Romance of the three domains: how cladistics transformed the classification of cellular organisms

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Automated Pangenomic Analysis in Target Selection for PCR Detection and Identification of Bacteria by Use of ssGeneFinder Webserver and Its Application to Salmonella enterica Serovar Typhi

(2012) Chi-Chun Ho et al.   JOURNAL OF CLINICAL MICROBIOLOGY

First Report of Spontaneous Intrapartum Atopobium vaginae Bacteremia

(2012) J. F. W. Chan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Identification of a Novel Bat Papillomavirus by Metagenomics

(2012) Herman Tse et al.   PLoS One

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

First Discovery of Two Polyketide Synthase Genes for Mitorubrinic Acid and Mitorubrinol Yellow Pigment Biosynthesis and Implications in Virulence of Penicillium marneffei

(2012) Patrick C. Y. Woo et al.   PLoS Neglected Tropical Diseases

The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

(2011) Ruben E Valas et al.   Biology Direct

Rapid Identification and Validation of Specific Molecular Targets for Detection of Escherichia coli O104:H4 Outbreak Strain by Use of High-Throughput Sequencing Data from Nine Genomes

(2011) C.-C. Ho et al.   JOURNAL OF CLINICAL MICROBIOLOGY

First Report of Disseminated Mycobacterium Skin Infections in Two Liver Transplant Recipients and Rapid Diagnosis byhsp65Gene Sequencing

(2011) Susanna K. P. Lau et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB

(2011) P. C. Y. Woo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Co-existence of multiple strains of two novel porcine bocaviruses in the same pig, a previously undescribed phenomenon in members of the family Parvoviridae, and evidence for inter- and intra-host genetic diversity and recombination

(2011) S. K. P. Lau et al.   JOURNAL OF GENERAL VIROLOGY

Complete Genome Sequence of a Coxsackievirus A22 Strain in Hong Kong Reveals a Natural Intratypic Recombination Event

(2011) C. C. Y. Yip et al.   JOURNAL OF VIROLOGY

Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination

(2011) S. K. P. Lau et al.   JOURNAL OF VIROLOGY

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

(2010) Sophie S Abby et al.   BMC BIOINFORMATICS

High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei

(2010) Patrick C. Y. Woo et al.   FEBS Journal

Genome Networks Root the Tree of Life between Prokaryotic Domains

(2010) Tal Dagan et al.   Genome Biology and Evolution

Ecoepidemiology and Complete Genome Comparison of Different Strains of Severe Acute Respiratory Syndrome-Related Rhinolophus Bat Coronavirus in China Reveal Bats as a Reservoir for Acute, Self-Limiting Infection That Allows Recombination Events

(2010) S. K. P. Lau et al.   JOURNAL OF VIROLOGY

Cladistic analysis or cladistic classification?

(2010) Ernst Mayr   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees

(2010) K. Schliep et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rooting the Ribosomal Tree of Life

(2010) G. P. Fournier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coronavirus Diversity, Phylogeny and Interspecies Jumping

(2009) Patrick C. Y. Woo et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

The Evolutionary History of the Structure of 5S Ribosomal RNA

(2009) Feng-Jie Sun et al.   JOURNAL OF MOLECULAR EVOLUTION

Genome beginnings: rooting the tree of life

(2009) J. A. Lake et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What, Exactly, is Cladistics? Re-writing the History of Systematics and Biogeography

(2008) D. M. Williams et al.   ACTA BIOTHEORETICA

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin 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

A Comparison of Phylogenetic Network Methods Using Computer Simulation

(2008) Steven M. Woolley 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

Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis Within Protist Cells in Termite Gut

(2008) Y. Hongoh et al.   SCIENCE

Evidence for a New Root of the Tree of Life

(2008) James A. Lake et al.   SYSTEMATIC BIOLOGY