Global Patterns of Protein Domain Gain and Loss in Superkingdoms

Emergence of novel domains in proteins

(2013) Macarena Toll-Riera et al.   BMC EVOLUTIONARY BIOLOGY

Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism

(2013) Kelsey Caetano-Anollés et al.   PLoS One

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

(2013) Patrick Forterre   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

(2013) Syed Abbas Bukhari et al.   PLoS Computational Biology

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

(2012) Kyung Mo Kim et al.   BMC EVOLUTIONARY BIOLOGY

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

(2012) Arshan Nasir et al.   BMC EVOLUTIONARY BIOLOGY

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

Ribosomal History Reveals Origins of Modern Protein Synthesis

(2012) Ajith Harish et al.   PLoS One

Gene gain and loss events in Rickettsia and Orientia species

(2011) Kalliopi Georgiades et al.   Biology Direct

Origin and evolution of gene families in Bacteria and Archaea

(2011) R Collins et al.   BMC BIOINFORMATICS

The proteomic complexity and rise of the primordial ancestor of diversified life

(2011) Kyung Mo Kim et al.   BMC EVOLUTIONARY BIOLOGY

Characterization and Inference of Gene Gain/Loss along Burkholderia Evolutionary History

(2011) Bo Zhu et al.   Evolutionary Bioinformatics

The Dynamics and Evolutionary Potential of Domain Loss and Emergence

(2011) A. D. Moore et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Reductive evolution of proteomes and protein structures

(2011) M. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

(2011) J. Cameron Thrash et al.   Scientific Reports

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

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

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

(2011) Christian M Zmasek et al.   GENOME BIOLOGY

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

(2011) Arshan Nasir et al.   Genes

Proteome Evolution and the Metabolic Origins of Translation and Cellular Life

(2010) Derek Caetano-Anollés et al.   JOURNAL OF MOLECULAR EVOLUTION

Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data

(2010) K. M. Kim et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation

(2010) Minglei Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

SUPERFAMILY 1.75 including a domain-centric gene ontology method

(2010) D. A. de Lima Morais et al.   NUCLEIC ACIDS RESEARCH

Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis

(2010) Anthony M. Poole et al.   RESEARCH IN MICROBIOLOGY

Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns

(2010) Christian M Zmasek et al.   GENOME BIOLOGY

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

The origin, evolution and structure of the protein world

(2009) Gustavo Caetano-Anollés et al.   BIOCHEMICAL JOURNAL

Chaperones and protein folding in the archaea

(2009) Andrew T. Large et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The evolution of protein domain families

(2009) Marija Buljan et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

(2009) Minglei Wang et al.   STRUCTURE

Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

(2009) David A. Morrison   SYSTEMATIC BIOLOGY

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

(2008) A. L. Davidson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

Arrangements in the modular evolution of proteins

(2008) Andrew D. Moore et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses

(2008) Feng-Jie Sun et al.   PLoS Computational Biology