Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

CRISPR/Cas9-enhanced ssDNA recombineering for Pseudomonas putida

(2019) Tomás Aparicio et al.   Microbial Biotechnology

Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair DefectiveEscherichia coli

(2018) Patricia L. Foster et al.   GENETICS

Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria

(2018) Hongan Long et al.   MOLECULAR BIOLOGY AND EVOLUTION

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

(2018) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair DefectiveEscherichia coli

(2018) Patricia L. Foster et al.   GENETICS

Improved Thermotolerance of Genome-Reduced Pseudomonas putida EM42 Enables Effective Functioning of the PL /c I857 System

(2018) Tomás Aparicio et al.   Biotechnology Journal

ReadTools : A universal toolkit for handling sequence data from different sequencing platforms

(2017) Daniel Gómez-Sánchez et al.   Molecular Ecology Resources

CRISPR/Cas9-Based Counterselection Boosts Recombineering Efficiency in Pseudomonas putida

(2017) Tomás Aparicio et al.   Biotechnology Journal

A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

(2017) Deirdre E. Ricaurte et al.   Microbial Biotechnology

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

Evolution of the methyl directed mismatch repair system in Escherichia coli

(2016) Christopher D. Putnam   DNA REPAIR

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

Mutation Rate, Spectrum, Topology, and Context-Dependency in the DNA Mismatch Repair-Deficient Pseudomonas fluorescens ATCC948

(2014) Hongan Long et al.   Genome Biology and Evolution

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

(2014) Esteban Martínez-García et al.   Microbial Cell Factories

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering

(2011) James A. Sawitzke et al.   JOURNAL OF MOLECULAR BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis

(2009) B. M. Hall et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

β Clamp Directs Localization of Mismatch Repair in Bacillus subtilis

(2008) Lyle A. Simmons et al.   MOLECULAR CELL

Dual role of NER in mutagenesis in Pseudomonas putida

(2007) Mariliis Tark et al.   DNA REPAIR