Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

The evolution and population diversity of human-specific segmental duplications

(2017) Megan Y. Dennis et al.   Nature Ecology & Evolution

The Divergence of Neandertal and Modern Human Y Chromosomes

(2016) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

Human adaptation and evolution by segmental duplication

(2016) Megan Y Dennis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Diverse regulatory interactions of long noncoding RNAs

(2016) Tae-Kyung Kim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Neocortex expansion in development and evolution — from cell biology to single genes

(2016) Michaela Wilsch-Bräuninger et al.   CURRENT OPINION IN NEUROBIOLOGY

Long noncoding RNAs: Central to nervous system development

(2016) Ronald P. Hart et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE

Schizophrenia

(2016) Michael J Owen et al.   LANCET

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Microcephaly Proteins Wdr62 and Aspm Define a Mother Centriole Complex Regulating Centriole Biogenesis, Apical Complex, and Cell Fate

(2016) Divya Jayaraman et al.   NEURON

How Wnt Signaling Builds the Brain: Bridging Development and Disease

(2016) Rivka Noelanders et al.   NEUROSCIENTIST

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Variation in the molecular clock of primates

(2016) Priya Moorjani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Long Noncoding RNA Localization and Function

(2016) Ling-Ling Chen   TRENDS IN BIOCHEMICAL SCIENCES

Neural progenitor cells and their role in the development and evolutionary expansion of the neocortex

(2016) Takashi Namba et al.   Wiley Interdisciplinary Reviews-Developmental Biology

A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

(2016) M. Florio et al.   Science Advances

GC-biased gene conversion links the recombination landscape and demography to genomic base composition

(2015) Carina F. Mugal et al.   BIOESSAYS

Can a few non-coding mutations make a human brain?

(2015) Lucía F. Franchini et al.   BIOESSAYS

Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex

(2015) Debra L. Silver   BIOESSAYS

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

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

Genetic Changes Shaping the Human Brain

(2015) Byoung-Il Bae et al.   DEVELOPMENTAL CELL

Phylogenetic Analysis Supports a Link between DUF1220 Domain Number and Primate Brain Expansion

(2015) Fabian Zimmer et al.   Genome Biology and Evolution

Massively parallel cis -regulatory analysis in the mammalian central nervous system

(2015) Susan Q. Shen et al.   GENOME RESEARCH

Comprehensive identification and analysis of human accelerated regulatory DNA

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

High throughput technologies for the functional discovery of mammalian enhancers: New approaches for understanding transcriptional regulatory network dynamics

(2015) Lisa Dailey   GENOMICS

Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences

(2015) Michael A. White   GENOMICS

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Replicated linear association between DUF1220 copy number and severity of social impairment in autism

(2015) J. M. Davis et al.   HUMAN GENETICS

Genomic and Network Patterns of Schizophrenia Genetic Variation in Human Evolutionary Accelerated Regions

(2015) Ke Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Beta-catenin in schizophrenia: Possibly deleterious novel mutation

(2015) Anastasia Levchenko et al.   PSYCHIATRY RESEARCH

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

(2015) M. Florio et al.   SCIENCE

DUF1220 copy number is associated with schizophrenia risk and severity: implications for understanding autism and schizophrenia as related diseases

(2015) V B Searles Quick et al.   Translational Psychiatry

The Cell Biology of Neurogenesis: Toward an Understanding of the Development and Evolution of the Neocortex

(2014) Elena Taverna et al.   Annual Review of Cell and Developmental Biology

DUF1220 protein domains drive proliferation in human neural stem cells and are associated with increased cortical volume in anthropoid primates

(2014) J. G. Keeney et al.   Brain Structure & Function

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

(2014) Melissa J Hubisz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

New genes contribute to genetic and phenotypic novelties in human evolution

(2014) Yong E Zhang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Neural progenitors, neurogenesis and the evolution of the neocortex

(2014) M. Florio et al.   DEVELOPMENT

Cux1andCux2selectively target basal and apical dendritic compartments of layer II-III cortical neurons

(2014) Beatriz Cubelos et al.   Developmental Neurobiology

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Dominant β-catenin mutations cause intellectual disability with recognizable syndromic features

(2014) Valter Tucci et al.   JOURNAL OF CLINICAL INVESTIGATION

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

(2014) Francesca Antonacci et al.   NATURE GENETICS

Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance

(2014) Christiane Schreiweis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

DUF1220 Dosage Is Linearly Associated with Increasing Severity of the Three Primary Symptoms of Autism

(2014) Jonathan M. Davis et al.   PLoS Genetics

Developmental Changes in the Transcriptome of Human Cerebral Cortex Tissue: Long Noncoding RNA Transcripts

(2013) Leonard Lipovich et al.   CEREBRAL CORTEX

An emerging role for Wnt and GSK3 signaling pathways in schizophrenia

(2013) KK Singh   CLINICAL GENETICS

Evolution and diversity of copy number variation in the great ape lineage

(2013) P. H. Sudmant et al.   GENOME RESEARCH

The Role of Human-Specific Gene Duplications During Brain Development and Evolution

