The genome of Nautilus pompilius illuminates eye evolution and biomineralization

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

Antarctic blackfin icefish genome reveals adaptations to extreme environments

(2019) Bo-Mi Kim et al.   Nature Ecology & Evolution

Integrated records of environmental change and evolution challenge the Cambrian Explosion

(2019) Rachel Wood et al.   Nature Ecology & Evolution

The survey and reference assisted assembly of the Octopus vulgaris genome

(2019) Ilaria Zarrella et al.   Scientific Data

Cephalopod cognition

(2019) Alexandra K. Schnell et al.   CURRENT BIOLOGY

Crystal growth kinetics as an architectural constraint on the evolution of molluscan shells

(2019) Vanessa Schoeppler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods

(2019) Elena A. Ritschard et al.   BIOESSAYS

Dorsoventral decoupling of Hox gene expression underpins the diversification of molluscs

(2019) Pin Huan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation

(2018) Leon Hilgers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Elucidating the control and development of skin patterning in cuttlefish

(2018) Sam Reiter et al.   NATURE

The Golden Section and beauty in nature: The perfection of symmetry and the charm of asymmetry

(2018) Ulrich Lüttge et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod laying aerial eggs

(2017) Huawei Mu et al.   Journal of Proteomics

Scallop genome provides insights into evolution of bilaterian karyotype and development

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

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258Klebsiella pneumoniaeStrains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones

(2016) María Soledad Ramirez et al.   Genome Biology and Evolution

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

The seahorse genome and the evolution of its specialized morphology

(2016) Qiang Lin et al.   NATURE

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

A revisited phylogeography ofNautilus pompilius

(2016) Lauren E. Vandepas et al.   Ecology and Evolution

Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

(2016) Chengxi Ye et al.   PeerJ

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

DNA Sequence-Specific Binding of CENP-B Enhances the Fidelity of Human Centromere Function

(2015) Daniele Fachinetti et al.   DEVELOPMENTAL CELL

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems

(2015) M. A. Yoshida et al.   INTEGRATIVE AND COMPARATIVE 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

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Massive expansion and functional divergence of innate immune genes in a protostome

(2015) Linlin Zhang et al.   Scientific Reports

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

Long-term cycles in the carbon reservoir of the Quaternary ocean: a perspective from the South China Sea

(2014) PinXian Wang et al.   National Science Review

Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

(2013) Iona M. MacLeod et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Atsushi Ogura et al.   Scientific Reports

IFN-Inducible GTPases in Host Cell Defense

(2012) Bae-Hoon Kim et al.   Cell Host & Microbe

The shell-forming proteome ofLottia giganteareveals both deep conservations and lineage-specific novelties

(2012) Benjamin Marie et al.   FEBS Journal

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

Delayed build-up of Arctic ice sheets during 400,000-year minima in insolation variability

(2012) Qingzhen Hao et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

Evolution of Ocean Temperature and Ice Volume Through the Mid-Pleistocene Climate Transition

(2012) H. Elderfield et al.   SCIENCE

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

(2011) Björn Kröger et al.   BIOESSAYS

Nautilin-63, a novel acidic glycoprotein from the shell nacre of Nautilus macromphalus

(2011) Benjamin Marie et al.   FEBS Journal

Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia

(2011) Michael S. Y. Lee et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Shell microstructure of the early bivalve Pojetaia and the independent origin of nacre within the mollusca

(2011) MICHAEL J. VENDRASCO et al.   PALAEONTOLOGY

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

(2009) Zia Khan et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Evolution of Flexible Behavioral Repertoires in Cephalopod Molluscs

(2009) Frank W. Grasso et al.   BRAIN BEHAVIOR AND EVOLUTION

Phototransduction Motifs and Variations

(2009) King-Wai Yau et al.   CELL

Purified RPE65 shows isomerohydrolase activity after reassociation with a phospholipid membrane

(2009) Olga Nikolaeva et al.   FEBS Journal

Memory of visual and topographical features suggests spatial learning in nautilus (Nautilus pompilius L.).

(2009) Robyn J. Crook et al.   JOURNAL OF COMPARATIVE PSYCHOLOGY

Parallel Evolution of Nacre Building Gene Sets in Molluscs

(2009) Daniel J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of eyes and visually guided behaviour

(2009) D.-E. Nilsson   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Eye Evolution: The Blurry Beginning

(2008) Dan-E. Nilsson et al.   CURRENT BIOLOGY

A biphasic memory curve in the chambered nautilus, Nautilus pompilius L. (Cephalopoda: Nautiloidea)

(2008) R. Crook et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS