Evolutionary History of Chordate PAX Genes: Dynamics of Change in a Complex Gene Family

Impact of asymmetric gene repertoire between cyclostomes and gnathostomes

(2013) Shigehiro Kuraku   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Pax2 modulates proliferation during specification of the otic and epibranchial placodes

(2012) Sabine Freter et al.   DEVELOPMENTAL DYNAMICS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

TimeTree2: species divergence times on the iPhone

(2011) S. Kumar et al.   BIOINFORMATICS

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

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

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

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Patterning and early cell lineage decisions in the developing kidney: the role of Pax genes

(2011) Gregory R. Dressler   PEDIATRIC NEPHROLOGY

Lineage-specific co-evolution of the Egf receptor/ligand signaling system

(2010) Juliette AGC Laisney et al.   BMC EVOLUTIONARY BIOLOGY

Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals

(2010) Víctor Quesada et al.   BMC GENOMICS

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish

(2010) H. Suga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal expression of Pax genes in amphioxus: Insights into Pax-related organogenesis and evolution

(2010) Lu Chen et al.   Science China-Life Sciences

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

ThePAX258gene subfamily: A comparative perspective

(2009) Debbie K. Goode et al.   DEVELOPMENTAL DYNAMICS

The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication

(2009) Shigehiro Kuraku et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Stepwise loss of motilin and its specific receptor genes in rodents

(2009) Jing He et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages

(2008) Susan Bassham et al.   BMC BIOLOGY

RESURRECTING THE ROLE OF TRANSCRIPTION FACTOR CHANGE IN DEVELOPMENTAL EVOLUTION

(2008) Vincent J. Lynch et al.   EVOLUTION

Support for the minimal essential MHC hypothesis: a parrot with a single, highly polymorphic MHC class II B gene

(2008) Colin R. Hughes et al.   IMMUNOGENETICS

The evolution of teleost pigmentation and the fish-specific genome duplication

(2008) I. Braasch et al.   JOURNAL OF FISH BIOLOGY

Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?

(2008) S. Kuraku et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis

(2008) M. Semon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA