Incorporating tree-thinking and evolutionary time scale into developmental biology

Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

(2015) Miyuki Noro et al.   BMC EVOLUTIONARY BIOLOGY

Lineage-specific loss of FGF17 within the avian orders Galliformes and Passeriformes

(2015) John Abramyan   GENE

Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians

(2015) N. V. Whelan et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

A phylogenomic analysis of turtles

(2015) Nicholas G. Crawford et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The deuterostome context of chordate origins

(2015) Christopher J. Lowe et al.   NATURE

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

(2014) Nathalie Feiner et al.   Genome Biology and Evolution

The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution

(2014) Jia-Xing Yue et al.   Genome Biology and Evolution

A transcriptome approach to ecdysozoan phylogeny

(2014) Janus Borner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics

(2014) Alexandra Louis et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Why coelacanths are not ‘living fossils’

(2013) Didier Casane et al.   BIOESSAYS

State-of the art methodologies dictate new standards for phylogenetic analysis

(2013) Maria Anisimova et al.   BMC EVOLUTIONARY BIOLOGY

Functions and Mechanisms of Fibroblast Growth Factor (FGF) Signalling in Drosophila melanogaster

(2013) Villö Muha et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

(2013) Shigehiro Kuraku et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes, Forged by Ancient Duplications and Divergences

(2013) Vydianathan Ravi et al.   PLoS Genetics

Evolution of the Tbx6/16 Subfamily Genes in Vertebrates: Insights from Zebrafish

(2012) Daegwon Ahn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

(2011) Huan Qiu et al.   BMC GENOMICS

Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses

(2011) Tereza Manousaki et al.   EVOLUTION & DEVELOPMENT

Genome-Wide Detection of Gene Extinction in Early Mammalian Evolution

(2011) Shigehiro Kuraku et al.   Genome Biology and Evolution

Revisiting the origin of the vertebrate Hox14 by including its relict sarcopterygian members

(2011) Nathalie Feiner et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Genome duplication in amphibians and fish: an extended synthesis

(2011) B. K. Mable et al.   JOURNAL OF ZOOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

(2011) R. Sanchez et al.   NUCLEIC ACIDS RESEARCH

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Palaeophylogenomics of the Vertebrate Ancestor--Impact of Hidden Paralogy on Hagfish and Lamprey Gene Phylogeny

(2010) S. Kuraku   INTEGRATIVE AND COMPARATIVE BIOLOGY

2R or not 2R is not the question anymore

(2010) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Watching the clock: Studying variation in rates of molecular evolution between species

(2010) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes

(2009) Nathalie Feiner et al.   BMC EVOLUTIONARY BIOLOGY

Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom

(2009) Lukasz Huminiecki et al.   BMC EVOLUTIONARY BIOLOGY

How Fast Is the Sessile Ciona?

(2009) Luisa Berná et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Evolution of developmental regulation in the vertebrate FgfD subfamily

(2009) Richard Jovelin et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into Cyclostome Phylogenomics: Pre-2R or Post-2R

(2009) Shigehiro Kuraku   ZOOLOGICAL SCIENCE

Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

(2008) Kevin E. Omland et al.   BIOESSAYS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Noncanonical role of Hox14 revealed by its expression patterns in lamprey and shark

(2008) S. Kuraku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid molecular evolution in a living fossil

(2008) Jennifer M. Hay et al.   TRENDS IN GENETICS

The evolutionary rate of tuatara revisited

(2008) Hilary C. Miller et al.   TRENDS IN GENETICS