Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

Tutorial on Structured Continuous-Time Markov Processes

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Structural properties of genotype–phenotype maps

(2017) S. E. Ahnert   Journal of the Royal Society Interface

The genotype-phenotype map of an evolving digital organism

(2017) Miguel A. Fortuna et al.   PLoS Computational Biology

Assessing similarity: on homology, characters and the need for a semantic approach to non-evolutionary comparative homology

(2016) Lars Vogt   CLADISTICS

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices

(2016) T. Alex Dececchi et al.   PLoS One

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

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development

(2015) Mark Rebeiz et al.   Annual Review of Genomics and Human Genetics

Co-option of an Ancestral Hox-Regulated Network Underlies a Recently Evolved Morphological Novelty

(2015) William J. Glassford et al.   DEVELOPMENTAL CELL

Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses

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

Finding Our Way through Phenotypes

(2015) Andrew R. Deans et al.   PLOS BIOLOGY

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

(2014) Victor A Vera-Ruiz et al.   BMC BIOINFORMATICS

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Calculating structural complexity in phylogenies using ancestral ontologies

(2014) Martín J. Ramírez et al.   CLADISTICS

Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms

(2014) Veronica F. Hinman et al.   GENESIS

Species coexistence and the dynamics of phenotypic evolution in adaptive radiation

(2013) Joseph A. Tobias et al.   NATURE

Insights into insect wing origin provided by functional analysis of vestigial in the red flour beetle, Tribolium castaneum

(2013) C. M. Clark-Hachtel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms

(2013) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Evolutionary Inferences from Phylogenies: A Review of Methods

(2012) Brian C. O'Meara   Annual Review of Ecology Evolution and Systematics

Gene regulatory networks reused to build novel traits

(2012) Antónia Monteiro   BIOESSAYS

Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits

(2012) Amy R. McCune et al.   CURRENT GENOMICS

The Wing-Patterning Network in the Wingless Castes of Myrmicine and Formicine Ant Species Is a Mix of Evolutionarily Labile and Non-Labile Genes

(2012) Seba Jamal Shbailat et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Problematic character coding methods in morphology and their effects

(2011) MARTIN D. BRAZEAU   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

(2011) D. B. Wake et al.   SCIENCE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Phenomics: the next challenge

(2010) David Houle et al.   NATURE REVIEWS GENETICS

Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor

(2010) M. Pigliucci   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenex: Ontological Annotation of Phenotypic Diversity

(2010) James P. Balhoff et al.   PLoS One

A Gross Anatomy Ontology for Hymenoptera

(2010) Matthew J. Yoder et al.   PLoS One

Gradual Adaptation Toward a Range-Expansion Phenotype Initiated the Global Radiation of Toads

(2010) I. Van Bocxlaer et al.   SCIENCE

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

On the origins of novelty in development and evolution

(2008) Armin P. Moczek   BIOESSAYS

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

(2008) Sean B. Carroll   CELL

Quantitative tests of primary homology

(2007) Ingi Agnarsson et al.   CLADISTICS