Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction–modification systems

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia

(2017) Christopher D. Johnston et al.   PLoS One

Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

(2017) Qiang Yan et al.   Frontiers in Microbiology

Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum

(2016) Liang Tian et al.   Biotechnology for Biofuels

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth

(2015) Nicholas R. Sandoval et al.   Biotechnology for Biofuels

The complete methylome of Helicobacter pylori UM032

(2015) Woon Ching Lee et al.   BMC GENOMICS

Elimination of formate production in Clostridium thermocellum

(2015) Thomas Rydzak et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum

(2015) Beth Papanek et al.   METABOLIC ENGINEERING

Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum

(2015) Paul P. Lin et al.   METABOLIC ENGINEERING

CATH FunFHMMer web server: protein functional annotations using functional family assignments

(2015) Sayoni Das et al.   NUCLEIC ACIDS RESEARCH

Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals

(2015) Benjamin M. Zeldes et al.   Frontiers in Microbiology

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Analysis of the Campylobacter jejuni Genome by SMRT DNA Sequencing Identifies Restriction-Modification Motifs

(2015) Jason L. O’Loughlin et al.   PLoS One

Technical guide for genetic advancement of underdeveloped and intractable Clostridium

(2014) Michael E. Pyne et al.   BIOTECHNOLOGY ADVANCES

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications

(2014) Hannah Akinosho et al.   Frontiers in Chemistry

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

(2013) Charlotte M Wilson et al.   Biotechnology for Biofuels

Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement

(2013) Daehwan Chung et al.   Biotechnology for Biofuels

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum

(2012) Adam M Guss et al.   Biotechnology for Biofuels

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

The methylomes of six bacteria

(2012) Iain A. Murray et al.   NUCLEIC ACIDS RESEARCH

Increased expression of β-glucosidase A in Clostridium thermocellum 27405 significantly increases cellulase activity

(2012) Miranda L. Maki et al.   Bioengineered

Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405)

(2011) Lucas D. Ellis et al.   BIORESOURCE TECHNOLOGY

Improvement of Transformation Efficiency by Strategic Circumvention of Restriction Barriers in Streptomyces griseus

(2011) Hirokazu Suzuki   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium thermocellum and Creation of a pta Mutant

(2010) S. A. Tripathi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA

(2010) Guang Liu et al.   PLoS Genetics

Impact of Pretreated Switchgrass and Biomass Carbohydrates on Clostridium thermocellum ATCC 27405 Cellulosome Composition: A Quantitative Proteomic Analysis

(2009) Babu Raman et al.   PLoS One

Improvement of bacterial transformation efficiency using plasmid artificial modification

(2008) Kazumasa Yasui et al.   NUCLEIC ACIDS RESEARCH