Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas

The effect of temperature on physiological energetics of a fast-growing selective strain and a hatchery population of the Pacific oyster (Crassostrea gigas )

(2018) Jingxiao Zhang et al.   AQUACULTURE RESEARCH

Gonad Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Identifies Potential Genes Regulating the Sex Determination and Differentiation Process

(2018) Chenyang Yue et al.   MARINE BIOTECHNOLOGY

Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

(2018) Chunyan Li et al.   BMC GENOMICS

Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction

(2018) Alejandro P. Gutierrez et al.   Frontiers in Genetics

The transcriptional response of the Pacific oyster Crassostrea gigas against acute heat stress

(2017) Chuanyan Yang et al.   FISH & SHELLFISH IMMUNOLOGY

Differential mantle transcriptomics and characterization of growth-related genes in the diploid and triploid pearl oyster Pinctada fucata

(2017) Yunyan Guan et al.   Marine Genomics

A New View into the Regulation of Purine Metabolism: The Purinosome

(2017) Anthony M. Pedley et al.   TRENDS IN BIOCHEMICAL SCIENCES

Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)

(2017) Haigang Qi et al.   PLoS One

Improvements in desirable traits of the Pacific oyster, Crassostrea gigas , as a result of five generations of selection on the West Coast, USA

(2016) Claudio Manoel Rodrigues de Melo et al.   AQUACULTURE

A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters ( Crassostrea gigas × Crassostrea angulata ) Using Genotyping-by-Sequencing

(2016) Jinpeng Wang et al.   G3-Genes Genomes Genetics

Identification, molecular characterization and expression analysis ofRPL24genes in three Cucurbitaceae family members: cucumber, melon and watermelon

(2015) Mehmet Cengiz Baloglu et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

Transcriptome analysis reveals strong and complex antiviral response in a mollusc

(2015) Yan He et al.   FISH & SHELLFISH IMMUNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.)

(2015) Li Jiang et al.   Scientific Reports

Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds

(2015) Dennis Hedgecock et al.   G3-Genes Genomes Genetics

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

(2015) Dandan Feng et al.   PLoS One

QTL mapping for glycogen content and shell pigmentation in the Pacific oyster Crassostrea gigas using microsatellites and SNPs

(2014) Xiaoxiao Zhong et al.   AQUACULTURE INTERNATIONAL

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Modulation of insulin-like receptor gene (MdIR) in response to feeding in the surf clam Mesodesma donacium (Lamarck, 1818)

(2014) Pamela Alarcón-Matus et al.   JOURNAL OF MOLLUSCAN STUDIES

Discovery and validation of genic single nucleotide polymorphisms in the Pacific oysterCrassostrea gigas

(2014) Jiafeng Wang et al.   Molecular Ecology Resources

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

A Scallop IGF Binding Protein Gene: Molecular Characterization and Association of Variants with Growth Traits

(2014) Liying Feng et al.   PLoS One

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heritability estimates for growth-related traits in the Pacific oyster (Crassostrea gigas) using a molecular pedigree

(2013) Ning Kong et al.   AQUACULTURE RESEARCH

Genome and Transcriptome Analyses Provide Insight into the Euryhaline Adaptation Mechanism of Crassostrea gigas

(2013) Jie Meng et al.   PLoS One

Polymorphism in the insulin-related peptide gene and its association with growth traits in the Pacific oyster Crassostrea gigas

(2012) Rihao Cong et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

The GTPase Gem and its partner Kif9 are required for chromosome alignment, spindle length control, and mitotic progression

(2012) Guillaume Andrieu et al.   FASEB JOURNAL

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

(2012) Mohamed Salem et al.   PLoS One

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

The physiological basis for inter-individual growth variability in the spat of clams (Ruditapes philippinarum)

(2011) David Tamayo et al.   AQUACULTURE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Suppression substractive hybridisation (SSH) and real time PCR reveal differential gene expression in the Pacific cupped oyster, Crassostrea gigas, challenged with Ostreid herpesvirus 1

(2011) T. Renault et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Selection response and realized heritability for growth in three stocks of the Pacific oyster Crassostrea gigas

(2011) Qi Li et al.   FISHERIES SCIENCE

Quantitative Trait Locus Analysis of Stage-Specific Inbreeding Depression in the Pacific OysterCrassostrea gigas

(2011) Louis V. Plough et al.   GENETICS

Genetic Mapping and QTL Analysis of Growth-Related Traits in the Pacific Oyster

(2011) Xiang Guo et al.   MARINE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas)

(2010) C. Sauvage et al.   ANIMAL GENETICS

HETEROZYGOSITY-FITNESS CORRELATIONS: A TIME FOR REAPPRAISAL

(2010) Marta Szulkin et al.   EVOLUTION

Causes and effects of a highly successful marine invasion: Case-study of the introduced Pacific oyster Crassostrea gigas in continental NW European estuaries

(2010) Karin Troost   JOURNAL OF SEA RESEARCH

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

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

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

BOTERO1 is required for normal orientation of cortical microtubules and anisotropic cell expansion in Arabidopsis

(2010) Adeline Bichet et al.   PLANT JOURNAL

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). II. Response to selection for survival and its influence on growth and yield

(2009) Lionel Dégremont et al.   AQUACULTURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

In situ expression of ribosomal protein L21 in developing tooth germ of the mouse lower first molar

(2009) Ming Xie et al.   JOURNAL OF MOLECULAR HISTOLOGY

Centromere mapping in triploid families of the Pacific oyster Crassostrea gigas (Thunberg)

(2008) Sophie Hubert et al.   AQUACULTURE

HNF-1  Regulates Transcription of the PKD Modifier Gene Kif12

(2008) Y. Gong et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols