Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

(2016) Morteza Mahmoudi Saber et al.   Genome Biology and Evolution

Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics

(2016) Isaac Adeyemi Babarinde et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

(2016) Marit W Vermunt et al.   NATURE NEUROSCIENCE

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex

(2015) J. Lomax Boyd et al.   CURRENT BIOLOGY

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

(2015) Daniel R. Schrider et al.   Genome Biology and Evolution

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

From trans to cis: transcriptional regulatory networks in neocortical development

(2015) Mikihito Shibata et al.   TRENDS IN GENETICS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

(2013) Alex S. Nord et al.   CELL

Conserved non-coding elements and cis regulation: actions speak louder than words

(2013) A. C. Nelson et al.   DEVELOPMENT

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

(2013) Isaac Adeyemi Babarinde et al.   Genome Biology and Evolution

The Developmental Brain Gene NPAS3 Contains the Largest Number of Accelerated Regulatory Sequences in the Human Genome

(2013) Gretel B. Kamm et al.   MOLECULAR BIOLOGY AND EVOLUTION

The mystery of extreme non-coding conservation

(2013) N. Harmston et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

(2013) C. R. Linnen et al.   SCIENCE

The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option

(2013) Aaron M. Wenger et al.   PLoS Genetics

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

(2012) S. Dimitrieva et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Vertebrate Paralogous Conserved Noncoding Sequences May Be Related to Gene Expressions in Brain

(2012) Masatoshi Matsunami et al.   Genome Biology and Evolution

Hundreds of conserved non-coding genomic regions are independently lost in mammals

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events

(2011) D. K. Goode et al.   DEVELOPMENT

Loss-of-Function Mutation in a Repressor Module of Human-Specifically Activated Enhancer HACNS1

(2011) K. Sumiyama et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution

(2011) Nelle Lambert et al.   PLoS One

Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions between Human Conserved Non-Coding Sequences

(2011) Daniel Robyr et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

(2010) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Contrasts between adaptive coding and noncoding changes during human evolution

(2010) Ralph Haygood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

(2010) Gizem Kalay et al.   PLoS Genetics

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements

(2009) Leila Taher et al.   BIOINFORMATICS

Testing significance relative to a fold-change threshold is a TREAT

(2009) D. J. McCarthy et al.   BIOINFORMATICS

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

(2009) Matthew B. Johnson et al.   NEURON

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

(2009) Gayle K. McEwen et al.   PLoS Genetics

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

(2008) Sean B. Carroll   CELL

Widespread Ultraconservation Divergence in Primates

(2008) I. Ovcharenko   MOLECULAR BIOLOGY AND EVOLUTION

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics