PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

DACTAL: divide-and-conquer trees (almost) without alignments

(2012) S. Nelesen et al.   BIOINFORMATICS

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

BioCreative III interactive task: an overview

(2011) Cecilia N Arighi et al.   BMC BIOINFORMATICS

The Genome of Th17 Cell-Inducing Segmented Filamentous Bacteria Reveals Extensive Auxotrophy and Adaptations to the Intestinal Environment

(2011) Andrew Sczesnak et al.   Cell Host & Microbe

Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae

(2011) Hiromi Nishida et al.   GENOMICS

Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies

(2011) L. Guo et al.   JOURNAL OF BACTERIOLOGY

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

(2011) Nicola Segata et al.   PLoS One

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients

(2010) Jaroslaw Zdziarski et al.   PLoS Pathogens

Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

(2009) K. Mori et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome-based phylogenetic analysis of Streptomyces and its relatives

(2009) Mohammad Tauqeer Alam et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Biogeography of the Sulfolobus islandicus pan-genome

(2009) M. L. Reno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages

(2009) Wataru Iwasaki et al.   PLoS Genetics

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

(2008) G. Aguileta et al.   SYSTEMATIC BIOLOGY

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY