Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad

Cross‐species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads

(2021) Hans Christoph Liedtke et al.   MOLECULAR ECOLOGY

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Herbivory by spadefoot toad tadpoles and reduced water level affect submerged plants in temporary ponds

(2021) Maria Jesús Pinero-Rodríguez et al.   Inland Waters

Frog nest foams exhibit pharmaceutical foam-like properties

(2021) Sarah Brozio et al.   Royal Society Open Science

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies

(2021) Diego Fuentes et al.   NUCLEIC ACIDS RESEARCH

A scalable pipeline for designing reconfigurable organisms

(2020) Sam Kriegman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Movement patterns, maximum distances traveled and microhabitat selection of spadefoot toad tadpoles in temporary ponds

(2020) María Jesús Pinero-Rodríguez et al.   AMPHIBIA-REPTILIA

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

(2020) Paul M Hime et al.   SYSTEMATIC BIOLOGY

Miniaturization, genome size, and biological size in a diverse clade of salamanders

(2020) Louis Paul Decena-Segarra et al.   AMERICAN NATURALIST

Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates )

(2019) Christophe Dufresnes et al.   MOLECULAR ECOLOGY

Call a spade a spade: taxonomy and distribution of Pelobates, with description of a new Balkan endemic

(2019) Christophe Dufresnes et al.   ZooKeys

De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate

(2019) H. Christoph Liedtke et al.   G3-Genes Genomes Genetics

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

(2019) Fabian Seidl et al.   G3-Genes Genomes Genetics

Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

(2018) Giulia I. M. Pasquesi et al.   Nature Communications

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

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

A rapid rate of sex-chromosome turnover and non-random transitions in true frogs

(2018) Daniel L. Jeffries et al.   Nature Communications

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Toxins and pharmacologically active compounds from species of the family Bufonidae (Amphibia, Anura)

(2017) Candelario Rodríguez et al.   JOURNAL OF ETHNOPHARMACOLOGY

Genetic accommodation via modified endocrine signalling explains phenotypic divergence among spadefoot toad species

(2017) Saurabh S. Kulkarni et al.   Nature Communications

Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans

(2017) Kristian Alfsnes et al.   Ecology and Evolution

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

(2016) Xuefeng Cui et al.   BIOINFORMATICS

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly

(2016) R. Rebecca Love et al.   BMC GENOMICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

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

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

Assembly of long error-prone reads using de Bruijn graphs

(2016) Yu Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

(2015) Lindell Bromham et al.   AMERICAN NATURALIST

Anuran Reproductive Modes: Evolving Perspectives

(2015) Martha L. Crump   JOURNAL OF HERPETOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Updated distribution and biogeography of amphibians and reptiles of Europe

(2014) Neftali Sillero et al.   AMPHIBIA-REPTILIA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

BESST - Efficient scaffolding of large fragmented assemblies

(2014) Kristoffer Sahlin et al.   BMC BIOINFORMATICS

Ecological consequences of amphibian larvae and their native and alien predators on the community structure of temporary ponds

(2014) Rosa Arribas et al.   FRESHWATER BIOLOGY

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

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

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

(2013) Aarti Desai et al.   PLoS One

Mechanisms and Consequences of Developmental Acceleration in Tadpoles Responding to Pond Drying

(2013) Ivan Gomez-Mestre et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

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

Evolutionary reduction of developmental plasticity in desert spadefoot toads

(2011) S. S. KULKARNI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY