Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

Hyoliths are Palaeozoic lophophorates

(2017) Joseph Moysiuk et al.   NATURE

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

(2017) Sabrina M. Schiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans

(2017) Andreas C. Fröbius et al.   Nature Communications

The nervous system of the lophophore in the ctenostome Amathia gracilis provides insight into the morphology of ancestral ectoprocts and the monophyly of the lophophorates

(2016) Elena N. Temereva et al.   BMC EVOLUTIONARY BIOLOGY

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

(2016) Takeshi Takeuchi et al.   Zoological Letters

Repurposed Transcriptomic Data Facilitate Discovery of Innate Immunity Toll-Like Receptor (TLR) Genes Across Lophotrochozoa

(2016) Kenneth M. Halanych et al.   BIOLOGICAL BULLETIN

Hox genes pattern the anterior-posterior axis of the juvenile but not the larva in a maximally indirect developing invertebrate, Micrura alaskensis (Nemertea)

(2015) Laurel S Hiebert et al.   BMC BIOLOGY

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

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

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

(2015) Bernhard Egger et al.   CURRENT BIOLOGY

The Magellania venosa Biomineralizing Proteome: A Window into Brachiopod Shell Evolution

(2015) Daniel J. Jackson et al.   Genome Biology and Evolution

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

The deuterostome context of chordate origins

(2015) Christopher J. Lowe et al.   NATURE

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

Stonefish toxin defines an ancient branch of the perforin-like superfamily

(2015) Andrew M. Ellisdon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modern Data on the Innervation of the Lophophore in Lingula anatina (Brachiopoda) Support the Monophyly of the Lophophorates

(2015) Elena N. Temereva et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

Nemertean Toxin Genes Revealed through Transcriptome Sequencing

(2014) Nathan V. Whelan et al.   Genome Biology and Evolution

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Illuminating the Base of the Annelid Tree Using Transcriptomics

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

Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue

(2014) David Jandzik et al.   NATURE

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

(2013) Maximilian P Nesnidal et al.   BMC EVOLUTIONARY BIOLOGY

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

(2013) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos 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 Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

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

Ancient deuterostome origins of vertebrate brain signalling centres

(2012) Ariel M. Pani et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The complex world of WNT receptor signalling

(2012) Christof Niehrs   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system

(2012) Scott Santagata et al.   EvoDevo

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Wnt gene loss in flatworms

(2011) Nick Riddiford et al.   DEVELOPMENT GENES AND EVOLUTION

The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals

(2011) D. H. Erwin et al.   SCIENCE

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida)

(2010) Bernhard Hausdorf et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Wnt Signaling and the Polarity of the Primary Body Axis

(2009) Christian P. Petersen et al.   CELL

Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha

(2009) J. Paps et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Nodal signalling is involved in left–right asymmetry in snails

(2008) Cristina Grande et al.   NATURE

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta

(2008) Yoichi Sekita et al.   NATURE GENETICS

Genomic Organization and Expression Demonstrate Spatial and Temporal Hox Gene Colinearity in the Lophotrochozoan Capitella sp. I

(2008) Andreas C. Fröbius et al.   PLoS One

Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

(2008) M. Helmkampf et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES