Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?

(2012) J. Paps et al.   Briefings in Functional Genomics

B2G-FAR, a species-centered GO annotation repository

(2011) Stefan Götz et al.   BIOINFORMATICS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

(2011) Carmel McDougall et al.   BMC EVOLUTIONARY BIOLOGY

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

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

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

The normal development of Platynereis dumerilii (Nereididae, Annelida)

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

Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization

(2011) J. H. L. Hui et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

(2010) Xiao-Wei Wang et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

(2010) Christopher J. Winchell et al.   DEVELOPMENT GENES AND EVOLUTION

Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster

(2010) Sebastian M. Shimeld et al.   DEVELOPMENTAL BIOLOGY

The homeodomain protein hmbx-1 maintains asymmetric gene expression in adult C. elegans olfactory neurons

(2010) B. J. Lesch et al.   GENES & DEVELOPMENT

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals

(2009) Tokiharu Takahashi et al.   BMC EVOLUTIONARY BIOLOGY

Paxβ: a novel family of lophotrochozoan Pax genes

(2009) Matthew Schmerer et al.   EVOLUTION & DEVELOPMENT

Orthologs of key vertebrate neural genes are expressed during neurogenesis in the annelidPlatynereis dumerilii

(2009) Pierre Kerner et al.   EVOLUTION & DEVELOPMENT

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

(2009) Sebastian M. Shimeld et al.   GENOMICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae

(2008) Naohito Takatori et al.   DEVELOPMENT GENES AND EVOLUTION

HomeoDB: a database of homeobox gene diversity

(2008) Ying-Fu Zhong et al.   EVOLUTION & DEVELOPMENT

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The transcription factorsHeBlimpandHeT-brainof an indirectly developing polychaete suggest ancestral endodermal, gastrulation, and sensory cell-type specification roles

(2008) Cesar Arenas-Mena   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

High-throughput functional annotation and data mining with the Blast2GO suite

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

The evolution of nervous system centralization

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