Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

(2014) C. Gilbert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms

(2013) Mark J Margres et al.   BMC GENOMICS

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator

(2013) Qiu-Hong Wan et al.   CELL RESEARCH

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

(2013) Daniel A. Dalquen et al.   Genome Biology and Evolution

The First Chameleon Transcriptome: Comparative Genomic Analysis of the OXPHOS System Reveals Loss of COX8 in Iguanian Lizards

(2013) Dan Bar-Yaacov et al.   Genome Biology and Evolution

Contrasted Evolution of the Vomeronasal Receptor Repertoires in Mammals and Squamate Reptiles

(2013) Urszula Brykczynska et al.   Genome Biology and Evolution

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

(2013) John A St John et al.   GENOME BIOLOGY

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

(2012) Hilary C Miller et al.   BMC GENOMICS

Uterine Gene Expression in the Live-Bearing Lizard, Chalcides ocellatus, Reveals Convergence of Squamate Reptile and Mammalian Pregnancy Mechanisms

(2012) Matthew C. Brandley et al.   Genome Biology and Evolution

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

(2011) Athanasia C Tzika et al.   EvoDevo

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

(2010) Tonia S Schwartz et al.   BMC GENOMICS

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

(2010) AXEL KÜNSTNER et al.   MOLECULAR ECOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

More than just orphans: are taxonomically-restricted genes important in evolution?

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology