The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss

(2018) James E Tarver et al.   Genome Biology and Evolution

Comparative genomics and the nature of placozoan species

(2018) Michael Eitel et al.   PLOS BIOLOGY

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

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

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

(2016) Seyed Alireza Zamani-Dahaj et al.   MOLECULAR BIOLOGY AND EVOLUTION

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Animal Phylogeny and Its Evolutionary Implications

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

A meta-approach for improving the prediction and the functional annotation of ortholog groups

(2014) Cécile Pereira et al.   BMC GENOMICS

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

(2014) Torsten H. Struck   Evolutionary Bioinformatics

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer in the acquisition of novel traits by metazoans

(2014) Luis Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans

(2014) Sven Leininger et al.   Nature Communications

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND 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 Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy

(2011) Daniel J Jackson et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

(2010) Joseph F Ryan et al.   EvoDevo

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem-cell differentiation

(2008) Georg Hemmrich et al.   BIOESSAYS

Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos

(2008) Alexander V. Alekseyenko et al.   SYSTEMATIC BIOLOGY

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY