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

Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

(2016) Bharat Bhusan Patnaik et al.   PLoS One

Transcriptome Analysis Revealed Changes of Multiple Genes Involved in Haliotis discus hannai Innate Immunity during Vibrio parahemolyticus Infection

(2016) Bo-Hye Nam et al.   PLoS One

Transcriptome Analysis of the Sydney Rock Oyster, Saccostrea glomerata: Insights into Molluscan Immunity

(2016) Nicole G. Ertl et al.   PLoS One

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

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

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

Transcriptome Analysis of Shell Color-Related Genes in the Clam Meretrix meretrix

(2015) Xin Yue et al.   MARINE BIOTECHNOLOGY

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Type material in the NCBI Taxonomy Database

(2014) Scott Federhen   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

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

A novel C1q-domain-containing (C1qDC) protein from Mytilus coruscus with the transcriptional analysis against marine pathogens and heavy metals

(2013) Hui-Hui Liu et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Effects of benzo(a)pyrene on differentially expressed genes and haemocyte parameters of the clam Venerupis philippinarum

(2013) Na Liu et al.   ECOTOXICOLOGY

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

(2012) T. Takeuchi et al.   DNA RESEARCH

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis

(2012) Eva E. R. Philipp et al.   PLoS One

Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

(2012) Rebeca Moreira et al.   PLoS One

A C1q Domain Containing Protein from Scallop Chlamys farreri Serving as Pattern Recognition Receptor with Heat-Aggregated IgG Binding Activity

(2012) Leilei Wang et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

(2011) Massimo Milan 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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Isolation and identification of Perkinsus olseni from feces and marine sediment using immunological and molecular techniques

(2010) Kyung-Il Park et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Diversity and pathogenecity of Vibrio species in cultured bivalve molluscs

(2010) Roxana Beaz-Hidalgo et al.   Environmental Microbiology Reports

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Virus-like particles associated with brown muscle disease in Manila clam,Ruditapes philippinarum, in Arcachon Bay (France)

(2009) C Dang et al.   JOURNAL OF FISH DISEASES

Noble tandem-repeat galectin of Manila clam Ruditapes philippinarum is induced upon infection with the protozoan parasite Perkinsus olseni

(2008) Jin Young Kim et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY