A Pluralistic Account of Homology: Adapting the Models to the Data

MosaicFinder: identification of fused gene families in sequence similarity networks

(2013) Pierre-Alain Jachiet et al.   BIOINFORMATICS

Gene similarity networks provide tools for understanding eukaryote origins and evolution

(2013) D. Alvarez-Ponce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

High-quality sequence clustering guided by network topology and multiple alignment likelihood

(2012) Vincent Miele et al.   BIOINFORMATICS

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

(2012) David A Fitzpatrick et al.   BMC GENOMICS

Increased Genome Sampling Reveals a Dynamic Relationship between Gene Duplicability and the Structure of the Primate Protein–Protein Interaction Network

(2012) Aoife Doherty et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metazoan opsin evolution reveals a simple route to animal vision

(2012) R. Feuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

(2012) E. Bapteste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data

(2012) Xiaoshu Chen et al.   PLoS Computational Biology

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

The public goods hypothesis for the evolution of life on Earth

(2011) James O McInerney et al.   Biology Direct

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Phylogenomic networks

(2011) Tal Dagan   TRENDS IN MICROBIOLOGY

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

(2011) Alinda Nagy et al.   Genes

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors

(2011) Alinda Nagy et al.   Genes

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Modular arrangement of proteins as inferred from analysis of homology

(2010) Erik L.L. Sonnhammer et al.   PROTEIN SCIENCE

Domain Recombination: A Workhorse for Evolutionary Innovation

(2010) G. Apic et al.   Science Signaling

Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective

(2009) Yan Boucher et al.   BIOESSAYS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Getting a better picture of microbial evolution en route to a network of genomes

(2009) T. Dagan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

A Database of Domain Definitions for Proteins with Complex Interdomain Geometry

(2009) Indraneel Majumdar et al.   PLoS One

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MACHOS: Markov clusters of homologous subsequences

(2008) Simon Wong et al.   BIOINFORMATICS

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(2008) Nan Song et al.   PLoS Computational Biology

Fusion and Fission of Genes Define a Metric between Fungal Genomes

(2008) Pascal Durrens et al.   PLoS Computational Biology