Comparative Transcriptome Analysis of Two Oysters, Crassostrea gigas and Crassostrea hongkongensis Provides Insights into Adaptation to Hypo-Osmotic Conditions

First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species,Pinus halepensisMill

(2014) S. Pinosio et al.   Molecular Ecology Resources

Inter-site differences of zinc susceptibility of the oyster Crassostrea hongkongensis

(2013) Fengjie Liu et al.   AQUATIC TOXICOLOGY

Mass flowering of the tropical treeShorea beccarianawas preceded by expression changes in flowering and drought-responsive genes

(2013) Masaki J. Kobayashi et al.   MOLECULAR ECOLOGY

SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

(2013) C. Schunter et al.   Molecular Ecology Resources

Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers

(2013) Z. C. Zhou et al.   Molecular Ecology Resources

Analysis of the black-chinned tilapiaSarotherodon melanotheron heudelotiireproducing under a wide range of salinities: from RNA-seq to candidate genes

(2013) J.-C. Avarre et al.   Molecular Ecology Resources

RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish

(2013) Shikai Liu et al.   PHYSIOLOGICAL GENOMICS

Transcriptome Sequencing of Zhikong Scallop (Chlamys farreri) and Comparative Transcriptomic Analysis with Yesso Scallop (Patinopecten yessoensis)

(2013) Shan Wang et al.   PLoS One

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

(2013) Iratxe Montes et al.   PLoS One

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

(2012) Shikai Liu et al.   BMC GENOMICS

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

(2012) Jun Chen et al.   BMC GENOMICS

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill

(2012) A. Whitehead et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

High-throughput and parallel SNP discovery in selected candidate genes inEucalyptus camaldulensisusing Illumina NGS platform

(2012) Prasad S. Hendre et al.   PLANT BIOTECHNOLOGY JOURNAL

Sequencing and de novo Analysis of Crassostrea angulata (Fujian Oyster) from 8 Different Developing Phases Using 454 GSFlx

(2012) Ji Qin et al.   PLoS One

Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas

(2012) Xuelin Zhao et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

(2011) Jianfeng Ren et al.   BMC EVOLUTIONARY BIOLOGY

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

(2011) Shikai Liu et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Transcriptomic Analysis of the Clam Meretrix meretrix on Different Larval Stages

(2011) Pin Huan et al.   MARINE BIOTECHNOLOGY

The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions

(2011) ROBERT W. CHAPMAN et al.   MOLECULAR ECOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus

(2010) Raul Bettencourt et al.   BMC GENOMICS

Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success

(2010) B. L. Lockwood et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

(2009) Yali Xue et al.   CURRENT BIOLOGY

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Type I interferon-dependent and -independent expression of tripartite motif proteins in immune cells

(2008) Ricardo Rajsbaum et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Comparative ORESTES-sampling of transcriptomes of immune-challenged Biomphalaria glabrata snails

(2008) Ben Hanelt et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Identification of Crassostrea ariakensis and Related Oysters by Multiplex Species-Specific PCR

(2008) Haiyan Wang et al.   JOURNAL OF SHELLFISH RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS