Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

(2017) Fidel Botero-Castro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

(2017) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conserved and divergent expression patterns of markers of axial development in reptilian embryos: Chinese soft-shell turtle and Madagascar ground gecko

(2016) Michio Yoshida et al.   DEVELOPMENTAL BIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Into the light: diurnality has evolved multiple times in geckos

(2015) Tony Gamble et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing

(2015) Kaori Tatsumi et al.   BIOTECHNIQUES

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

(2015) Yuichiro Hara et al.   BMC GENOMICS

Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3

(2015) Shen Gu et al.   HUMAN MOLECULAR GENETICS

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration

(2015) Yan Liu et al.   Nature Communications

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity

(2015) Laura W. Dillon et al.   Cell Reports

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Genetic manipulation of reptilian embryos: toward an understanding of cortical development and evolution

(2015) Tadashi Nomura et al.   Frontiers in Neuroscience

Dact genes are chordate specific regulators at the intersection of Wnt and Tgf-β signaling pathways

(2014) Frank Schubert et al.   BMC EVOLUTIONARY BIOLOGY

Gene duplication in an African cichlid adaptive radiation

(2014) Heather E Machado et al.   BMC GENOMICS

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

(2014) Nathalie Feiner 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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

On the origin of POU5F1

(2013) Stephen Frankenberg et al.   BMC BIOLOGY

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

(2013) Walter L Eckalbar et al.   BMC GENOMICS

NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits

(2013) P. Dittwald et al.   GENOME RESEARCH

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

(2013) Yinhua Huang et al.   NATURE GENETICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Repeated Origin and Loss of Adhesive Toepads in Geckos

(2012) Tony Gamble et al.   PLoS One

Novel origins of copy number variation in the dog genome

(2012) Jonas Berglund et al.   GENOME BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Rbfox-regulated alternative splicing is critical for zebrafish cardiac and skeletal muscle functions

(2011) Thomas L. Gallagher et al.   DEVELOPMENTAL BIOLOGY

The Anolis Lizard Genome: An Amniote Genome without Isochores

(2011) Matthew K. Fujita et al.   Genome Biology and Evolution

Genome-Wide Detection of Gene Extinction in Early Mammalian Evolution

(2011) Shigehiro Kuraku et al.   Genome Biology and Evolution

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes

(2009) Nathalie Feiner et al.   BMC EVOLUTIONARY BIOLOGY

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Normal developmental stages of the Madagascar ground geckoParoedura pictuswith special reference to limb morphogenesis

(2008) Miyuki Noro et al.   DEVELOPMENTAL DYNAMICS

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

(2008) M. A.M. Groenen et al.   GENOME RESEARCH

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH