/nar/gkz1165openalex-snapshot
Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics
inferred← citeshttps://doi.org/10.1093/nar/gkz907openalex-snapshot
Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations
inferred← citeshttps://doi.org/10.1093/sysbio/syae027openalex-snapshot
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield
inferred← citeshttps://doi.org/10.1093/ve/veab042openalex-snapshot
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
inferred← citeshttps://doi.org/10.1093/ve/veac114openalex-snapshot
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples
inferred← citeshttps://doi.org/10.1093/ve/veae019openalex-snapshot
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies
inferred← citeshttps://doi.org/10.1094/mpmi-11-20-0329-taopenalex-snapshot
Application of Target Enrichment Sequencing for Population Genetic Analyses of the Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli in Michigan
inferred← citeshttps://doi.org/10.1096/fj.201903036rropenalex-snapshot
Activation‐induced cytidine deaminase can target multiple topologies of double‐stranded DNA in a transcription‐independent manner
inferred← citeshttps://doi.org/10.1097/im9.0000000000000134openalex-snapshot
Evaluation of 10 Different Pipelines for Bacterial Single-Nucleotide Variant Detection
inferred← citeshttps://doi.org/10.1099/jgv.0.001395openalex-snapshot
Sequencing of serially passaged measles virus affirms its genomic stability and reveals a nonrandom distribution of consensus mutations
inferred← citeshttps://doi.org/10.1099/jgv.0.001708openalex-snapshot
Physiological magnesium concentrations increase fidelity of diverse reverse transcriptases from HIV-1, HIV-2, and foamy virus, but not MuLV or AMV
inferred← citeshttps://doi.org/10.1101/2020.04.26.061747openalex-snapshot
Detecting and Quantitating Low Fraction DNA Variants with Low-Depth Sequencing
inferred← citeshttps://doi.org/10.1101/2020.06.25.171595openalex-snapshot
A targeted next generation sequencing approach to develop robust, genotype-specific mutation profiles and uncover novel variants in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1101/2020.12.18.423488openalex-snapshot
Sensitive detection of DNA contamination in tumor samples via microhaplotypes
inferred← citeshttps://doi.org/10.1101/2021.05.24.443729openalex-snapshot
De novo mutation rates at the single-mutation resolution in a human HBB gene-region associated with adaptation and genetic disease
inferred← citeshttps://doi.org/10.1101/2022.03.15.484480openalex-snapshot
OnRamp: rapid nanopore plasmid validation
inferred← citeshttps://doi.org/10.1101/2022.04.12.488100openalex-snapshot
Improving the fidelity of uridine analog incorporation during in vitro transcription
inferred← citeshttps://doi.org/10.1101/2022.09.20.22279947openalex-snapshot
A quantitative universal NGS-based ctDNA assay for hepatoblastoma
inferred← citeshttps://doi.org/10.1101/2022.11.15.516560openalex-snapshot
Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisisae
inferred← citeshttps://doi.org/10.1101/2022.12.10.519890openalex-snapshot
SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python
inferred← citeshttps://doi.org/10.1101/2023.02.19.526140openalex-snapshot
Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing
inferred← citeshttps://doi.org/10.1101/2023.10.09.561356openalex-snapshot
Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells
inferred← citeshttps://doi.org/10.1101/2024.08.14.607907openalex-snapshot
GENOMICON-Seq: A comprehensive tool for the simulation of mutations in amplicon and whole exome sequencing
inferred← citeshttps://doi.org/10.1101/2024.10.30.24316422openalex-snapshot
Somatic mutation and selection at epidemiological scale
inferred← citeshttps://doi.org/10.1101/2025.08.01.668007openalex-snapshot
Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy
inferred← citeshttps://doi.org/10.1101/2025.08.20.671269openalex-snapshot
Improving RNA-seq protocols
inferred← citeshttps://doi.org/10.1101/314815openalex-snapshot
Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
inferred← citeshttps://doi.org/10.1101/645903openalex-snapshot
Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
inferred← citeshttps://doi.org/10.1101/679852openalex-snapshot
Spontaneous Mutations in HIV-1 Gag, protease, RT p66 in the first replication cycle and how they appear: Insights from an in vitro BSL2 assay on mutation rates and types
inferred← citeshttps://doi.org/10.1101/706788openalex-snapshot
Evidence that APP gene copy number changes reflect recombinant vector contamination
inferred← citeshttps://doi.org/10.1101/807073openalex-snapshot
Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects
inferred← citeshttps://doi.org/10.1101/gr.239186.118openalex-snapshot
Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
inferred← citeshttps://doi.org/10.1101/gr.277369.122openalex-snapshot
Multiplexed long-read plasmid validation and analysis using OnRamp
inferred← citeshttps://doi.org/10.1101/gr.281717.125openalex-snapshot
Pattern-Filter structural validation of single-cell RNA-seq reads reduces artifactual barcodes and improves biological resolution
inferred← citeshttps://doi.org/10.1109/isit63088.2025.11195505openalex-snapshot
Spectral Analysis of Nanopore DNA Signatures Under Geometric Duplication
inferred← citeshttps://doi.org/10.1109/tit.2020.3030569openalex-snapshot
Trace Reconstruction Problems in Computational Biology
inferred← citeshttps://doi.org/10.1111/1755-0998.12760openalex-snapshot
A fungal mock community control for amplicon sequencing experiments
inferred← citeshttps://doi.org/10.1111/1755-0998.12928openalex-snapshot
Capture enrichment of aquatic environmental DNA: A first proof of concept
inferred← citeshttps://doi.org/10.1111/1755-0998.13008openalex-snapshot
Metabarcoding a diverse arthropod mock community
inferred← citeshttps://doi.org/10.1111/1755-0998.13143openalex-snapshot
A method to generate multilocus barcodes of pinned insect specimens using MiSeq
inferred← citeshttps://doi.org/10.1111/1755-0998.13733openalex-snapshot
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation
inferred← citeshttps://doi.org/10.1111/1755-0998.13746openalex-snapshot
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses
inferred← citeshttps://doi.org/10.1111/1755-0998.70023openalex-snapshot
gmmDenoise : A New Method and R Package for High‐Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis
inferred← citeshttps://doi.org/10.1111/bjh.16382openalex-snapshot
Novel Illumina‐based next generation sequencing approach with one‐round amplification provides early and reliable detection of BCR‐ABL1 kinase domain mutations in chronic myeloid leukemia
inferred← citeshttps://doi.org/10.1111/imb.12564openalex-snapshot
Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis
inferred← citeshttps://doi.org/10.1111/jam.14380openalex-snapshot
Generating amplicon reads for microbial community assessment with next‐generation sequencing
inferred← citeshttps://doi.org/10.1111/mec.16036openalex-snapshot
Long‐term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions
inferred← citeshttps://doi.org/10.1111/nph.14776openalex-snapshot
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
inferred← citeshttps://doi.org/10.1111/nph.15625openalex-snapshot
Loop assembly: a simple and open system for recursive fabrication of DNA circuits
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