The sea cucumber genome provides insights into morphological evolution and visceral regeneration

Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants

(2017) Jihoon Jo et al.   GigaScience

Evolution of a pentameral body plan was not linked to translocation of anterior Hox genes: the echinoderm HOX cluster revisited

(2016) Maria Byrne et al.   EVOLUTION & DEVELOPMENT

Gut Regeneration in Holothurians: A Snapshot of Recent Developments

(2016) V. S. Mashanov et al.   BIOLOGICAL BULLETIN

Angiopoietin-1 enhances skeletal muscle regeneration in mice

(2015) Mahroo Mofarrahi et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

(2015) Yaping Wang et al.   NATURE GENETICS

How was the notochord born?

(2015) Nori Satoh et al.   EVOLUTION & DEVELOPMENT

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Transcriptomic changes during regeneration of the central nervous system in an echinoderm

(2014) Vladimir S Mashanov et al.   BMC GENOMICS

Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network

(2014) Zhongling Sun et al.   GENE EXPRESSION PATTERNS

On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates

(2014) Noriyuki Satoh et al.   GENESIS

Genomic organization of Hox and ParaHox clusters in the echinoderm,Acanthaster planci

(2014) Kenneth W. Baughman et al.   GENESIS

Specification to Biomineralization: Following a Single Cell Type as It Constructs a Skeleton

(2014) D. C. Lyons et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The role of thePax1/9gene in the early development of amphioxus pharyngeal gill slits

(2014) Xin Liu et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The cost of being valuable: predictors of extinction risk in marine invertebrates exploited as luxury seafood

(2014) S. W. Purcell et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomic analysis of echinoderm class relationships supports Asterozoa

(2014) M. J. Telford et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MSMBvariation and prostate cancer risk: Clues towards a possible fungal etiology

(2014) Siobhan Sutcliffe et al.   PROSTATE

The Fox/Forkhead transcription factor family of the hemichordate Saccoglossus kowalevskii

(2014) Jens H Fritzenwanker et al.   EvoDevo

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Radial glial cells play a key role in echinoderm neural regeneration

(2013) Vladimir S Mashanov et al.   BMC BIOLOGY

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

Hemichordata (Pterobranchia, Enteropneusta) and the fossil record

(2013) Jörg Maletz   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas

(2013) Lina Sun et al.   PLoS One

Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’

(2013) Thomas C. Mathers et al.   PeerJ

Extracellular matrix protein tenascin-C is required in the bone marrow microenvironment primed for hematopoietic regeneration

(2012) A. Nakamura-Ishizu et al.   BLOOD

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms

(2012) Brenna S McCauley et al.   EvoDevo

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphniaand their coevolution with chaoborid predators

(2011) Alexey A Kotov et al.   BMC EVOLUTIONARY BIOLOGY

Sea cucumber fisheries: global analysis of stocks, management measures and drivers of overfishing

(2011) Steven W Purcell et al.   FISH AND FISHERIES

Hepassocin regulates cell proliferation of the human hepatic cells L02 and hepatocarcinoma cells through different mechanisms

(2011) Meng-Meng Cao et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Expression of Hox4 during development of the pentamerous juvenile sea star, Parvulastra exigua

(2010) Paula Cisternas et al.   DEVELOPMENT GENES AND EVOLUTION

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Gene expression profiling of intestinal regeneration in the sea cucumber

(2009) Pablo A Ortiz-Pineda et al.   BMC GENOMICS

A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos

(2009) Brenna S. McCauley et al.   DEVELOPMENTAL BIOLOGY

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fossil steroids record the appearance of Demospongiae during the Cryogenian period

(2009) Gordon D. Love et al.   NATURE

FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis and regulate gastrulation during sea urchin development

(2008) E. Rottinger et al.   DEVELOPMENT

Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis

(2008) C. A. Ettensohn   DEVELOPMENT

Longevity and lack of senescence in the red sea urchin Strongylocentrotus franciscanus

(2008) Thomas A. Ebert   EXPERIMENTAL GERONTOLOGY

Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

(2008) B. J Swalla et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES