Comparative genomics and the nature of placozoan species

Placozoa

(2018) Bernd Schierwater et al.   CURRENT BIOLOGY

Neuropeptidergic integration of behavior inTrichoplax adhaerens, an animal without synapses

(2017) Adriano Senatore et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Ctenophore relationships and their placement as the sister group to all other animals

(2017) Nathan V. Whelan et al.   Nature Ecology & Evolution

Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon

(2017) Hans-Jürgen Osigus et al.   PLoS One

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex

(2016) Nicolas Debortoli et al.   CURRENT BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

The invisible dimension of fungal diversity

(2016) David Hibbett   SCIENCE

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

(2016) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

Genomics and the animal tree of life: conflicts and future prospects

(2016) Gonzalo Giribet   ZOOLOGICA SCRIPTA

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Bioinformatic prediction of Trichoplax adhaerens regulatory peptides

(2015) Mikhail Nikitin   GENERAL AND COMPARATIVE ENDOCRINOLOGY

The Early MetazoanTrichoplax adhaerensPossesses a FunctionalO-GlcNAc System

(2015) Nithya Selvan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

(2015) Yana Safonova et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Species Delimitation's Coming of Age: Figure 1.

(2015) Jean-François Flot   SYSTEMATIC BIOLOGY

Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora

(2015) Paul Simion et al.   ZOOLOGY

Guidelines for DNA taxonomy, with a focus on the meiofauna

(2015) Diego Fontaneto et al.   Marine Biodiversity

Phylogenetic Signal Dissection Identifies the Root of Starfishes

(2015) Roberto Feuda et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Heatmap3: an improved heatmap package with more powerful and convenient features

(2014) Shilin Zhao et al.   BMC BIOINFORMATICS

Novel Cell Types, Neurosecretory Cells, and Body Plan of the Early-Diverging Metazoan Trichoplax adhaerens

(2014) Carolyn L. Smith et al.   CURRENT BIOLOGY

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

How to describe a cryptic species? Practical challenges of molecular taxonomy

(2013) Katharina M Jörger et al.   Frontiers in Zoology

Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont

(2013) Timothy Driscoll et al.   Genome Biology and Evolution

Towards a Molecular Taxonomy for Protists: Benefits, Risks, and Applications in Plankton Ecology

(2013) David A. Caron   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Global Diversity of the Placozoa

(2013) Michael Eitel et al.   PLoS One

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

Mitochondrial Genome of a Japanese Placozoan

(2012) Hideyuki Miyazawa et al.   ZOOLOGICAL SCIENCE

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Difficult phylogenetic questions: more data, maybe; better methods, certainly

(2011) Hervé Philippe et al.   BMC BIOLOGY

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

(2011) Filip Husník et al.   BMC BIOLOGY

Concepts in protistology: Species definitions and boundaries

(2011) Jens Boenigk et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Ultrastructural analyses support different morphological lineages in the phylum placozoa Grell, 1971

(2011) Loretta Guidi et al.   JOURNAL OF MORPHOLOGY

Extreme mitochondrial evolution in the ctenophoreMnemiopsis leidyi: Insight from mtDNA and the nuclear genome

(2011) Walker Pett et al.   Mitochondrial DNA

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

New Insights into Placozoan Sexual Reproduction and Development

(2011) Michael Eitel et al.   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Early evolution of the LIM homeobox gene family

(2010) Mansi Srivastava et al.   BMC BIOLOGY

Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

(2010) Jean-François Flot et al.   BMC EVOLUTIONARY BIOLOGY

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

(2010) Alexandre Alié et al.   BMC EVOLUTIONARY BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters

(2010) M. EITEL et al.   MOLECULAR ECOLOGY

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

(2008) A. Bhutkar et al.   GENETICS

Placozoa and the evolution of Metazoa and intrasomatic cell differentiation

(2008) Bernd Schierwater et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity

(2008) Masatoshi Nei et al.   NATURE REVIEWS GENETICS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

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

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

The Early ANTP Gene Repertoire: Insights from the Placozoan Genome

(2008) Bernd Schierwater et al.   PLoS One