(2013) Takayuki Sassa   JOURNAL OF NEUROGENETICS

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

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice

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

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Long noncoding RNAs in development and disease of the central nervous system

(2013) Shi-Yan Ng et al.   TRENDS IN GENETICS

The role of AUTS2 in neurodevelopment and human evolution

(2013) Nir Oksenberg et al.   TRENDS IN GENETICS

Evolutionary History and Genome Organization of DUF1220 Protein Domains

(2013) Majesta S. O’Bleness et al.   G3-Genes Genomes Genetics

Function and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution

(2013) Nir Oksenberg et al.   PLoS Genetics

DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution

(2012) Laura J. Dumas et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A System-Level Transcriptomic Analysis of Schizophrenia Using Postmortem Brain Tissue Samples

(2012) Panos Roussos et al.   ARCHIVES OF GENERAL PSYCHIATRY

Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation

(2012) Cécile Charrier et al.   CELL

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication

(2012) Megan Y. Dennis et al.   CELL

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

(2012) D. D. Licatalosi et al.   GENES & DEVELOPMENT

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Evolution of genetic and genomic features unique to the human lineage

(2012) Majesta O'Bleness et al.   NATURE REVIEWS GENETICS

Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes

(2012) Hernán A. Burbano et al.   PLoS One

Investigating Embryonic Expression Patterns and Evolution of AHI1 and CEP290 Genes, Implicated in Joubert Syndrome

(2012) Yu-Zhu Cheng et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

ASPM regulates Wnt signaling pathway activity in the developing brain

(2011) J. J. Buchman et al.   GENES & DEVELOPMENT

Chromosome 1p21.3 microdeletions comprising DPYD and MIR137 are associated with intellectual disability

(2011) M. H. Willemsen et al.   JOURNAL OF MEDICAL GENETICS

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

(2011) D. Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Transcriptional regulation of neurodevelopmental and metabolic pathways by NPAS3

(2011) L Sha et al.   MOLECULAR PSYCHIATRY

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

Immunohistochemical Analyses of NPAS3 Expression in the Developing Human Fetal Brain

(2011) P. Gould et al.   ANATOMIA HISTOLOGIA EMBRYOLOGIA

Accelerated Recruitment of New Brain Development Genes into the Human Genome

(2011) Yong E. Zhang et al.   PLOS BIOLOGY

Foxp2 Regulates Gene Networks Implicated in Neurite Outgrowth in the Developing Brain

(2011) Sonja C. Vernes et al.   PLoS Genetics

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Hemizygous deletions on chromosome 1p21.3 involving the DPYD gene in individuals with autism spectrum disorder

(2010) MT Carter et al.   CLINICAL GENETICS

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

srGAP2 Arginine Methylation Regulates Cell Migration and Cell Spreading through Promoting Dimerization

(2010) Shaoshi Guo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein 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

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

Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex

(2010) F. Bedogni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice

(2009) Wolfgang Enard et al.   CELL

Disrupted in Schizophrenia 1 Regulates Neuronal Progenitor Proliferation via Modulation of GSK3β/β-Catenin Signaling

(2009) Yingwei Mao et al.   CELL

The F-BAR Domain of srGAP2 Induces Membrane Protrusions Required for Neuronal Migration and Morphogenesis

(2009) Sabrice Guerrier et al.   CELL

Autism susceptibility candidate 2 (Auts2) encodes a nuclear protein expressed in developing brain regions implicated in autism neuropathology

(2009) Francesco Bedogni et al.   GENE EXPRESSION PATTERNS

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Human-specific transcriptional regulation of CNS development genes by FOXP2

(2009) Genevieve Konopka et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Evolution of the neocortex: a perspective from developmental biology

(2009) Pasko Rakic   NATURE REVIEWS NEUROSCIENCE

Wnt signaling in development and disease

(2009) Jennifer L. Freese et al.   NEUROBIOLOGY OF DISEASE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment

(2009) Eulàlia Salichs et al.   PLoS Genetics

Characterization of the proneural gene regulatory network during mouse telencephalon development

(2008) Julia M Gohlke et al.   BMC BIOLOGY

A genome-wide screen for noncoding elements important in primate evolution

(2008) Eliot C Bush et al.   BMC EVOLUTIONARY BIOLOGY

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

SOX2Plays a Critical Role in the Pituitary, Forebrain, and Eye during Human Embryonic Development

(2008) Daniel Kelberman et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

SLC25A12 expression is associated with neurite outgrowth and is upregulated in the prefrontal cortex of autistic subjects

(2008) A-M Lepagnol-Bestel et al.   MOLECULAR PSYCHIATRY

Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder

(2008) B S Pickard et al.   MOLECULAR PSYCHIATRY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Distinctive structures between chimpanzee and humanin a brain noncoding RNA

(2008) A. Beniaminov et al.   RNA

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

Genetic basis of human brain evolution

(2008) Eric J. Vallender et al.   TRENDS IN NEUROSCIENCES