Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

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

(2021) Hao Song et al.   BMC BIOLOGY

High spatial resolution mapping of the mucosal proteome of the gills of Crassostrea virginica: implication in particle processing

(2021) Emmanuelle Pales Espinosa et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Erection of a New Genus and Species for the Pathogen of Hard Clams ‘Quahog Parasite Unknown’ (QPX): Mucochytrium quahogii gen. nov., sp. nov.

(2021) Sabrina Geraci-Yee et al.   PROTIST

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

(2021) Carolina Peñaloza et al.   GigaScience

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

(2021) Nadège Guiglielmoni et al.   BMC BIOINFORMATICS

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

The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus

(2020) Ronghua Li et al.   Frontiers in Genetics

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

(2020) Min Wei et al.   iScience

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

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

Computer vision for pattern detection in chromosome contact maps

(2020) Cyril Matthey-Doret et al.   Nature Communications

Transcriptome analysis of shell color-related genes in the hard clam Mercenaria mercenaria

(2019) Zhi Hu et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

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

Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba

(2019) Nicholas B. Stewart et al.   PLoS Genetics

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

(2019) Marco Gerdol et al.   Marine Drugs

A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe

(2019) Marisa A Yonemitsu et al.   eLife

Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies

(2019) Binh Thanh Thai et al.   Frontiers in Genetics

Effects of Thermal Stress and Ocean Acidification on the Expression of the Retrotransposon Steamer in the Softshell Mya arenaria

(2019) Michael P. Lesser et al.   JOURNAL OF SHELLFISH RESEARCH

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Identification of clam plasma proteins that bind its pathogen Quahog Parasite Unknown

(2018) Rachel Hartman et al.   FISH & SHELLFISH IMMUNOLOGY

Reverse genetics demonstrate the role of mucosal C-type lectins in food particle selection in the oyster Crassostrea virginica

(2018) Emmanuelle Pales Espinosa et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics

(2018) Camille Thomas-Bulle et al.   BMC GENOMICS

Hemocyanin genes as indicators of habitat shifts in Panpulmonata?

(2018) Gabriela Giannina Schäfer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The TNF Family of Ligands and Receptors: Communication Modules in the Immune System and Beyond

(2018) Catherine Dostert et al.   PHYSIOLOGICAL REVIEWS

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

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

Detection of invasive and cryptic species in marine mussels (Bivalvia, Mytilidae): A chromosomal perspective

(2017) Daniel García-Souto et al.   JOURNAL FOR NATURE CONSERVATION

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

(2017) Marcela Uliano-Silva et al.   GigaScience

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

Alterations of the immune transcriptome in resistant and susceptible hard clams ( Mercenaria mercenaria ) in response to Quahog Parasite Unknown (QPX) and temperature

(2016) Kailai Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Widespread transmission of independent cancer lineages within multiple bivalve species

(2016) Michael J. Metzger et al.   NATURE

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

(2015) Michael J. Metzger et al.   CELL

The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia

(2015) Marco Gerdol et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Repertoire and evolution of TNF superfamily in Crassostrea gigas: Implications for expansion and diversification of this superfamily in Mollusca

(2015) Dahai Gao et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to Brown Ring Disease

(2014) Bassem Allam et al.   FISH & SHELLFISH IMMUNOLOGY

The impact of chromosomal rearrangements on regulation of gene expression

(2014) L. Harewood et al.   HUMAN MOLECULAR GENETICS

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward 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

LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

(2013) Mathieu Piednoël et al.   PLoS One

Correction: Three-Dimensional Phase-Sensitive Inversion-Recovery Turbo FLASH Sequence for the Assessment of Left Ventricular Myocardial Scar in Swine

(2013) Xiuyu Chen et al.   PLoS One

Identification of Relevant Cancer Related-Genes in the Flat Oyster Ostrea edulis Affected by Disseminated Neoplasia

(2012) Laura Martín-Gómez et al.   MARINE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

BEL/Pao retrotransposons in metazoan genomes

(2011) Nicole de la Chaux et al.   BMC EVOLUTIONARY BIOLOGY

Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis

(2011) Paola Venier et al.   BMC GENOMICS

The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: A widespread and diverse family of immune-related molecules

(2011) Marco Gerdol et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

DNA Transposons: Nature and Applications in Genomics

(2010) Martin Munoz-Lopez et al.   CURRENT GENOMICS

The C1q domain containing proteins: Where do they come from and what do they do?

(2010) Tristan M. Carland et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Induction of transposase and polyprotein RNA levels in disseminated neoplastic hemocytes of soft-shell clams: Mya arenaria

(2010) Ahmed Siah et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

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

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Karyotypes of Diploid and Triploid Mercenaria mercenaria (Linnaeus)

(2008) Lin Zhi-Hua et al.   JOURNAL OF SHELLFISH RESEARCH

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS