A transcriptional blueprint for a spiral-cleaving embryo

De Novo assembly and annotation of the freshwater crayfish Astacus astacus transcriptome

(2016) Kathrin Theissinger et al.   Marine Genomics

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

(2016) Michal Levin et al.   NATURE

Current status of annelid phylogeny

(2016) Anne Weigert et al.   ORGANISMS DIVERSITY & EVOLUTION

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)

(2015) Shaadi Mehr et al.   BMC GENOMICS

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

(2015) Christopher E. Laumer et al.   CURRENT BIOLOGY

The Evolution of Annelids Reveals Two Adaptive Routes to the Interstitial Realm

(2015) Torsten Hugo Struck et al.   CURRENT BIOLOGY

Phylogenomic Insights into Animal Evolution

(2015) Maximilian J. Telford et al.   CURRENT BIOLOGY

MED GATA factors promote robust development of the C. elegans endoderm

(2015) Morris F. Maduro et al.   DEVELOPMENTAL BIOLOGY

Reinforcing the Egg-Timer: Recruitment of Novel Lophotrochozoa Homeobox Genes to Early and Late Development in the Pacific Oyster

(2015) Jordi Paps et al.   Genome Biology and Evolution

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

Structure, phylogeny, and expression of the frizzled-related gene family in the lophotrochozoan annelid Platynereis dumerilii

(2015) Benjamin R. Bastin et al.   EvoDevo

Variation in spiralian development: insights from polychaetes

(2015) Elaine C. Seaver   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Spiralian model systems

(2015) Jonathan Q. Henry   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Expression of the wnt gene complement in a spiral-cleaving embryo and trochophore larva

(2015) Margaret M. Pruitt et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

(2014) Miler T. Lee et al.   Annual Review of Cell and Developmental Biology

Animal Phylogeny and Its Evolutionary Implications

(2014) Casey W. Dunn et al.   Annual Review of Ecology Evolution and Systematics

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

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

(2014) Clara Collart et al.   DEVELOPMENT

Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii

(2014) Juliane Zantke et al.   GENETICS

Illuminating the Base of the Annelid Tree Using Transcriptomics

(2014) Anne Weigert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maternal Inheritance of Twist and Analysis of MAPK Activation in Embryos of the Polychaete Annelid Platynereis dumerilii

(2014) Kathrin Pfeifer et al.   PLoS One

The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species

(2014) Patricia Heyn et al.   Cell Reports

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

(2013) Sarita S Paranjpe et al.   BMC GENOMICS

Identification of the zebrafish maternal and paternal transcriptomes

(2013) Steven A. Harvey et al.   DEVELOPMENT

Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis

(2013) S.-J. Park et al.   GENES & DEVELOPMENT

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

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

(2013) Miler T. Lee et al.   NATURE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

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

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo

(2013) Zehra Ali-Murthy et al.   PLoS Genetics

Scaffolding low quality genomes using orthologous protein sequences

(2012) Y. I. Li et al.   BIOINFORMATICS

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

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

(2011) Marten Jäger et al.   BMC GENOMICS

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Profiling by Image Registration Reveals Common Origin of Annelid Mushroom Bodies and Vertebrate Pallium

(2010) Raju Tomer et al.   CELL

Characterizing the Embryonic Transcriptome of the Snail Ilyanassa

(2010) J. D. Lambert et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Differential Localization of mRNAs During Early Development in the Mollusc, Crepidula fornicata

(2010) Jonathan J. Henry et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

A Twist in Time--The Evolution of Spiral Cleavage in the Light of Animal Phylogeny

(2010) A. Hejnol   INTEGRATIVE AND COMPARATIVE BIOLOGY

Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective

(2010) S.-J. Cho et al.   MOLECULAR BIOLOGY AND EVOLUTION

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes

(2009) Jerome HL Hui et al.   BMC BIOLOGY

The evolution of protostome GATA factors: Molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships

(2009) William Q Gillis et al.   BMC EVOLUTIONARY BIOLOGY

The Schistosoma japonicum genome reveals features of host–parasite interplay

(2009)   NATURE

The genome of the blood fluke Schistosoma mansoni

(2009) Matthew Berriman et al.   NATURE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

SpBase: the sea urchin genome database and web site

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