Constrained vertebrate evolution by pleiotropic genes

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

(2017) Ryohei Seki et al.   Nature Communications

Animal Evolution: Are Phyla Real?

(2016) Andreas Hejnol et al.   CURRENT BIOLOGY

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Constraints Evolve: Context Dependency of Gene Effects Allows Evolution of Pleiotropy

(2015) Mihaela Pavličev et al.   Annual Review of Ecology Evolution and Systematics

What to compare and how: Comparative transcriptomics for Evo-Devo

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

A “Developmental Hourglass” in Fungi

(2015) Xuanjin Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Facts and fancies about early fossil chordates and vertebrates

(2015) Philippe Janvier   NATURE

The developmental hourglass model: a predictor of the basic body plan?

(2014) N. Irie et al.   DEVELOPMENT

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

(2014) J. J. Tena et al.   GENOME RESEARCH

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

(2014) J. J. Li et al.   GENOME RESEARCH

Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle

(2014) Linda Z. Holland   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Chordate evolution and the three-phylum system

(2014) N. Satoh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

(2014) Spiros Papakostas et al.   Nature Communications

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates

(2013) Barbara Piasecka et al.   PLoS Genetics

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

(2013) Benjamin Georgi et al.   PLoS Genetics

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

A transcriptomic hourglass in plant embryogenesis

(2012) Marcel Quint et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The evolution of early animal embryos: conservation or divergence?

(2012) Alex T. Kalinka et al.   TRENDS IN ECOLOGY & EVOLUTION

A model of developmental evolution: selection, pleiotropy and compensation

(2012) Mihaela Pavlicev et al.   TRENDS IN ECOLOGY & EVOLUTION

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh 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

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

(2011) M. W. Perry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals

(2011) D. H. Erwin et al.   SCIENCE

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS