MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

(2011) Garret Suen et al.   PLoS Genetics

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

(2011) Christian M Zmasek et al.   GENOME BIOLOGY

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite Scavenging Amino Acids from Its Host's Lungs

(2010) Philippe M. Hauser et al.   PLoS One

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade

(2010) Simon W. Baxter et al.   PLoS Genetics

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

(2010) C André Lévesque et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

The genome of the blood fluke Schistosoma mansoni

(2009) Matthew Berriman et al.   NATURE

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

(2009) Carol Soderlund et al.   PLoS Genetics

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

(2009) Fusheng Wei et al.   PLoS Genetics

nGASP - the nematode genome annotation assessment project

(2008) Avril Coghlan et al.   BMC BIOINFORMATICS