PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

(2018) Kaia Achim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord ofPlatynereis dumerilii

(2017) Hernando Martínez Vergara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell lineage and cell cycling analyses of the 4d micromere using live imaging in the marine annelid Platynereis dumerilii

(2017) B Duygu Özpolat et al.   eLife

A transcriptional blueprint for a spiral-cleaving embryo

(2016) Hsien-Chao Chou et al.   BMC GENOMICS

Towards a systems-level understanding of development in the marine annelid Platynereis dumerilii

(2016) Elizabeth A Williams et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2016) Michal Levin et al.   NATURE

Formation of body appendages during caudal regeneration in Platynereis dumerilii: adaptation of conserved molecular toolsets

(2016) Jan Grimmel et al.   EvoDevo

The evolutionary origin of bilaterian smooth and striated myocytes

(2016) Thibaut Brunet et al.   eLife

NxTrim: optimized trimming of Illumina mate pair reads: Table 1.

(2015) Jared O’Connell et al.   BIOINFORMATICS

Comparative Toxicity of Chlorinated Saline and Freshwater Wastewater Effluents to Marine Organisms

(2015) Mengting Yang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

(2015) Sheila A. Kitchen et al.   G3-Genes Genomes Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Melatonin Signaling Controls Circadian Swimming Behavior in Marine Zooplankton

(2014) Maria Antonietta Tosches et al.   CELL

Platynereis dumerilii

(2014) Florian Raible et al.   CURRENT BIOLOGY

Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode

(2014) Jianbin Wang et al.   CURRENT BIOLOGY

TALENs Mediate Efficient and Heritable Mutation of Endogenous Genes in the Marine Annelid Platynereis dumerilii

(2014) Stephanie Bannister et al.   GENETICS

Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii

(2014) Juliane Zantke et al.   GENETICS

Tools for Gene-Regulatory Analyses in the Marine Annelid Platynereis dumerilii

(2014) Benjamin Backfisch et al.   PLoS One

Development of the annelid axochord: Insights into notochord evolution

(2014) A. Lauri et al.   SCIENCE

Neuronal connectome of a sensory-motor circuit for visual navigation

(2014) Nadine Randel et al.   eLife

Characterization of differential transcript abundance through time during Nematostella vectensis development

(2013) Rebecca Helm et al.   BMC GENOMICS

The neuropeptide complement of the marine annelid Platynereis dumerilii

(2013) Markus Conzelmann et al.   BMC GENOMICS

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Identification of the zebrafish maternal and paternal transcriptomes

(2013) Steven A. Harvey et al.   DEVELOPMENT

Posterior elongation in the annelid Platynereis dumerilii involves stem cells molecularly related to primordial germ cells

(2013) Eve Gazave et al.   DEVELOPMENTAL BIOLOGY

Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus

(2013) Qiang Tu et al.   DEVELOPMENTAL BIOLOGY

Mesoteloblast-Like Mesodermal Stem Cells in the Polychaete AnnelidPlatynereis dumerilii(Nereididae)

(2013) Antje H.L. Fischer et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL 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

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Conditional and Specific Cell Ablation in the Marine Annelid Platynereis dumerilii

(2013) Vinoth Babu Veedin-Rajan et al.   PLoS One

Circadian and Circalunar Clock Interactions in a Marine Annelid

(2013) Juliane Zantke et al.   Cell Reports

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems

(2013) Sarah Tulin et al.   EvoDevo

Activation of Hox genes during caudal regeneration of the polychaete annelid Platynereis dumerilii

(2012) Kathrin Pfeifer et al.   DEVELOPMENT GENES AND EVOLUTION

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

(2012) M. H. Tan et al.   GENOME RESEARCH

Algorithm for Predicting Functionally Equivalent Proteins from BLAST and HMMER Searches

(2012) Dong Su Yu   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Hidden in the crowd: primordial germ cells and somatic stem cells in the mesodermal posterior growth zone of the polychaete Platynereis dumerillii are two distinct cell populations

(2012) Nicole Rebscher et al.   EvoDevo

The normal development of Platynereis dumerilii (Nereididae, Annelida)

(2011) Antje HL Fischer et al.   Frontiers in Zoology

Neuropeptides regulate swimming depth of Platynereis larvae

(2011) M. Conzelmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hedgehog Signaling Regulates Segment Formation in the Annelid Platynereis

(2010) N. Dray et al.   SCIENCE

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

KEGG Atlas mapping for global analysis of metabolic pathways

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

SpBase: the sea urchin genome database and web site

(2008) R. A. Cameron et al.   NUCLEIC ACIDS RESEARCH