Development of SNP markers for identification of thermo-resistant families of the Pacific oyster Crassostrea gigas based on RNA-seq

Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis

(2019) Zhuang Yang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Histological Alterations in Pacific Oysters Crassostrea gigas that Survived a Summer Mortality Event in Baja California, Mexico

(2018) Jorge Cáceres-Martínez et al.   JOURNAL OF AQUATIC ANIMAL HEALTH

Genomic Tools and Selective Breeding in Molluscs

(2018) Christopher M. Hollenbeck et al.   Frontiers in Genetics

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

Biallelic COLGALT1 variants are associated with cerebral small vessel disease

(2018) Satoko Miyatake et al.   ANNALS OF NEUROLOGY

Transcriptomic and metabolic response to chronic and acute thermal exposure of juvenile geoduck clams Panopea globosa

(2018) Oscar E. Juárez et al.   Marine Genomics

Performance of Diploid and TriploidCrassostrea gigas(Thunberg, 1793) Grown in Tropical Versus Temperate Natural Environmental Conditions

(2017) Ana M. Ibarra et al.   JOURNAL OF SHELLFISH RESEARCH

Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond

(2017) Jisca Huisman   Molecular Ecology Resources

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

Collagen Accumulation in Osteosarcoma Cells lacking GLT25D1 Collagen Galactosyltransferase

(2016) Stephan Baumann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

(2014) Ross D Houston et al.   BMC GENOMICS

Aha1 Can Act as an Autonomous Chaperone to Prevent Aggregation of Stressed Proteins

(2014) Vishwadeepak Tripathi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Computational Screening and Molecular Dynamic Simulation of Breast Cancer Associated Deleterious Non-Synonymous Single Nucleotide Polymorphisms in TP53 Gene

(2014) Kumaraswamy Naidu Chitrala et al.   PLoS One

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

Essential Role of the Zinc Transporter ZIP9/SLC39A9 in Regulating the Activations of Akt and Erk in B-Cell Receptor Signaling Pathway in DT40 Cells

(2013) Masanari Taniguchi et al.   PLoS One

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evidence of herpesvirus (OsHV-1) resistance in juvenile Crassostrea gigas selected for high resistance to the summer mortality phenomenon

(2011) Lionel Dégremont   AQUACULTURE

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Cloning and expression of a heat shock protein (HSP) 90 gene in the haemocytes of Crassostrea hongkongensis under osmotic stress and bacterial challenge

(2011) Dingkun Fu et al.   FISH & SHELLFISH IMMUNOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Identification of Domains and Amino Acids Essential to the Collagen Galactosyltransferase Activity of GLT25D1

(2011) Claire Perrin-Tricaud et al.   PLoS One

Expression analysis of global gene response to chronic heat exposure in broiler chickens (Gallus gallus) reveals new reactive genes

(2011) C. Li et al.   POULTRY SCIENCE

Antioxidant responses in gills of mussel (Mytilus galloprovincialis) as biomarkers of environmental stress along the Spanish Mediterranean coast

(2010) B. Fernández et al.   AQUATIC TOXICOLOGY

Toward the estimation of the absolute quality of individual protein structure models

(2010) Pascal Benkert et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective

(2010) Nicolas Guex et al.   ELECTROPHORESIS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties

(2010) Tao Huang et al.   PLoS One

Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008

(2010) Amélie Segarra et al.   VIRUS RESEARCH

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

A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity

(2009) Abdellah Allali-Hassani et al.   BIOCHEMICAL JOURNAL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait

(2009) Thomas Moen et al.   BMC GENOMICS

The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL

(2009) R D Houston et al.   HEREDITY

Small but influential: the role of microRNAs on gene regulatory network and 3′UTR evolution

(2009) Rui Zhang et al.   Journal of Genetics and Genomics

Transcriptome Profiling of Selectively Bred Pacific Oyster Crassostrea gigas Families that Differ in Tolerance of Heat Shock

(2009) R. Paul Lang et al.   MARINE BIOTECHNOLOGY

COLONY: a program for parentage and sibship inference from multilocus genotype data

(2009) OWEN R. JONES et al.   Molecular Ecology Resources

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Transcriptional expression levels of cell stress marker genes in the Pacific oyster Crassostrea gigas exposed to acute thermal stress

(2008) Émilie Farcy et al.   CELL STRESS & CHAPERONES

3′ UTRs Are the Primary Regulators of Gene Expression in the C. elegans Germline

(2008) Christopher Merritt et al.   CURRENT BIOLOGY

Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar)

(2008) R. D. Houston et al.   GENETICS

Core Glycosylation of Collagen Is Initiated by Two  (1-O)Galactosyltransferases

(2008) B. Schegg et al.   MOLECULAR AND CELLULAR BIOLOGY

Cadmium affects the expression of heat shock protein 90 and metallothionein mRNA in the Pacific oyster, Crassostrea gigas

(2007) Yong Ki Choi et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY