Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

(2013) Brett J Baker et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico

(2013) Marie Ragon et al.   Frontiers in Microbiology

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

The genome of the ammonia-oxidizingCandidatusNitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral gene transfer as a support for the tree of life

(2012) S. S. Abby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea

(2012) S. Nelson-Sathi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

(2011) Céline Brochier-Armanet et al.   ISME Journal

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing

(2010) Rohit Ghai et al.   ISME Journal

Lateral acquisition of genes is affected by the friendliness of their products

(2010) U. Gophna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

On the need for widespread horizontal gene transfers under genome size constraint

(2009) Hervé Isambert et al.   Biology Direct

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

(2009) Aditi Kanhere et al.   BMC EVOLUTIONARY BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

(2008) José R. de la Torre et al.   ENVIRONMENTAL MICROBIOLOGY

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY