Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

A comparison of gene expression and DNA methylation patterns across tissues and species

(2020) Lauren E. Blake et al.   GENOME RESEARCH

Differential DNA methylation of vocal and facial anatomy genes in modern humans

(2020) David Gokhman et al.   Nature Communications

Recently Evolved Enhancers Emerge with High Interindividual Variability and Less Frequently Associate with Disease

(2020) Bas Castelijns et al.   Cell Reports

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Massively parallel discovery of human-specific substitutions that alter enhancer activity

(2020) Severin Uebbing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neocortical Expansion Due to Increased Proliferation of Basal Progenitors Is Linked to Changes in Their Morphology

(2019) Nereo Kalebic et al.   Cell Stem Cell

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

(2019) Martin Kuhlwilm et al.   Scientific Reports

Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates

(2019) Ittai E. Eres et al.   PLoS Genetics

Human-specific features of spatial gene expression and regulation in eight brain regions

(2018) Chuan Xu et al.   GENOME RESEARCH

Familial paroxysmal kinesigenic dyskinesia is associated with mutations in the KCNA1 gene

(2018) Xiao-Meng Yin et al.   HUMAN MOLECULAR GENETICS

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

Repurposing of promoters and enhancers during mammalian evolution

(2018) Francesco N. Carelli et al.   Nature Communications

Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder

(2018) Ditte Demontis et al.   NATURE GENETICS

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Detecting ancient positive selection in humans using extended lineage sorting

(2017) Stéphane Peyrégne et al.   GENOME RESEARCH

Transposable elements are the primary source of novelty in primate gene regulation

(2017) Marco Trizzino et al.   GENOME RESEARCH

A Specialist Macaque MHC Class I Molecule with HLA-B*27–like Peptide-Binding Characteristics

(2017) Natasja G. de Groot et al.   JOURNAL OF IMMUNOLOGY

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

The population genomics of rhesus macaques ( Macaca mulatta ) based on whole-genome sequences

(2016) Cheng Xue et al.   GENOME RESEARCH

Archaic adaptive introgression in TBX15/WARS2

(2016) Fernando Racimo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of 15 genetic loci associated with risk of major depression in individuals of European descent

(2016) Craig L Hyde et al.   NATURE GENETICS

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

(2016) Marit W Vermunt et al.   NATURE NEUROSCIENCE

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Evolution of Epigenetic Regulation in Vertebrate Genomes

(2016) Rebecca F. Lowdon et al.   TRENDS IN GENETICS

The evolutionary history of genes involved in spoken and written language: beyond FOXP2

(2016) Alessandra Mozzi et al.   Scientific Reports

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

(2016) David Juan et al.   Cell Reports

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

(2015) F. Racimo   GENETICS

Comprehensive identification and analysis of human accelerated regulatory DNA

(2015) Rachel M. Gittelman et al.   GENOME RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The interplay between DNA methylation and sequence divergence in recent human evolution

(2015) Irene Hernando-Herraez et al.   NUCLEIC ACIDS RESEARCH

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques

(2013) Gaby G. M. Doxiadis et al.   IMMUNOGENETICS

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

(2013) Julia Lasserre et al.   PLoS Computational Biology

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

(2013) John A. Capra et al.   PLoS Genetics

Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution

(2012) Jia Zeng et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Nonoverlapping Functions of the Polycomb Group Cbx Family of Proteins in Embryonic Stem Cells

(2012) Lluis Morey et al.   Cell Stem Cell

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

Comprehensive DNA methylation analysis of human peripheral blood leukocytes and lymphoblastoid cell lines

(2011) Hiroko Sugawara et al.   Epigenetics

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Sexual Selection and the Molecular Evolution of ADAM Proteins

(2010) Scott Finn et al.   JOURNAL OF MOLECULAR EVOLUTION

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Clavesin Family, Neuron-specific Lipid- and Clathrin-binding Sec14 Proteins Regulating Lysosomal Morphology

(2009) Yohei Katoh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MEF2C haploinsufficiency caused by either microdeletion of the 5q14.3 region or mutation is responsible for severe mental retardation with stereotypic movements, epilepsy and/or cerebral malformations

(2009) N. Le Meur et al.   JOURNAL OF MEDICAL GENETICS

Relaxed selection in the wild

(2009) David C. Lahti et al.   TRENDS IN ECOLOGY & EVOLUTION

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS