Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico

(2019) Alicia Scocchia et al.   npj Genomic Medicine

EnDisease: a manually curated database for enhancer-disease associations

(2019) Wanwen Zeng et al.   Database-The Journal of Biological Databases and Curation

Multiple genomic copy number variants associated with periventricular nodular heterotopia indicate extreme genetic heterogeneity

(2019) Elena Cellini et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Predicting enhancers in mammalian genomes using supervised hidden Markov models

(2019) Tobias Zehnder et al.   BMC BIOINFORMATICS

InTAD: chromosome conformation guided analysis of enhancer target genes

(2019) Konstantin Okonechnikov et al.   BMC BIOINFORMATICS

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

(2019) Michelle M. Clark et al.   Science Translational Medicine

The evolution of Great Apes has shaped the functional enhancers' landscape in human embryonic stem cells

(2019) Gennadi Glinsky et al.   Stem Cell Research

De novo mutations in GRIN1 cause extensive bilateral polymicrogyria

(2018) Andrew E Fry et al.   BRAIN

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

(2018) Tahsin Stefan Barakat et al.   Cell Stem Cell

A survey of recently emerged genome-wide computational enhancer predictor tools

(2018) Leonard Whye Kit Lim et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Germline variants in SMARCB1 and other members of the BAF chromatin-remodeling complex across human disease entities: a meta-analysis

(2018) Till Holsten et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Comprehensive genomic analysis of patients with disorders of cerebral cortical development

(2018) Wojciech Wiszniewski et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

TLE1, a key player in neurogenesis, a new candidate gene for autosomal recessive postnatal microcephaly

(2018) Mara Cavallin et al.   European Journal of Medical Genetics

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

Analysis of 17 genes detects mutations in 81% of 811 patients with lissencephaly

(2018) Nataliya Di Donato et al.   GENETICS IN MEDICINE

A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb–polysyndactyly syndrome

(2018) Jacob W P Potuijt et al.   GENETICS IN MEDICINE

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

The mechanistic basis for chromatin regulation by pioneer transcription factors

(2018) Makiko Iwafuchi-Doi   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Identification of genes associated with cortical malformation using a transposon-mediated somatic mutagenesis screen in mice

(2018) I-Ling Lu et al.   Nature Communications

Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization

(2018) Ruth B. McCole et al.   Cell Reports

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

(2018) Jean Monlong et al.   PLoS Genetics

Development and Evolution of Cerebral and Cerebellar Cortex

(2018) David C. Van Essen et al.   BRAIN BEHAVIOR AND EVOLUTION

Genome-wide investigation of an ID cohort reveals de novo 3′UTR variants affecting gene expression

(2018) Paolo Devanna et al.   HUMAN GENETICS

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders

(2018) Mari E. K. Niemi et al.   NATURE

De novo mutations in regulatory elements in neurodevelopmental disorders

(2018) Patrick J. Short et al.   NATURE

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

(2018) Stephane E. Castel et al.   NATURE GENETICS

MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance

(2018) William B. Dobyns et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

(2018) Tiago C Silva et al.   BIOINFORMATICS

Mutated zinc finger protein of the cerebellum 1 leads to microcephaly, cortical malformation, callosal agenesis, cerebellar dysplasia, tethered cord and scoliosis

(2018) Laura V. Vandervore et al.   European Journal of Medical Genetics

A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity

(2018) Brett B Maricque et al.   NATURE BIOTECHNOLOGY

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Human brain development and its in vitro recapitulation

(2018) Yusuke Seto et al.   NEUROSCIENCE RESEARCH

SEdb: a comprehensive human super-enhancer database

(2018) Yong Jiang et al.   NUCLEIC ACIDS RESEARCH

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

(2018) Xinchen Wang et al.   Nature Communications

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

(2018) Marc S. Halfon   TRENDS IN GENETICS

Regulatory variants of FOXG1 in the context of its topological domain organisation

(2017) Mana M Mehrjouy et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Cerebral cortex development: an outside-in perspective

(2017) Gulistan Agirman et al.   FEBS LETTERS

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test

(2017) Anath C Lionel et al.   GENETICS IN MEDICINE

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Mutations of conserved non-coding elements of PITX2 in patients with ocular dysgenesis and developmental glaucoma

(2017) Meredith E. Protas et al.   HUMAN MOLECULAR GENETICS

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci

(2017) Matthew C Canver et al.   NATURE GENETICS

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

DiseaseEnhancer: a resource of human disease-associated enhancer catalog

(2017) Guanxiong Zhang et al.   NUCLEIC ACIDS RESEARCH

HEDD: Human Enhancer Disease Database

(2017) Zhen Wang et al.   NUCLEIC ACIDS RESEARCH

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Assessment of de novo copy-number variations in Italian patients with schizophrenia: Detection of putative mutations involving regulatory enhancer elements

