Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Time-series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray

(2010) Virginia I. Rich et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic and functional adaptation in surface ocean planktonic prokaryotes

(2010) Shibu Yooseph et al.   NATURE

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Bosque: integrated phylogenetic analysis software

(2008) S. Ramirez-Flandes et al.   BIOINFORMATICS

Genomic sequencing of single microbial cells from environmental samples

(2008) Thomas Ishoey et al.   CURRENT OPINION IN MICROBIOLOGY

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

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

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

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

(2008) Stephen J. Callister et al.   PLoS One

Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell

(2008) Y. Hongoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH