The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties

Genome and transcriptome mechanisms driving cephalopod evolution

(2022) Caroline B. Albertin et al.   Nature Communications

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization

(2022) Hannah Schmidbaur et al.   Nature Communications

Cell type diversity in a developing octopus brain

(2022) Ruth Styfhals et al.   Nature Communications

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 genome of Nautilus pompilius illuminates eye evolution and biomineralization

(2021) Yang Zhang et al.   Nature Ecology & Evolution

Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”

(2021) Zekun Huang et al.   Molecular Ecology Resources

Comparative brain structure and visual processing in octopus from different habitats

(2021) Wen-Sung Chung et al.   CURRENT BIOLOGY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo genome assembly of limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae), the first reference genome of a deep-sea gastropod endemic to cold seeps

(2020) Ruoyu Liu et al.   Genome Biology and Evolution

The Scaly-foot Snail genome and implications for the origins of biomineralised armour

(2020) Jin Sun et al.   Nature Communications

The gene-rich genome of the scallop Pecten maximus

(2020) Nathan J Kenny et al.   GigaScience

Chromosome‐level genome assembly of the East Asian common octopus ( Octopus sinensis ) using PacBio sequencing and Hi‐C technology

(2020) Fenghui Li et al.   Molecular Ecology Resources

Use of Peripheral Sensory Information for Central Nervous Control of Arm Movement by Octopus vulgaris

(2020) Tamar Gutnick et al.   CURRENT BIOLOGY

The iron-responsive genome of the chiton Acanthopleura Granulata

(2020) Rebecca M Varney 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

Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

(2019) Elena A. Ritschard et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The survey and reference assisted assembly of the Octopus vulgaris genome

(2019) Ilaria Zarrella et al.   Scientific Data

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

(2019) Chang-Ming Bai et al.   GigaScience

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

(2019) Dong Zhang et al.   Molecular Ecology Resources

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

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Cephalopod Brains: An Overview of Current Knowledge to Facilitate Comparison With Vertebrates

(2018) Shuichi Shigeno et al.   Frontiers in Physiology

Draft genome of the Peruvian scallop Argopecten purpuratus

(2018) Chao Li et al.   GigaScience

OUP accepted manuscript

(2018)   DNA RESEARCH

A Brain Atlas of the Long Arm Octopus, Octopus minor

(2018) Seung-Hyun Jung et al.   Experimental Neurobiology

The genome of the jellyfish Aurelia and the evolution of animal complexity

(2018) David A. Gold et al.   Nature Ecology & Evolution

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Cadherin genes and evolutionary novelties in the octopus

(2017) Z. Yan Wang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

(2017) Yi-Jyun Luo et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

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

Evolution of highly diverse forms of behavior in molluscs

(2016) Binyamin Hochner et al.   CURRENT BIOLOGY

Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues

(2016) Jean-René Arseneau et al.   Molecular Ecology Resources

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast

(2016) Xiaoshu Chen et al.   Cell Systems

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Nautilus: biology, systematics, and paleobiology as viewed from 2015

(2016) Peter Ward et al.   Swiss Journal of Palaeontology

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

(2015) Caroline B. Albertin et al.   NATURE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Molecular cytogenetic study in Octopus (Amphioctopus) areolatus from Japan

(2014) Kenta Adachi et al.   FISHERIES SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

(2014) Bruce J. Walker 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

Cephalopod Cognition in an Evolutionary Context: Implications for Ethology

(2013) Joseph J. Vitti   Biosemiotics

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

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

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

Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation

(2011) Masa-aki Yoshida et al.   GENE

Comparative Analysis of Chromosome Counts Infers Three Paleopolyploidies in the Mollusca

(2011) Nathaniel M. Hallinan et al.   Genome Biology and Evolution

Combinatorial homophilic interaction between  -protocadherin multimers greatly expands the molecular diversity of cell adhesion

(2010) D. Schreiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY