Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oyster Crassostrea ariakensis

Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas

(2021) Haigang Qi et al.   Molecular Ecology Resources

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

(2021) Carolina Peñaloza et al.   GigaScience

Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

(2021) Ao Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Acetylome Analysis Reveals Population Differentiation of the Pacific Oyster Crassostrea gigas in Response to Heat Stress

(2020) Ao Li et al.   MARINE BIOTECHNOLOGY

Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves

(2020) Jinxia Peng et al.   Molecular Ecology Resources

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

(2019) Mahdi Belcaid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis

(2019) A. Xingyu Liu et al.   MARINE BIOTECHNOLOGY

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cysteine dioxygenase is essential for mouse sperm osmoadaptation and male fertility

(2018) Atsushi Asano et al.   FEBS Journal

Inducible variation in anaerobic energy metabolism reflects hypoxia tolerance across the intertidal and subtidal distribution of the Pacific oyster ( Crassostrea gigas )

(2018) Jie Meng et al.   MARINE ENVIRONMENTAL RESEARCH

OUP accepted manuscript

(2018)   DNA RESEARCH

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Erratum to: A reference human genome dataset of the BGISEQ-500 sequencer

(2018) Jie Huang et al.   GigaScience

Response a chronic effects of PBDE-47: Up-regulations of HSP60 and HSP70 expression in freshwater bivalve Anodonta woodiana

(2017) Xichao Xia et al.   FISH & SHELLFISH IMMUNOLOGY

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response

(2017) Hongtao Nie et al.   Scientific Reports

Intraspecific Variation in Mitogenomes of Five Crassostrea Species Provides Insight into Oyster Diversification and Speciation

(2016) Jianfeng Ren et al.   MARINE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Osmoregulated Chloride Currents in Hemocytes from Mytilus galloprovincialis

(2016) Monica Bregante et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

Non-Lethal Heat Shock of the Asian Green Mussel, Perna viridis, Promotes Hsp70 Synthesis, Induces Thermotolerance and Protects Against Vibrio Infection

(2015) Nor Afiqah Aleng et al.   PLoS One

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Interactive Effects of Ocean Acidification, Elevated Temperature, and Reduced Salinity on Early-Life Stages of the Pacific Oyster

(2014) Ginger W. K. Ko et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2014) Xuelin Zhao et al.   PLoS One

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

(2013) Jie Meng et al.   PLoS One

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas

(2012) Xuelin Zhao et al.   PLoS One

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Osmoregulation in decapod crustaceans: implications to aquaculture productivity, methods for potential improvement and interactions with elevated ammonia exposure

(2011) Nicholas Romano et al.   AQUACULTURE

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals

(2011) D. H. Erwin et al.   SCIENCE

Mechanosensitive signalling in fish gill and other ion transporting epithelia

(2010) W. S. Marshall   Acta Physiologica

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Eleven novel microsatellite markers for the Asian oysterCrassostrea ariakensis

(2008) JIE XIAO et al.   Molecular Ecology Resources