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

Life in Changing Fluids: A Critical Appraisal of Swimming Animals Before the Cambrian

(2018) David A Gold   INTEGRATIVE AND COMPARATIVE BIOLOGY

A gonad-expressed opsin mediates light-induced spawning in the jellyfish Clytia

(2018) Gonzalo Quiroga Artigas et al.   eLife

Ctenophore relationships and their placement as the sister group to all other animals

(2017) Nathan V. Whelan et al.   Nature Ecology & Evolution

Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

(2016) Emily S. Bellis et al.   BMC GENOMICS

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

The earliest pelagic jellyfish with rhopalia from Cambrian Chengjiang Lagerstätte

(2016) Jian Han et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

Transcriptome profiling of the dynamic life cycle of the scypohozoan jellyfish Aurelia aurita

(2015) Vera Brekhman et al.   BMC GENOMICS

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

(2015) Selene L Fernandez-Valverde et al.   BMC GENOMICS

Patterns of Wnt signaling in the life cycle ofPodocoryna carneaand its implications for medusae evolution in Hydrozoa (Cnidaria)

(2015) Steven M. Sanders et al.   EVOLUTION & DEVELOPMENT

Interspecific Differential Expression Analysis of RNA-Seq Data Yields Insight into Life Cycle Variation in Hydractiniid Hydrozoans

(2015) Steven M. Sanders et al.   Genome Biology and Evolution

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Structural and Developmental Disparity in the Tentacles of the Moon Jellyfish Aurelia sp.1

(2015) David A. Gold et al.   PLoS One

Gene Expression Data from the Moon Jelly, Aurelia, Provide Insights into the Evolution of the Combinatorial Code Controlling Animal Sense Organ Development

(2015) Nagayasu Nakanishi et al.   PLoS One

Self-repairing symmetry in jellyfish through mechanically driven reorganization

(2015) Michael J. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome ofAiptasia, a sea anemone model for coral symbiosis

(2015) Sebastian Baumgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adoption of conserved developmental genes in development and origin of the medusa body plan

(2015) Johanna E. M. Kraus et al.   EvoDevo

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

(2015) Felipe Zapata et al.   PLoS One

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

Regulation of Polyp-to-Jellyfish Transition in Aurelia aurita

(2014) Björn Fuchs et al.   CURRENT BIOLOGY

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Jellyfish nervous systems

(2013) Takeo Katsuki et al.   CURRENT BIOLOGY

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 Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

The “Eyes absent” (eya) Gene in the Eye-Bearing Hydrozoan Jellyfish Cladonema radiatum: Conservation of the Retinal Determination Network

(2012) DARIA FEDERICA GRAZIUSSI et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

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

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

FoxO is a critical regulator of stem cell maintenance in immortal Hydra

(2012) A.-M. Boehm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of vision

(2012) Walter J. Gehring   Wiley Interdisciplinary Reviews-Developmental Biology

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Evolutionary crossroads in developmental biology: Cnidaria

(2011) U. Technau et al.   DEVELOPMENT

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

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

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

(2011) Eunji Park et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems

(2011) R. H. Condon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals

(2011) D. H. Erwin et al.   SCIENCE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Evolutionary origin of rhopalia: insights from cellular-level analyses of Otx and POU expression patterns in the developing rhopalial nervous system

(2010) Nagayasu Nakanishi et al.   EVOLUTION & DEVELOPMENT

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

What's on the mind of a jellyfish? A review of behavioural observations on Aurelia sp. jellyfish

(2010) David J. Albert   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

FoxO and Stress Responses in the Cnidarian Hydra vulgaris

(2010) Diane Bridge et al.   PLoS One

Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish

(2010) H. Suga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Convergent origins and rapid evolution of spliced leader trans-splicing in Metazoa: Insights from the Ctenophora and Hydrozoa

(2010) R. Derelle et al.   RNA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Development of the rhopalial nervous system in Aurelia sp.1 (Cnidaria, Scyphozoa)

(2009) Nagayasu Nakanishi et al.   DEVELOPMENT GENES AND EVOLUTION

A transcription co-factor integrates cell adhesion and motility with the p53 response

(2009) A. S. Coutts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genesis and Expansion of Metazoan Transcription Factor Gene Classes

(2008) Claire Larroux et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

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

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Evolution and Functional Diversity of Jellyfish Opsins

(2007) Hiroshi Suga et al.   CURRENT BIOLOGY