Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the EarthwormEisenia fetida

Reinforcing the Egg-Timer: Recruitment of Novel Lophotrochozoa Homeobox Genes to Early and Late Development in the Pacific Oyster

(2015) Jordi Paps et al.   Genome Biology and Evolution

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Illuminating the Base of the Annelid Tree Using Transcriptomics

(2014) Anne Weigert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication

(2014) Kyle J. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri

(2012) Susan J Stasiuk et al.   EvoDevo

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Additional duplicated Hox genes in the earthworm: Perionyx excavatus Hox genes consist of eleven paralog groups

(2011) Sung-Jin Cho et al.   GENE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

(2010) Joseph F Ryan et al.   EvoDevo

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

HomeoDB: a database of homeobox gene diversity

(2008) Ying-Fu Zhong et al.   EVOLUTION & DEVELOPMENT

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

(2008) L. Z. Holland et al.   GENOME RESEARCH