(2017) Giulio Piluso et al.   WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

(2017) Deborah Y. Kwon et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Genomic copy number variation analysis in multiple system atrophy

(2017) Yuka Hama et al.   Molecular Brain

Characterizing the Pattern of Anomalies in Congenital Zika Syndrome for Pediatric Clinicians

(2017) Cynthia A. Moore et al.   JAMA Pediatrics

Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers

(2017) Julia B. Carleton et al.   Cell Systems

Germline and somatic mutations in cortical malformations: Molecular defects in Argentinean patients with neuronal migration disorders

(2017) Dolores González-Morón et al.   PLoS One

Mutations in CRADD Result in Reduced Caspase-2-Mediated Neuronal Apoptosis and Cause Megalencephaly with a Rare Lissencephaly Variant

(2016) Nataliya Di Donato et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Histone Acetylome-wide Association Study of Autism Spectrum Disorder

(2016) Wenjie Sun et al.   CELL

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Evaluation of non-coding variation in GLUT1 deficiency

(2016) Yu-Chi Liu et al.   DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Annual Research Review: Quality of life and childhood mental and behavioural disorders - a critical review of the research

(2016) Ulf Jonsson et al.   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

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

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

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

(2016) Marit W Vermunt et al.   NATURE NEUROSCIENCE

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

(2016) Feng Liu et al.   Scientific Reports

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

(2016) Dimitri J Stavropoulos et al.   npj Genomic Medicine

Familial recurrences ofFOXG1-related disorder: Evidence for mosaicism

(2015) Kelly Q. McMahon et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Progress and challenges in bioinformatics approaches for enhancer identification

(2015) Dimitrios Kleftogiannis et al.   BRIEFINGS IN BIOINFORMATICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Chromatin deregulation in disease

(2015) Anne C. Mirabella et al.   CHROMOSOMA

Mosaic parental germline mutations causing recurrent forms of malformations of cortical development

(2015) Julia Lauer Zillhardt et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

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

Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene

(2015) Minaka Ishibashi et al.   HUMAN GENETICS

A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

(2015) Elisa Giorgio et al.   HUMAN MOLECULAR GENETICS

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Coexpression networks identify brain region–specific enhancer RNAs in the human brain

(2015) Pu Yao et al.   NATURE NEUROSCIENCE

SEA: a super-enhancer archive

(2015) Yanjun Wei et al.   NUCLEIC ACIDS RESEARCH

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications

(2015) Yiming Lu et al.   PLoS One

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Costs of caring for children with an intellectual developmental disorder

(2015) Dallas Genereaux et al.   Disability and Health Journal

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

(2015) Nergiz Dogan et al.   Epigenetics & Chromatin

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

(2015) Qiongshi Lu et al.   Scientific Reports

Aberrant Gene Expression in Humans

(2015) Yong Zeng et al.   PLoS Genetics

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Homozygous loss of DIAPH1 is a novel cause of microcephaly in humans

(2014) A Gulhan Ercan-Sencicek et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Malformations of cortical development: clinical features and genetic causes

(2014) Renzo Guerrini et al.   LANCET NEUROLOGY

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Somatic Mutations in Cerebral Cortical Malformations

(2014) Saumya S. Jamuar et al.   NEW ENGLAND JOURNAL OF MEDICINE

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Evolutionarily Dynamic Alternative Splicing of GPR56 Regulates Regional Cerebral Cortical Patterning

(2014) B.-I. Bae et al.   SCIENCE

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain

(2014) Marit W. Vermunt et al.   Cell Reports

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

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

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability

(2013) Anne Gregor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Disruption of Autoregulatory Feedback by a Mutation in a Remote, Ultraconserved PAX6 Enhancer Causes Aniridia

(2013) Shipra Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies

(2013) Alexander R. Ball et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Optical control of mammalian endogenous transcription and epigenetic states

(2013) Silvana Konermann et al.   NATURE

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

(2013) Michael N Weedon et al.   NATURE GENETICS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

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

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

Computational Identification of Active Enhancers in Model Organisms

(2013) Chengqi Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

RTTN Mutations Link Primary Cilia Function to Organization of the Human Cerebral Cortex

(2012) Sima Kheradmand Kia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

(2012) Scott Smemo et al.   HUMAN MOLECULAR GENETICS

A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb

(2012) Tobias Laurell et al.   HUMAN MUTATION

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

(2012) Michael Fernández et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano 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

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia

(2011) Vladimir Vacic et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

(2010) E. Lidor Nili et al.   GENOME RESEARCH

Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations

(2010) Kaya Bilgüvar et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim 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

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

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

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

Cortical Brain Malformations

(2008) Marie Claire Yvette de Wit et al.   ARCHIVES OF NEUROLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein

(2008) Yongsu Jeong et al.   NATURE GENETICS

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS