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

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

(2020) Le Qin Choo et al.   BMC GENOMICS

A draft genome sequence of the elusive giant squid, Architeuthis dux

(2020) Rute R da Fonseca et al.   GigaScience

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

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

Giant African snail genomes provide insights into molluscan whole‐genome duplication and aquatic–terrestrial transition

(2020) Conghui Liu et al.   Molecular Ecology Resources

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black and White Abalone Species

(2019) Rick Masonbrink et al.   Genome Biology and Evolution

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

A draft genome assembly of the solar-powered sea slug Elysia chlorotica

(2019) Huimin Cai et al.   Scientific Data

Calcium carbonate unit realignment under acidification: A potential compensatory mechanism in an edible estuarine oyster

(2019) Yuan Meng et al.   MARINE POLLUTION BULLETIN

Signatures of Divergence, Invasiveness, and Terrestrialization Revealed by Four Apple Snail Genomes

(2019) Jin Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Seasonal fluctuations of metal bioaccumulation and reproductive health of local oyster populations in a large contaminated estuary

(2019) Nanyan Weng et al.   ENVIRONMENTAL POLLUTION

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

Greenlip Abalone (Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning

(2019) Natasha A. Botwright et al.   G3-Genes Genomes Genetics

Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)

(2019) Han Ming Gan et al.   Frontiers in Genetics

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

A chromosomal-level genome assembly for the giant African snail Achatina fulica

(2019) Yunhai Guo et al.   GigaScience

A revised spiralian homeobox gene classification incorporating new polychaete transcriptomes reveals a diverse TALE class and a divergent Hox gene

(2018) Thomas Barton-Owen et al.   Genome Biology and Evolution

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

OUP accepted manuscript

(2018)   DNA RESEARCH

An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

(2017) Tilman Schell et al.   Genome Biology and Evolution

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

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

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj 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

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae

(2017) Bo-Hye Nam 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

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

(2016) Roy N. Platt et al.   Genome Biology and Evolution

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Takeshi Takeuchi et al.   Zoological Letters

The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal

(2015) David E.K. Ferrier   Briefings in Functional Genomics

Reinforcing the Egg-Timer: Recruitment of Novel Lophotrochozoa Homeobox Genes to Early and Late Development in the Pacific Oyster

(2015) Jordi Paps et al.   Genome Biology and Evolution

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Antibiotic resistance monitoring in heterotrophic bacteria from anthropogenic-polluted seawater and the intestines of oyster Crassostrea hongkongensis

(2014) Rui Xuan Wang et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

(2014) Daniele Salvi et al.   PLoS One

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

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

Evolution of homeobox genes

(2012) Peter W. H. Holland   Wiley Interdisciplinary Reviews-Developmental Biology

Copper and zinc contamination in oysters: Subcellular distribution and detoxification

(2011) Wen-Xiong Wang et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

(2011) Ying-fu Zhong et al.   EVOLUTION & DEVELOPMENT

Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization

(2011) J. H. L. Hui et al.   MOLECULAR BIOLOGY AND EVOLUTION

A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia

(2010) Maureen E Mazza et al.   EvoDevo

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Urbilaterian Super-Hox cluster

(2008) Thomas Butts et al.   TRENDS IN GENETICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY