The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

(2021) Hao Song et al.   BMC BIOLOGY

A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)

(2021) Chase H Smith   Genome Biology and Evolution

Genomic Insights into the Origin and Evolution of Molluscan Red-Bloodedness in the Blood Clam Tegillarca granosa

(2021) Yongbo Bao et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

(2021) André Gomes-dos-Santos et al.   DNA RESEARCH

Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome

(2021) Michael A. McCartney   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics and transcriptomics of the green mussel explain the durability of its byssus

(2021) Koji Inoue et al.   Scientific Reports

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

The gene-rich genome of the scallop Pecten maximus

(2020) Nathan J Kenny et al.   GigaScience

Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus

(2020) Xiao Liu et al.   Scientific Data

Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle

(2020) Min Wei et al.   iScience

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

(2020) Yiqian Li et al.   BMC GENOMICS

Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

(2020) Jack Chi-Ho Ip et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa

(2020) Rebekah L. Rogers et al.   MOLECULAR ECOLOGY

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

(2019) Chang-Ming Bai et al.   GigaScience

The quagga mussel genome and the evolution of freshwater tolerance

(2019) Andrew D Calcino et al.   DNA RESEARCH

Chromosome‐level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

(2019) Zhaoshou Ran et al.   Molecular Ecology Resources

Dispersal mechanisms for zebra mussels: population genetics supports clustered invasions over spread from hub lakes in Minnesota

(2018) Sophie Mallez et al.   BIOLOGICAL INVASIONS

Genome Survey of the Freshwater Mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) Using a Hybrid De Novo Assembly Approach

(2018) Sébastien Renaut et al.   Genome Biology and Evolution

Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla

(2018) Michael J. Metzger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OUP accepted manuscript

(2018)   DNA RESEARCH

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

(2018) Emily L. Wynn et al.   G3-Genes Genomes Genetics

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Next-generation sequencing of Dreissena polymorpha transcriptome sheds light on its mitochondrial DNA

(2017) Marianna Soroka et al.   HYDROBIOLOGIA

25 years of serving the community with ribosomal RNA gene reference databases and tools

(2017) Frank Oliver Glöckner et al.   JOURNAL OF BIOTECHNOLOGY

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

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

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

(2017) Yuli Li et al.   Nature Communications

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei

(2017) Marcela Uliano-Silva et al.   GigaScience

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

(2017) Xiaodong Du et al.   GigaScience

Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs

(2017) Ekaterina Shelest   Frontiers in Genetics

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

(2017) Jin Sun et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

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

Overland transport of recreational boats as a spreading vector of zebra mussel Dreissena polymorpha

(2016) Lukas De Ventura et al.   BIOLOGICAL INVASIONS

Detachment rates of dreissenid mussels after boat hull-mediated overland dispersal

(2016) F. P. L. Collas et al.   HYDROBIOLOGIA

Mussels blow rings: Jet behavior affects local mixing

(2016) Michael Nishizaki et al.   LIMNOLOGY AND OCEANOGRAPHY

Widespread transmission of independent cancer lineages within multiple bivalve species

(2016) Michael J. Metzger et al.   NATURE

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

(2016) Takeshi Takeuchi et al.   Zoological Letters

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams

(2015) Michael J. Metzger et al.   CELL

Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica

(2015) Marta Gómez-Chiarri et al.   FISH & SHELLFISH IMMUNOLOGY

The future of species invasions in the Great Lakes-St. Lawrence River basin

(2015) Katie S. Pagnucco et al.   JOURNAL OF GREAT LAKES RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Cloning and characterization of the shell matrix protein Shematrin in scallop Chlamys farreri

(2014) Ya Lin et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Twenty five years of changes in Dreissena spp. populations in Lake Erie

(2014) Alexander Y. Karatayev et al.   JOURNAL OF GREAT LAKES RESEARCH

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

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

Activation of transcription and retrotransposition of a novel retroelement,Steamer, in neoplastic hemocytes of the molluskMya arenaria

(2014) Gloria Arriagada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Rapid range expansion of the invasive quagga mussel in relation to zebra mussel presence in The Netherlands and Western Europe

(2013) J. Matthews et al.   BIOLOGICAL INVASIONS

Bibliography ofDreissena polymorpha(Zebra Mussels) andDreissena rostriformis Bugensis(QUAGGA Mussels): 1989 to 2011

(2013) Don W. Schloesser et al.   JOURNAL OF SHELLFISH RESEARCH

Rapid evolution of pearl oyster shell matrix proteins with repetitive, low-complexity domains

(2013) C. McDougall et al.   Journal of the Royal Society Interface

Novel Proteins Identified in the Insoluble Byssal Matrix of the Freshwater Zebra Mussel

(2013) Arpita Gantayet et al.   MARINE BIOTECHNOLOGY

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Byssal proteins of the freshwater zebra mussel, Dreissena polymorpha

(2012) Arpita Gantayet et al.   BIOFOULING

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Contrasting Rates of Spread of Two Congeners,Dreissena polymorphaandDreissena Rostriformis Bugensis, at Different Spatial Scales

(2012) Alexander Y. Karatayev et al.   JOURNAL OF SHELLFISH RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

(2012) Steven P. Lund et al.   Statistical Applications in Genetics and Molecular Biology

Biological and ecological mechanisms for overcoming sperm limitation in invasive dreissenid mussels

(2011) Noel P. Quinn et al.   AQUATIC SCIENCES

Low dissolved ions may limit secondary invasion of inland waters by exotic round gobies and dreissenid mussels in North America

(2011) Brad S. Baldwin et al.   BIOLOGICAL INVASIONS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Population genetic history of the dreissenid mussel invasions: expansion patterns across North America

(2010) Joshua E. Brown et al.   BIOLOGICAL INVASIONS

Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA

(2010) Hélène Doucet-Beaupré et al.   BMC EVOLUTIONARY BIOLOGY

What a difference a species makes: a meta–analysis of dreissenid mussel impacts on freshwater ecosystems

(2010) S. N. Higgins et al.   ECOLOGICAL MONOGRAPHS

Differences in growth and survivorship of zebra and quagga mussels: size matters

(2010) Alexander Y. Karatayev et al.   HYDROBIOLOGIA

The good, the bad, and the algae: Perceiving ecosystem services and disservices generated by zebra and quagga mussels

(2010) Karin E. Limburg et al.   JOURNAL OF GREAT LAKES RESEARCH

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): Identification of the “missing” ATPase 8 gene

(2010) Sophie Breton et al.   Marine Genomics

Gene expression profiling during the byssogenesis of zebra mussel (Dreissena polymorpha)

(2010) Wei Xu et al.   MOLECULAR GENETICS AND GENOMICS

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

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

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

Collagen Structure and Stability

(2009) Matthew D. Shoulders et al.   Annual Review of Biochemistry

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Non-indigenous invasive bivalves as ecosystem engineers

(2009) Ronaldo Sousa et al.   BIOLOGICAL INVASIONS

Parallel Evolution of Nacre Building Gene Sets in Molluscs

(2009) Daniel J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY