Nanopore Sequencing and De Novo Assembly of a Black-Shelled Pacific Oyster (Crassostrea gigas) Genome

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

(2019) Huimin Cai et al.   Scientific Data

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

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

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

N 6 -Methyladenine DNA Modification in the Human Genome

(2018) Chuan-Le Xiao et al.   MOLECULAR CELL

OUP accepted manuscript

(2018)   DNA RESEARCH

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

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

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

Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

(2018) Li Gong et al.   Molecular Ecology Resources

Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters

(2018) Julien de Lorgeril et al.   Nature Communications

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Xiaodong Du et al.   GigaScience

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

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

Molecular Basis for Adaptation of Oysters to Stressful Marine Intertidal Environments

(2016) Guofan Zhang et al.   Annual Review of Animal Biosciences

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Constraints on the timescale of animal evolutionary history

(2015) MJ Benton et al.   PALAEONTOLOGIA ELECTRONICA

Extraction and Identification of the Pigment in the Adductor Muscle Scar of Pacific Oyster Crassostrea gigas

(2015) Shixin Hao et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana

(2012) Zoé Joly-Lopez et al.   PLoS Genetics

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

(2011) Michael W. Beck et al.   BIOSCIENCE

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

(2011) Jianfeng Ren et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Towards a molecular phylogeny of Mollusks: Bivalves’ early evolution as revealed by mitochondrial genes

(2010) Federico Plazzi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Massive settlements of the Pacific oyster, Crassostrea gigas, in Scandinavia

(2009) Anna-Lisa Wrange et al.   BIOLOGICAL INVASIONS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY