The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

(2020) Jialin Liu et al.   BMC BIOLOGY

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

(2020) James P. Reddington et al.   DEVELOPMENTAL CELL

The role of chromatin accessibility in cis-regulatory evolution

(2019) Pei-Chen Peng et al.   Genome Biology and Evolution

Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle

(2019) Marta Coronado-Zamora et al.   Genome Biology and Evolution

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Gene Editing on Center Stage

(2018) Rasmus O. Bak et al.   TRENDS IN GENETICS

Developmental Constraints on Genome Evolution in Four Bilaterian Model Species

(2018) Jialin Liu et al.   Genome Biology and Evolution

Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo

(2018) Jialin Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

(2017) Pierre Khoueiry et al.   eLife

Constrained vertebrate evolution by pleiotropic genes

(2017) Haiyang Hu et al.   Nature Ecology & Evolution

Developmental constraints shape the evolution of the nematode mid-developmental transition

(2017) Harel Zalts et al.   Nature Ecology & Evolution

gkmSVM: an R package for gapped-kmer SVM

(2016) Mahmoud Ghandi et al.   BIOINFORMATICS

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

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

(2016) Michal Levin et al.   NATURE

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) N. Irie et al.   DEVELOPMENT

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development

(2013) Alicia N. Schep et al.   PLoS One

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

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

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

(2008) Sangyun Jeong et al.   CELL

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

(2008) Sean B. Carroll   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY