Genome of Spea multiplicata, a Rapidly Developing, Phenotypically Plastic, and Desert-Adapted Spadefoot Toad

Variation in hybrid gene expression: implications for the evolution of genetic incompatibilities in interbreeding species

(2019) Fabian Seidl et al.   MOLECULAR ECOLOGY

Morphological novelty emerges from pre-existing phenotypic plasticity

(2018) Nicholas A. Levis et al.   Nature Ecology & Evolution

Genomic takeover by transposable elements in the Strawberry poison frog

(2018) Rebekah L Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome assembly of the invasive cane toad, Rhinella marina

(2018) Richard J Edwards et al.   GigaScience

Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate

(2018) H. Christoph Liedtke et al.   Nature Ecology & Evolution

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Jumping genomic gigantism

(2018) Rachel Lockridge Mueller et al.   Nature Ecology & Evolution

Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement

(2017) N. A. Levis et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Xenbase: a genomic, epigenomic and transcriptomic model organism database

(2017) Kamran Karimi et al.   NUCLEIC ACIDS RESEARCH

Genetic variation during range expansion: effects of habitat novelty and hybridization

(2017) Amanda A. Pierce et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs

(2017) Rebekah M. Charney et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

(2017) S. Austin Hammond et al.   Nature Communications

Hybridization as a facilitator of species range expansion

(2016) Karin S. Pfennig et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

(2016) Gaik Tamazian et al.   GigaScience

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Whole-genome sequence of the Tibetan frogNanorana parkeriand the comparative evolution of tetrapod genomes

(2015) Yan-Bo Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An inducible offense: carnivore morph tadpoles induced by tadpole carnivory

(2015) Nicholas A. Levis et al.   Ecology and Evolution

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Evolution of Rapid Development in Spadefoot Toads Is Unrelated to Arid Environments

(2014) Cen Zeng et al.   PLoS One

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.)

(2012) KARIN S. PFENNIG et al.   Molecular Ecology Resources

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

(2012) Ruibang Luo et al.   GigaScience

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Distinct Xenopus Nodal ligands sequentially induce mesendoderm and control gastrulation movements in parallel to the Wnt/PCP pathway

(2010) G. Luxardi et al.   DEVELOPMENT

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups

(2009) Jindřich Chrtek et al.   ANNALS OF BOTANY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS