Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Blue: correcting sequencing errors using consensus and context

(2014) Paul Greenfield et al.   BIOINFORMATICS

Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

(2014) G. P. Flowers et al.   DEVELOPMENT

Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders

(2014) C. Sun et al.   Genome Biology and Evolution

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Highly efficient targeted mutagenesis in one-cell mouse embryos mediated by the TALEN and CRISPR/Cas systems

(2014) Akihiro Yasue et al.   Scientific Reports

Efficient high-throughput sequencing of a laser microdissected chromosome arm

(2013) Eva Seifertova et al.   BMC GENOMICS

Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain Transcription

(2013) Robert B. Page et al.   Genome Biology and Evolution

Variation in Salamander Tail Regeneration Is Associated with Genetic Factors That Determine Tail Morphology

(2013) Gareth J. Voss et al.   PLoS One

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Germline Transgenic Methods for Tracking Cells and Testing Gene Function during Regeneration in the Axolotl

(2013) Shahryar Khattak et al.   Stem Cell Reports

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

Visualization of retinoic acid signaling in transgenic axolotls during limb development and regeneration

(2012) James R. Monaghan et al.   DEVELOPMENTAL BIOLOGY

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

(2011) Stephen R. Voss et al.   GENOME RESEARCH

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration

(2009) James R Monaghan et al.   BMC BIOLOGY

Genic regions of a large salamander genome contain long introns and novel genes

(2009) Jeramiah J Smith et al.   BMC GENOMICS

Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes

(2009) Peng Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)

(2008) Robert B Page et al.   BMC GENOMICS