Corrected score methods for estimating Bayesian networks with error-prone nodes.
Sign Up to like & getrecommendations! Published in 2021 at "Statistics in medicine"
DOI: 10.1002/sim.8925
Abstract: Motivated by inferring cellular signaling networks using noisy flow cytometry data, we develop procedures to draw inference for Bayesian networks based on error-prone data. Two methods for inferring causal relationships between nodes in a network… read more here.
Keywords: bayesian networks; corrected score; methods estimating; error prone ... See more keywords
Antigenic Variation in the Lyme Spirochete: Insights into Recombinational Switching with a Suggested Role for Error-Prone Repair.
Sign Up to like & getrecommendations! Published in 2018 at "Cell reports"
DOI: 10.1016/j.celrep.2018.04.117
Abstract: The Lyme disease spirochete, Borrelia burgdorferi, uses antigenic variation as a strategy to evade the host's acquired immune response. New variants of surface-localized VlsE are generated efficiently by unidirectional recombination from 15 unexpressed vls cassettes… read more here.
Keywords: prone repair; variation; antigenic variation; recombinational switching ... See more keywords
Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes
Sign Up to like & getrecommendations! Published in 2020 at "iScience"
DOI: 10.1016/j.isci.2020.101223
Abstract: Summary Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length and are therefore particularly relevant for microbiome studies. However, owing to the higher per-base error… read more here.
Keywords: long read; implications error; prone long; error prone ... See more keywords
Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates.
Sign Up to like & getrecommendations! Published in 2019 at "Molecular cell"
DOI: 10.1016/j.molcel.2019.01.001
Abstract: Post-replication repair (PRR) allows tolerance of chemical- and UV-induced DNA base lesions in both an error-free and an error-prone manner. In classical PRR, PCNA monoubiquitination recruits translesion synthesis (TLS) DNA polymerases that can replicate through… read more here.
Keywords: dna; dna polymerases; error prone; ssdna gaps ... See more keywords
Learning Context-Dependent DNA Mutation Patterns in Error-Prone Polymerase Chain Reaction.
Sign Up to like & getrecommendations! Published in 2022 at "Biochemistry"
DOI: 10.1021/acs.biochem.2c00292
Abstract: We present a novel statistical learning method for studying context-dependent error rates in error-prone polymerase chain reaction (PCR) experiments. We demonstrate the method by applying it to error-prone PCR sequencing data and show how it… read more here.
Keywords: chain reaction; polymerase chain; error prone; context dependent ... See more keywords
Ethanol exposure increases mutation rate through error-prone polymerases
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-17447-3
Abstract: Ethanol is a ubiquitous environmental stressor that is toxic to all lifeforms. Here, we use the model eukaryote Saccharomyces cerevisiae to show that exposure to sublethal ethanol concentrations causes DNA replication stress and an increased… read more here.
Keywords: prone polymerases; exposure; mutation rate; ethanol ... See more keywords
Fam72a enforces error-prone DNA repair during antibody diversification.
Sign Up to like & getrecommendations! Published in 2021 at "Nature"
DOI: 10.1038/s41586-021-04093-y
Abstract: Efficient humoral responses rely on DNA damage, mutagenesis and error-prone DNA repair. Diversification of B cell receptors through somatic hypermutation and class-switch recombination are initiated by cytidine deamination in DNA mediated by activation-induced cytidine deaminase (AID)1… read more here.
Keywords: prone dna; dna repair; dna; fam72a ... See more keywords
Error-prone bypass of DNA lesions during lagging strand replication is a common source of germline and cancer mutations
Sign Up to like & getrecommendations! Published in 2018 at "Nature genetics"
DOI: 10.1038/s41588-018-0285-7
Abstract: Studies in experimental systems have identified a multitude of mutational mechanisms including DNA replication infidelity and DNA damage followed by inefficient repair or replicative bypass. However, the relative contributions of these mechanisms to human germline… read more here.
Keywords: bypass; dna; strand; error prone ... See more keywords
Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Genetics"
DOI: 10.1101/2021.05.27.446004
Abstract: The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway depends on specialized DNA polymerases that incorporate nucleotides in front of… read more here.
Keywords: dna polymerases; rad55 rad57; dna; error prone ... See more keywords
Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR1
Sign Up to like & getrecommendations! Published in 2018 at "Plant Physiology"
DOI: 10.1104/pp.17.01618
Abstract: A novel method of studying chloroplast proteins, which combines error-prone PCR with mutant complementation, is demonstrated using petD in Chlamydomonas reinhardtii. Site-directed mutagenesis of chloroplast genes was developed three decades ago and has greatly advanced… read more here.
Keywords: mutagenesis; chloroplast proteins; chloroplast; error prone ... See more keywords
Asynchronous and error-prone longitudinal data analysis via functional calibration.
Sign Up to like & getrecommendations! Published in 2022 at "Biometrics"
DOI: 10.1111/biom.13866
Abstract: In many longitudinal settings, time-varying covariates may not be measured at the same time as responses and are often prone to measurement error. Naive last-observation-carried-forward methods incur estimation biases, and existing kernel-based methods suffer from… read more here.
Keywords: time; error prone; error; functional calibration ... See more keywords