Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

(2016) Rebekah L. Horn et al.   Molecular Ecology Resources

Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

(2016) Bharat Bhusan Patnaik et al.   PLoS One

RNA sequencing,de novoassembly, and functional annotation of an endangered Nymphalid butterfly,Fabriciana nerippe Felder, 1862

(2016) Hee-Ju Hwang et al.   ENTOMOLOGICAL RESEARCH

Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

(2016) So Park et al.   Genes

Salt-Responsive Transcriptome Profiling of Suaeda glauca via RNA Sequencing

(2016) Hangxia Jin et al.   PLoS One

Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti

(2016) Hui Luo et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways

(2015) Bas Verbruggen et al.   BMC GENOMICS

De novo transcriptome sequencing and analysis of Coccinella septempunctata L. in non-diapause, diapause and diapause-terminated states to identify diapause-associated genes

(2015) Xiaoyang Qi et al.   BMC GENOMICS

Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing

(2015) Bharat Patnaik et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

De-novo transcriptome analysis of the banana shrimp (Fenneropenaeus merguiensis) and identification of genes associated with reproduction and development

(2015) Daniel Powell et al.   Marine Genomics

Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes inDaphnia

(2015) Jana Asselman et al.   MOLECULAR ECOLOGY

De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

(2015) Mei Liang et al.   PLoS One

Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress

(2015) Ke Chen et al.   PLoS One

Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity

(2015) Ke Chen et al.   PLoS One

Genetic diversity and population structure of the Tibetan poplar (Populus szechuanica var. tibetica) along an altitude gradient

(2014) Dengfeng Shen et al.   BMC GENETICS

Ade novotranscriptome of European pollen beetle populations and its analysis, with special reference to insecticide action and resistance

(2014) C. T. Zimmer et al.   INSECT MOLECULAR BIOLOGY

Evolutionary relationships within Triops (Branchiopoda: Notostraca) using complete mitochondrial genomes

(2014) Rebekah L. Horn et al.   JOURNAL OF CRUSTACEAN BIOLOGY

Sex-dependent transcriptome analysis and single nucleotide polymorphism (SNP) discovery in the brine shrimp Artemia franciscana

(2014) Diego Valenzuela-Miranda et al.   Marine Genomics

Transcriptomic Analysis of Endangered Chinese Salamander: Identification of Immune, Sex and Reproduction-Related Genes and Genetic Markers

(2014) Rongbo Che et al.   PLoS One

Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery

(2014) Jianjian Lv et al.   PLoS One

Transcriptome Analysis of the Mud Crab (Scylla paramamosain) by 454 Deep Sequencing: Assembly, Annotation, and Marker Discovery

(2014) Hongyu Ma et al.   PLoS One

Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

(2013) Hui Guo et al.   FISH & SHELLFISH IMMUNOLOGY

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

De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids

(2013) Ramasamy S. Annadurai et al.   PLoS One

Correction: Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Growth-Related Traits in Litopenaeus vannamei for Selective Breeding Applications

(2013) Farafidy Andriantahina et al.   PLoS One

Cys2His2 zinc finger protein family: Classification, functions, and major members

(2012) S. V. Razin et al.   BIOCHEMISTRY-MOSCOW

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

(2012) Dejun Li et al.   BMC GENOMICS

Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster

(2012) Adam D. Miller et al.   MOLECULAR BIOLOGY REPORTS

De Novo Sequencing and Transcriptome Analysis of the Central Nervous System of Mollusc Lymnaea stagnalis by Deep RNA Sequencing

(2012) Hisayo Sadamoto et al.   PLoS One

Isolation and characterization of twenty-six microsatellite loci for the tetraploid fish Dabry’s sturgeon (Acipenser dabryanus)

(2012) Shu-Huan Zhang et al.   Conservation Genetics Resources

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

(2011) Victor Zeng et al.   BMC GENOMICS

Morphologic and Genetic Variation in Triops (Branchiopoda: Notostraca) from Ephemeral Waters of the Northern Chihuahuan Desert of North America

(2011) Kenneth S. Macdonald et al.   JOURNAL OF CRUSTACEAN BIOLOGY

The first insight into the Taxus genome via fosmid library construction and end sequencing

(2011) DaCheng Hao et al.   MOLECULAR GENETICS AND GENOMICS

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

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

Complete mitochondrial genome of the longtail tadpole shrimpTriops longicaudatus(Crustacea, Branchiopoda, Notostraca)

(2010) Ju-Sun Ryu et al.   Mitochondrial DNA

Comprehensive Analysis of Simple Sequence Repeats in Pre-miRNAs

(2010) Ming Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Gene discovery from an ovary cDNA library of oriental river prawn Macrobrachium nipponense by ESTs annotation

(2008) Ping Wu et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Use and misuse of the gene ontology annotations

(2008) Seung Yon Rhee et al.   NATURE REVIEWS GENETICS