Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding

Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq

(2018) Yu Kong et al.   GENOME RESEARCH

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

(2018) Vivek Behera et al.   Nature Communications

Functional Variants Identified Efficiently through an Integrated Transcriptome and Epigenome Analysis

(2018) Fanlin Meng et al.   Scientific Reports

Whole-genome bisulfite sequencing with improved accuracy and cost

(2018) Masako Suzuki et al.   GENOME RESEARCH

Integrated analysis of motif activity and gene expression changes of transcription factors

(2017) Jesper Grud Skat Madsen et al.   GENOME RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

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

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Precise and efficient scarless genome editing in stem cells using CORRECT

(2017) Dylan Kwart et al.   Nature Protocols

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression

(2017) Henriette O’Geen et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Yimeng Yin et al.   SCIENCE

Stabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells

(2017) Masahiro Okada et al.   Epigenetics & Chromatin

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

(2017) Herbert Schulz et al.   Nature Communications

Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

(2017) Yong Lei et al.   Nature Communications

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

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

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

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

Targeted DNA methylation in human cells using engineered dCas9-methyltransferases

(2017) Tina Xiong et al.   Scientific Reports

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

(2017) Chao Ren et al.   Scientific Reports

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner

(2016) David Cano-Rodriguez et al.   Nature Communications

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke 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

Cooperation between SMYD3 and PC4 drives a distinct transcriptional program in cancer cells

(2015) Jin-Man Kim et al.   NUCLEIC ACIDS RESEARCH

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

(2015) Julie Nadel et al.   Epigenetics & Chromatin

Cell Specific eQTL Analysis without Sorting Cells

(2015) Harm-Jan Westra et al.   PLoS Genetics

Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

(2014) Xin Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

(2014) Ida Moltke et al.   NATURE

Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers

(2014) Xuefei Gao et al.   NUCLEIC ACIDS RESEARCH

The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

(2014) Yuanbin Ru et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

(2014) Mark D. Szczelkun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The NF-κB Genomic Landscape in Lymphoblastoid B Cells

(2014) Bo Zhao et al.   Cell Reports

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

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

(2013) Luke A. Gilbert et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Robust, synergistic regulation of human gene expression using TALE activators

(2013) Morgan L Maeder et al.   NATURE METHODS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera 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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

An Atlas of the Epstein-Barr Virus Transcriptome and Epigenome Reveals Host-Virus Regulatory Interactions

(2012) Aaron Arvey et al.   Cell Host & Microbe

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012)   NATURE

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

Measuring reproducibility of high-throughput experiments

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

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

Cooperative transcription factor associations discovered using regulatory variation

(2011) Konrad J. Karczewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection and interpretation of expression quantitative trait loci (eQTL)

(2009) Jacob J. Michaelson et al.   METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

A truncation mutation in TBC1D4 in a family with acanthosis nigricans and postprandial hyperinsulinemia

(2009) S. Dash et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two Modes of Transcriptional Activation at Native Promoters by NF-κB p65

(2009) Dominic van Essen et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY