De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

Enabling comparative gene expression studies of thyroid hormone action through the development of a flexible real-time quantitative PCR assay for use across multiple anuran indicator and sentinel species

(2014) Nik Veldhoen et al.   AQUATIC TOXICOLOGY

Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes

(2014) Anna E. Savage et al.   GENE

Amphibians acquire resistance to live and dead fungus overcoming fungal immunosuppression

(2014) Taegan A. McMahon et al.   NATURE

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish

(2014) S. K. McMenamin et al.   SCIENCE

Differential transcription of fathead minnow immune-related genes following infection with frog virus 3, an emerging pathogen of ectothermic vertebrates

(2014) Kwang Cheng et al.   VIROLOGY

De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms

(2014) Kyle R. Frischkorn et al.   Frontiers in Microbiology

RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei

(2013) Suchonma Sookruksawong et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

An insight into the sialome of the frog biting fly, Corethrella appendiculata

(2013) José M.C. Ribeiro et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Combining Different mRNA Capture Methods to Analyze the Transcriptome: Analysis of the Xenopus laevis Transcriptome

(2013) Michael D. Blower et al.   PLoS One

Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study

(2013) Adam L. Bazinet et al.   PLoS One

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication

(2012) K M Kiemnec-Tyburczy et al.   HEREDITY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Xenbase: expansion and updates of the Xenopus model organism database

(2012) Christina James-Zorn et al.   NUCLEIC ACIDS RESEARCH

Immune Evasion Strategies of Ranaviruses and Innate Immune Responses to These Emerging Pathogens

(2012) Leon Grayfer et al.   Viruses-Basel

The Metamorphosis of Amphibian Toxicogenomics

(2012) Caren C. Helbing   Frontiers in Genetics

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Expression Profiles of Reproduction- and Thyroid Hormone-Related Transcripts in the Brains of Chemically-Induced Intersex Frogs

(2011) V.S. Langlois et al.   Sexual Development

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Regulation of Thyroid Hormone-, Oestrogen- and Androgen-Related Genes by Triiodothyronine in the Brain of Silurana tropicalis

(2010) Paula Duarte-Guterman et al.   JOURNAL OF NEUROENDOCRINOLOGY

Transcript profiles and triiodothyronine regulation of sex steroid- and thyroid hormone-related genes in the gonad–mesonephros complex of Silurana tropicalis

(2010) Paula Duarte-Guterman et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Gene switching at Xenopus laevis metamorphosis

(2009) Sandeep Mukhi et al.   DEVELOPMENTAL BIOLOGY

Comparative and developmental study of the immune system inXenopus

(2009) Jacques Robert et al.   DEVELOPMENTAL DYNAMICS

THE TOXICITY OF ROUNDUP ORIGINAL MAX® TO 13 SPECIES OF LARVAL AMPHIBIANS

(2009) Rick A. Relyea et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Expression and T3 regulation of thyroid hormone- and sex steroid-related genes during Silurana (Xenopus) tropicalis early development

(2009) Paula Duarte-Guterman et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Fadrozole and finasteride exposures modulate sex steroid- and thyroid hormone-related gene expression in Silurana (Xenopus) tropicalis early larval development

(2009) Valérie S. Langlois et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

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

(2009)   JOURNAL OF HEREDITY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Genome-Wide Transcriptional Response of Silurana (Xenopus) tropicalis to Infection with the Deadly Chytrid Fungus

(2009) Erica Bree Rosenblum et al.   PLoS One

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH