De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

(2017) Daniel Blande et al.   Scientific Data

Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal

(2017) J. I. Khudyakov et al.   Scientific Reports

FRAMA: from RNA-seq data to annotated mRNA assemblies

(2016) Martin Bens et al.   BMC GENOMICS

Identification and function annotation of long intervening noncoding RNAs

(2016) Haitao Luo et al.   BRIEFINGS IN BIOINFORMATICS

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Comparative analysis of ear-hole closure identifies epimorphic regeneration as a discrete trait in mammals

(2016) Thomas R. Gawriluk et al.   Nature Communications

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

(2016) Mary Shimoyama et al.   Database-The Journal of Biological Databases and Curation

Gene expression defines natural changes in mammalian lifespan

(2015) Alexey A. Fushan et al.   AGING CELL

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Ontogenetic Change in the Regional Distribution of Dehydroepiandrosterone-Synthesizing Enzyme and the Glucocorticoid Receptor in the Brain of the Spiny Mouse (Acomys cahirinus)

(2015) Tracey A. Quinn et al.   DEVELOPMENTAL NEUROSCIENCE

First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics

(2015) Lianming Du et al.   Molecular Ecology Resources

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences

(2015) Mnirnal D Maudhoo et al.   GigaScience

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs

(2014) Zhong-Yin Zhou et al.   Genome Biology and Evolution

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon," Israel

(2014) Y. Hadid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

Ontogeny of the Adrenal Gland in the Spiny Mouse, With Particular Reference to Production of the Steroids Cortisol and Dehydroepiandrosterone

(2013) Tracey A. Quinn et al.   ENDOCRINOLOGY

The “Vampirome”: Transcriptome and proteome analysis of the principal and accessory submaxillary glands of the vampire bat Desmodus rotundus, a vector of human rabies

(2013) Ivo M.B. Francischetti et al.   Journal of Proteomics

Transcriptome resources for the frogsLithobates clamitansandPseudacris regilla, emphasizing antimicrobial peptides and conserved loci for phylogenetics

(2013) Laura S. Robertson et al.   Molecular Ecology Resources

Development, validation and high-throughput analysis of sequence markers in nonmodel species

(2013) P. Zieliński et al.   Molecular Ecology Resources

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

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

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam et al.   GENOME RESEARCH

Creatine pretreatment prevents birth asphyxia–induced injury of the newborn spiny mouse kidney

(2012) Stacey J. Ellery et al.   PEDIATRIC RESEARCH

The evolution of menstruation: A new model for genetic assimilation

(2011) Deena Emera et al.   BIOESSAYS

The Placental Response to Excess Maternal Glucocorticoid Exposure Differs Between the Male and Female Conceptus in Spiny Mice1

(2011) Bree A. O'Connell et al.   BIOLOGY OF REPRODUCTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

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

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

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

Developmental changes in the expression of creatine synthesizing enzymes and creatine transporter in a precocial rodent, the spiny mouse

(2009) Zoe Ireland et al.   BMC DEVELOPMENTAL BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH