The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

(2018) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

(2018) Chiara Sinigaglia et al.   DEVELOPMENTAL BIOLOGY

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

(2018) Gonzalo Quiroga Artigas et al.   eLife

High doses of CRISPR/Cas9 ribonucleoprotein efficiently induce gene knockout with low mosaicism in the hydrozoan Clytia hemisphaerica through microhomology-mediated deletion

(2018) Tsuyoshi Momose et al.   Scientific Reports

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

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

Diversification of C. elegans Motor Neuron Identity via Selective Effector Gene Repression

(2017) Sze Yen Kerk et al.   NEURON

Gut-like ectodermal tissue in a sea anemone challenges germ layer homology

(2017) Patrick R. H. Steinmetz et al.   Nature Ecology & Evolution

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

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

Hydrozoan insights in animal development and evolution

(2016) Lucas Leclère et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals

(2016) Hidenori Nishihara et al.   Genome Biology and Evolution

The cellular and molecular basis of cnidarian neurogenesis

(2016) Fabian Rentzsch et al.   Wiley Interdisciplinary Reviews-Developmental Biology

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

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani 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

The nerve ring in cnidarians: its presence and structure in hydrozoan medusae

(2015) Osamu Koizumi et al.   ZOOLOGY

Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints

(2015) Grigory Genikhovich et al.   Cell Reports

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

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

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

(2015) Felipe Zapata et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Larval body patterning and apical organs are conserved in animal evolution

(2014) Heather Marlow et al.   BMC BIOLOGY

RGM Regulates BMP-Mediated Secondary Axis Formation in the Sea Anemone Nematostella vectensis

(2014) Lucas Leclère et al.   Cell Reports

An endogenous green fluorescent protein-photoprotein pair in Clytia hemisphaerica eggs shows co-targeting to mitochondria and efficient bioluminescence energy transfer

(2014) C. Fourrage et al.   Open Biology

Differential Responses to Wnt and PCP Disruption Predict Expression and Developmental Function of Conserved and Novel Genes in a Cnidarian

(2014) Pascal Lapébie et al.   PLoS Genetics

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Evolution of bilaterian central nervous systems: a single origin?

(2013) Linda Z Holland et al.   EvoDevo

The Bilaterian Head Patterning Gene six3/6 Controls Aboral Domain Development in a Cnidarian

(2013) Chiara Sinigaglia et al.   PLOS BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

(2012) M. Irimia et al.   GENOME RESEARCH

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

(2012) Cole Trapnell et al.   Nature Protocols

A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling

(2012) Eric Röttinger et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians

(2011) Ehsan Kayal et al.   Genome Biology and Evolution

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

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

(2011) Chuya Shinzato et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Multiple Sox genes are expressed in stem cells or in differentiating neuro-sensory cells in the hydrozoan Clytia hemisphaerica

(2011) Muriel Jager et al.   EvoDevo

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

Stem cell-specific activation of an ancestral myc protooncogene with conserved basic functions in the early metazoan Hydra

(2010) M. Hartl 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

Clytia hemisphaerica: a jellyfish cousin joins the laboratory

(2010) Evelyn Houliston et al.   TRENDS IN GENETICS

A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia

(2010) Maureen E Mazza et al.   EvoDevo

Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters

(2009) Sebastian M. Shimeld et al.   GENOMICS

Are Hox Genes Ancestrally Involved in Axial Patterning? Evidence from the Hydrozoan Clytia hemisphaerica (Cnidaria)

(2009) Roxane Chiori et al.   PLoS One

BMPs and Chordin regulate patterning of the directive axis in a sea anemone

(2009) M. Saina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Early evolution of symmetry and polarity in metazoan body plans

(2008) Michaël Manuel   COMPTES RENDUS BIOLOGIES