Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Genetic diversity ofBartonella quintanain macaques suggests zoonotic origin of trench fever

(2013) Hao Li et al.   MOLECULAR ECOLOGY

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome

(2009) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)

(2009) R. Logares et al.   MOLECULAR BIOLOGY AND EVOLUTION

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of pathogenicity in the Bacillus cereus group

(2009) Xavier Didelot et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Inference of Microbial Recombination Rates from Metagenomic Data

(2009) Philip L. F. Johnson et al.   PLoS Genetics

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

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

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

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS