Toward community standards in the quest for orthologs

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

Editorial: Orthology and applications

(2011) C. Dessimoz   BRIEFINGS IN BIOINFORMATICS

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   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

The what, where, how and why of gene ontology--a primer for bioinformaticians

(2011) L. du Plessis et al.   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

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

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

(2011) Chuming Chen et al.   PLoS One

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

RNAcentral: A vision for an international database of RNA sequences

(2011) A. Bateman et al.   RNA

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

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

Orthology confers intron position conservation

(2010) Anna Henricson et al.   BMC GENOMICS

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

A Problem With the Correlation Coefficient as a Measure of Gene Expression Divergence

(2009) Vini Pereira et al.   GENETICS

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity

(2009) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

Evolutionary constraints on structural similarity in orthologs and paralogs

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

miROrtho: computational survey of microRNA genes

(2008) D. Gerlach et al.   NUCLEIC ACIDS RESEARCH

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(2008) Nan Song et al.   PLoS Computational Biology

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY