Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture

A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition

(2021) Damien E. Barrett et al.   PLoS One

Extensive genome-wide duplications in the eastern oyster ( Crassostrea virginica )

(2021) Tejashree H. Modak et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Digging into bivalve miRNAomes: between conservation and innovation

(2021) Umberto Rosani et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2021) Carolina Peñaloza et al.   GigaScience

Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia

(2021) Jin-Long Yang et al.   GigaScience

Transcriptomic Response to Perkinsus marinus in Two Crassostrea Oysters Reveals Evolutionary Dynamics of Host-Parasite Interactions

(2021) Jiulin Chan et al.   Frontiers in Genetics

miR-148 targets CiGadd45ba and CiGadd45bb to modulate the inflammatory response to bacterial infection in grass carp

(2020) Yuan Fang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The gene-rich genome of the scallop Pecten maximus

(2020) Nathan J Kenny et al.   GigaScience

Transcriptional Alteration of Gene Biomarkers in Hemocytes of Wild Ostrea edulis with Molecular Evidence of Infections with Bonamia spp. and/or Marteilia refringens Parasites

(2020) Paolo Cocci et al.   Pathogens

Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

(2020) Songqian Huang et al.   RNA Biology

Characterization of the ScghC1q-1 gene in Sinonovacula constricta and its role in innate immune responses

(2019) Yan Li et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Signatures of selection for bonamiosis resistance in European flat oyster ( Ostrea edulis ): New genomic tools for breeding programs and management of natural resources

(2019) Manuel Vera et al.   Evolutionary Applications

Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C

(2019) Chang-Ming Bai et al.   GigaScience

Solute carriers in scallop genome: Gene expansion and expression regulation after exposure to toxic dinoflagellate

(2019) Xiaogang Xun et al.   CHEMOSPHERE

Transmembrane (TMEM) protein family members: Poorly characterized even if essential for the metastatic process

(2019) Sébastien Marx et al.   SEMINARS IN CANCER BIOLOGY

Involvement of apoptosis in the dialogue between the parasite Bonamia ostreae and the flat oyster Ostrea edulis

(2019) Ophélie Gervais et al.   FISH & SHELLFISH IMMUNOLOGY

Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves

(2019) Marco Gerdol et al.   Marine Drugs

Diversity of cilia-based mechanosensory systems and their functions in marine animal behaviour

(2019) Luis Alberto Bezares-Calderón et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Clinical and Functional Relevance of the Monocarboxylate Transporter Family in Disease Pathophysiology and Drug Therapy

(2018) Pascale Fisel et al.   CTS-Clinical and Translational Science

Long-term affected flat oyster ( Ostrea edulis ) haemocytes show differential gene expression profiles from naïve oysters in response to Bonamia ostreae

(2018) P. Ronza et al.   GENOMICS

Genomic Tools and Selective Breeding in Molluscs

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

OUP accepted manuscript

(2018)   DNA RESEARCH

Regulation of apoptosis-related genes during interactions between oyster hemocytes and the alveolate parasite Perkinsus marinus

(2018) Yuk-Ting Lau et al.   FISH & SHELLFISH IMMUNOLOGY

The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum)

(2017) Seyoung Mun et al.   Genome Biology and Evolution

MicroRNA-3570 Modulates the NF-κB Pathway in Teleost Fish by Targeting MyD88

(2017) Qing Chu et al.   JOURNAL OF IMMUNOLOGY

Harnessing the Power of Genomics to Secure the Future of Seafood

(2017) Louis Bernatchez et al.   TRENDS IN ECOLOGY & EVOLUTION

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization

(2017) Xiaodong Du et al.   GigaScience

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray

(2016) Belén G. Pardo et al.   FISH & SHELLFISH IMMUNOLOGY

Epigenetics: A New Model for Intracellular Parasite–Host Cell Regulation

(2016) W. Robert McMaster et al.   TRENDS IN PARASITOLOGY

Decreased expression of SLC39A14 is associated with tumor aggressiveness and biochemical recurrence of human prostate cancer

(2016) Qian-De Liao et al.   OncoTargets and Therapy

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The immune system and its modulation mechanism in scallop

(2015) Linsheng Song et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis reveals strong and complex antiviral response in a mollusc

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

Analysis of synonymous codon usage patterns in sixty-four different bivalve species

(2015) Marco Gerdol et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV)

(2014) Guofu Chen et al.   FISH & SHELLFISH IMMUNOLOGY

Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis

(2014) Laura Martín-Gómez et al.   INFECTION GENETICS AND EVOLUTION

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Temporal expression patterns of rainbow trout immune-related genes in response to Myxobolus cerebralis exposure

(2013) Melinda R. Baerwald   FISH & SHELLFISH IMMUNOLOGY

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Retrotransposons

(2012) David J. Finnegan   CURRENT BIOLOGY

Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica)

(2012) Yan He et al.   FISH & SHELLFISH IMMUNOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Identification and Comparative Analysis of MicroRNAs Associated with Low-N Tolerance in Rice Genotypes

(2012) Lata Nischal et al.   PLoS One

MicroRNAs and the cell cycle

(2011) María José Bueno et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Oyster Reefs at Risk and Recommendations for Conservation, Restoration, and Management

(2011) Michael W. Beck et al.   BIOSCIENCE

tRNA genes in eukaryotic genome organization and reorganization

(2011) Ramsay J. McFarlane et al.   CELL CYCLE

Polymorphism in a serine protease inhibitor gene and its association with disease resistance in the eastern oyster (Crassostrea virginica Gmelin)

(2011) Haiyang Yu et al.   FISH & SHELLFISH IMMUNOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Matrix metalloproteinases as therapeutic targets in protozoan parasitic infections

(2011) Nathalie Geurts et al.   PHARMACOLOGY & THERAPEUTICS

Trypanosoma cruzi Utilizes the Host Low Density Lipoprotein Receptor in Invasion

(2011) Fnu Nagajyothi et al.   PLoS Neglected Tropical Diseases

Genomic organization of eukaryotic tRNAs

(2010) Clara Bermudez-Santana et al.   BMC GENOMICS

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

tRNA as an active chemical scaffold for diverse chemical transformations

(2009) Christopher S. Francklyn et al.   FEBS LETTERS

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

(2009) Da Wei Huang et al.   Nature Protocols

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

(2008) I. Milne et al.   BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS