Functional and evolutionary implications of gene orthology

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

Alternative splicing: decoding an expansive regulatory layer

(2012) Manuel Irimia et al.   CURRENT OPINION IN CELL BIOLOGY

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

Phylogenetic Analyses Uncover a Novel Clade of Transferrin in Nonmammalian Vertebrates

(2012) Hirzahida Mohd-Padil et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

(2012) Paul D. Thomas et al.   PLoS Computational Biology

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

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

Domain architecture conservation in orthologs

(2011) Kristoffer Forslund et al.   BMC BIOINFORMATICS

Ortholog identification in the presence of domain architecture rearrangement

(2011) K. Sjolander et al.   BRIEFINGS IN BIOINFORMATICS

Obituary: Walter Fitch and the orthology paradigm

(2011) E. V. Koonin   BRIEFINGS IN BIOINFORMATICS

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

(2011) J. Huerta-Cepas et al.   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Degrees of similarity

(2011) Tanita Casci   NATURE REVIEWS GENETICS

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

(2011) Khalid Mahmood et al.   NUCLEIC ACIDS RESEARCH

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

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

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

(2010) Marina V Omelchenko et al.   Biology Direct

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

An ontology to clarify homology-related concepts

(2010) Julien Roux et al.   TRENDS IN GENETICS

Domain mobility in proteins: functional and evolutionary implications

(2009) M. K. Basu et al.   BRIEFINGS IN BIOINFORMATICS

Decrypting the genome's alternative messages

(2009) Britta Hartmann et al.   CURRENT OPINION IN CELL BIOLOGY

Evolutionary constraints on structural similarity in orthologs and paralogs

(2009) Mark E. Peterson et al.   PROTEIN SCIENCE

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

RESURRECTING THE ROLE OF TRANSCRIPTION FACTOR CHANGE IN DEVELOPMENTAL EVOLUTION

(2008) Vincent J. Lynch et al.   EVOLUTION

Global alignment of multiple protein interaction networks with application to functional orthology detection

(2008) R. Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY

The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species

(2007) Stéphane Descorps-Declère et al.   BIOCHIMIE