Detecting epigenetic motifs in low coverage and metagenomics settings

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

(2013) Zhixing Feng et al.   PLoS Computational Biology

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

(2013) Maria Lluch-Senar et al.   PLoS Genetics

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled usingVibrio harveyimyovirus like

(2012) S. Bochow et al.   JOURNAL OF APPLIED MICROBIOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

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

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

The methylomes of six bacteria

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

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Phylogeny of Methylomes

(2010) A. Jeltsch   SCIENCE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Degenerative diseases, oxidative stress and cytochrome c oxidase function

(2009) Bernhard Kadenbach et al.   TRENDS IN MOLECULAR MEDICINE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH