Identifying Single Copy Orthologs in Metazoa

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

(2013) Albert J Vilella et al.   GENOME BIOLOGY

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Error and Error Mitigation in Low-Coverage Genome Assemblies

(2011) Melissa J. Hubisz et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Getting Started in Gene Orthology and Functional Analysis

(2010) Gang Fang et al.   PLoS Computational Biology

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

AQUA: automated quality improvement for multiple sequence alignments

(2009) J. Muller et al.   BIOINFORMATICS

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

(2009) Scott DiGuistini et al.   GENOME BIOLOGY

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

(2008) Jorge MC Mondego et al.   BMC GENOMICS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH