Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called “species signal”

Nuclear β-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development

(2015) Jacob M. Musser et al.   EVOLUTION & DEVELOPMENT

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

(2015) Cong Liang et al.   Nature Communications

Cell-type Phylogenetics and the Origin of Endometrial Stromal Cells

(2015) Koryu Kin et al.   Cell Reports

Cyclic Decidualization of the Human Endometrium in Reproductive Health and Failure

(2014) Birgit Gellersen et al.   ENDOCRINE REVIEWS

Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria

(2014) Craig B. Lowe et al.   MOLECULAR BIOLOGY AND EVOLUTION

A relative shift in cloacal location repositions external genitalia in amniote evolution

(2014) Patrick Tschopp et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

PNAS Plus: From the Cover: Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

(2014) M. S. Pankey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrative approach to understanding bird origins

(2014) X. Xu et al.   SCIENCE

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

A model based criterion for gene expression calls using RNA-seq data

(2013) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Next Gen Devo-Evo

(2012) Gunter P. Wagner   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Identity of the avian wing digits: Problems resolved and unsolved

(2011) Rebecca L. Young et al.   DEVELOPMENTAL DYNAMICS

Regulation of limb bud initiation and limb-type morphology

(2011) Veronique Duboc et al.   DEVELOPMENTAL DYNAMICS

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds

(2011) Zhe Wang et al.   NATURE

Global Gene Expression Analysis of Murine Limb Development

(2011) Leila Taher et al.   PLoS One

Evolutionary origin of the insect wing via integration of two developmental modules

(2010) Nao Niwa et al.   EVOLUTION & DEVELOPMENT

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Divergent transcriptional activities determine limb identity

(2010) Jean-François Ouimette et al.   Nature Communications

Genomics and the evolutionary origins of nervous system complexity

(2009) Todd H Oakley et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

The evolution of hierarchical gene regulatory networks

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS