The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

An Endogenous Foamy Virus in the Aye-Aye (Daubentonia madagascariensis)

(2012) G.-Z. Han et al.   JOURNAL OF VIROLOGY

An Endogenous Foamy-like Viral Element in the Coelacanth Genome

(2012) Guan-Zhu Han et al.   PLoS Pathogens

Graph accordance of next-generation sequence assemblies

(2011) G. Yao et al.   BIOINFORMATICS

Expression regulation triggers oncogenicity of xmrk alleles in the Xiphophorus melanoma system

(2011) Janine Regneri et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

(2011) Angel Amores et al.   GENETICS

Comprehensive Field Synopsis and Systematic Meta-analyses of Genetic Association Studies in Cutaneous Melanoma

(2011) F. Chatzinasiou et al.   JNCI-Journal of the National Cancer Institute

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genetic and environmental melanoma models in fish

(2010) E. Elizabeth Patton et al.   Pigment Cell & Melanoma Research

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Evolution of Placentas in the Fish Family Poeciliidae: An Empirical Study of Macroevolution

(2009) B.J.A. Pollux et al.   Annual Review of Ecology Evolution and Systematics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

(2009) D. H. E. Setiamarga et al.   Biology Letters

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

(2009) Ingo Braasch et al.   Genome Biology and Evolution

Automated identification of conserved synteny after whole-genome duplication

(2009) J. M. Catchen et al.   GENOME RESEARCH

Macroevolution of Complex Retroviruses

(2009) A. Katzourakis et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation

(2008) David Brawand et al.   PLOS BIOLOGY