Quantifying Homologous Replacement of Loci between Haloarchaeal Species

Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia

(2012) Ines Boujelben et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Quartet decomposition server: a platform for analyzing phylogenetic trees

(2012) Fenglou Mao et al.   BMC BIOINFORMATICS

Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales

(2012) Cheryl P Andam et al.   BMC EVOLUTIONARY BIOLOGY

A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T

(2012) Shivakumara Siddaramappa et al.   BMC GENOMICS

Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids

(2012) Adit Naor et al.   CURRENT BIOLOGY

Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

(2012) Erin A. Lynch et al.   PLoS One

Complete genome sequence of Halopiger xanaduensis type strain (SH-6T)

(2012) Iain Anderson et al.   Standards in Genomic Sciences

A Rooted Net of Life

(2011) David Williams et al.   Biology Direct

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Parallel evolution of transcriptome architecture during genome reorganization

(2011) S. H. Yoon et al.   GENOME RESEARCH

A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales

(2011) R. T. Papke et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Comparison of Phylogenetic Trees and Search for a Central Trend in the “Forest of Life”

(2011) Eugene V. Koonin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator

(2011) Y. Lin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Association between translation efficiency and horizontal gene transfer within microbial communities

(2011) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes

(2011) Iain Anderson et al.   PLoS One

Haloquadratum walsbyi : Limited Diversity in a Global Pond

(2011) Mike L. Dyall-Smith et al.   PLoS One

A Methylaspartate Cycle in Haloarchaea

(2011) M. Khomyakova et al.   SCIENCE

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Phylogenomic networks

(2011) Tal Dagan   TRENDS IN MICROBIOLOGY

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

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

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

The myth of bacterial species and speciation

(2010) Jeffrey G. Lawrence et al.   BIOLOGY & PHILOSOPHY

Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon

(2010) S. W. Roh et al.   JOURNAL OF BACTERIOLOGY

Evolution in Regulatory Regions Rapidly Compensates the Cost of Nonoptimal Codon Usage

(2010) D. Amoros-Moya et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying Nonvertical Inheritance in the Evolution of Legionella pneumophila

(2010) M. Coscolla et al.   MOLECULAR BIOLOGY AND EVOLUTION

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

(2010) Amber L. Hartman et al.   PLoS One

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

Complete genome sequence of Haloterrigena turkmenica type strain (4kT)

(2010) Elisabeth Saunders et al.   Standards in Genomic Sciences

AQUA: automated quality improvement for multiple sequence alignments

(2009) J. Muller et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

(2009) Talima Pearson et al.   BMC BIOLOGY

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene

(2009) H. Minegishi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Are Protein Domains Modules of Lateral Genetic Transfer?

(2009) Cheong Xin Chan et al.   PLoS One

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

(2009) O. Zhaxybayeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete genome sequence of Halogeometricum borinquense type strain (PR3T)

(2009) Stephanie Malfatti et al.   Standards in Genomic Sciences

Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)

(2009) Iain Anderson et al.   Standards in Genomic Sciences

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)

(2009) Brian J. Tindall et al.   Standards in Genomic Sciences

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Metabolism of halophilic archaea

(2008) Michaela Falb et al.   EXTREMOPHILES

Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1

(2008) F. Pfeiffer et al.   GENOMICS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION