Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes

Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface

(2017) Mihaela Pavličev et al.   GENOME RESEARCH

Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast)

(2017) Jian-Rong Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Brownian model of transcriptome evolution and phylogenetic network visualization between tissues

(2017) Xun Gu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts

(2016) Koryu Kin et al.   Genome Biology and Evolution

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes

(2016) N. Di-Poi  et al.   Science Advances

Understanding tissue expression evolution: from expression phylogeny to phylogenetic network

(2015) Xun Gu   BRIEFINGS IN BIOINFORMATICS

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

Wiring for independence: Positive feedback motifs facilitate individuation of traits in development and evolution

(2015) Mihaela Pavličev et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

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

(2015) Jacob M. Musser et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Neighboring Genes Show Correlated Evolution in Gene Expression

(2015) Avazeh T. Ghanbarian et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

(2015) Nikolaos Stefanakis et al.   NEURON

Cell-type Phylogenetics and the Origin of Endometrial Stromal Cells

(2015) Koryu Kin et al.   Cell Reports

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

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

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

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Independent evolution of striated muscles in cnidarians and bilaterians

(2012) Patrick R. H. Steinmetz et al.   NATURE

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

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

(2011) Zhe Wang et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks

(2009) L. Pu et al.   PLANT PHYSIOLOGY

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Pleiotropic scaling of gene effects and the ‘cost of complexity’

(2008) Günter P. Wagner et al.   NATURE

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

(2008) Detlev Arendt   NATURE REVIEWS GENETICS