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

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

(2020) Kang Du et al.   Nature Ecology & Evolution

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

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

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

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

The survey and reference assisted assembly of the Octopus vulgaris genome

(2019) Ilaria Zarrella et al.   Scientific Data

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties

(2019) Caroline B. Albertin et al.   Annual Review of Animal Biosciences

Inferring synteny between genome assemblies: a systematic evaluation

(2018) Dang Liu et al.   BMC BIOINFORMATICS

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation

(2018) Conghui Liu et al.   GigaScience

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

(2017) Coen M. Adema et al.   Nature Communications

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

(2017) Yuli Li et al.   Nature Communications

Scallop genome provides insights into evolution of bilaterian karyotype and development

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

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

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

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

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Eye-independent, light-activated chromatophore expansion (LACE) and expression of phototransduction genes in the skin of Octopus bimaculoides

(2015) M. D. Ramirez et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The genetic structure ofNautilus pompiliuspopulations surrounding Australia and the Philippines

(2015) Rachel C. Williams et al.   MOLECULAR ECOLOGY

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

(2015) Caroline B. Albertin et al.   NATURE

The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

(2015) Yi-Jyun Luo et al.   Nature Communications

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Population Assessments of Nautilus sp. in the Philippines, Australia, Fiji, and American Samoa Using Baited Remote Underwater Video Systems

(2014) Gregory J. Barord et al.   PLoS One

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

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

An eye on eye development

(2013) Rebecca Sinn et al.   MECHANISMS OF DEVELOPMENT

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Transcriptome Analysis of Nautilus and Pygmy Squid Developing Eye Provides Insights in Lens and Eye Evolution

(2013) Konstantinos Sousounis et al.   PLoS One

Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus

(2013) Atsushi Ogura et al.   Scientific Reports

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules

(2011) Björn Kröger et al.   BIOESSAYS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics

(2011) Anthony Levasseur et al.   Biology Direct

Assessing the impact of international trade on chambered nautilus

(2011) Patricia De Angelis   GEOBIOS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Nautilus at Risk – Estimating Population Size and Demography of Nautilus pompilius

(2011) Andrew Dunstan et al.   PLoS One

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Transposable element insertions have strongly affected human evolution

(2010) R. J. Britten   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY

The role of Pax genes in eye evolution

(2007) Zbynek Kozmik   BRAIN RESEARCH BULLETIN