Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Cistromic and genetic evidence that the vitamin D receptor mediates susceptibility to latitude-dependent autoimmune diseases

(2016) D R Booth et al.   GENES AND IMMUNITY

Genetically decreased vitamin D and risk of Alzheimer disease

(2016) Lauren E. Mokry et al.   NEUROLOGY

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Vitamin D and Risk of Multiple Sclerosis: A Mendelian Randomization Study

(2015) Lauren E. Mokry et al.   PLOS MEDICINE

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Aromatase and regulation of the estrogen-to-androgen ratio in synovial tissue inflammation: common pathway in both sexes

(2014) Silvia Capellino et al.   Annals of the New York Academy of Sciences

Spurious transcription factor binding: Non-functional or genetically redundant?

(2014) Mikhail Spivakov   BIOESSAYS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes

(2014) John D. Eicher et al.   NUCLEIC ACIDS RESEARCH

Patterns of Genome-Wide VDR Locations

(2014) Pauli Tuoresmäki et al.   PLoS One

Genetically low vitamin D concentrations and increased mortality: mendelian randomisation analysis in three large cohorts

(2014) S. Afzal et al.   BMJ-British Medical Journal

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Vitamin D deficiency and coronary artery disease: A review of the evidence

(2013) Vijay Kunadian et al.   AMERICAN HEART JOURNAL

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

(2013) Parameswaran Ramachandran et al.   BIOINFORMATICS

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

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

(2013) H. Kilpinen et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

The UCSC genome browser and associated tools

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

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

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

P-value-based regulatory motif discovery using positional weight matrices

(2012) H. Hartmann et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Vitamin D receptor as a master regulator of the c-MYC/MXD1 network

(2012) R. Salehi-Tabar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA

(2011) Igor Orlov et al.   EMBO JOURNAL

The effects of EBV transformation on gene expression levels and methylation profiles

(2011) Minal Çalışkan et al.   HUMAN MOLECULAR GENETICS

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

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

(2011) Jason Ernst et al.   NATURE

DNA binding alters coactivator interaction surfaces of the intact VDR–RXR complex

(2011) Jun Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

(2010) S. V. Ramagopalan et al.   GENOME RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ZNF423 Is Critically Required for Retinoic Acid-Induced Differentiation and Is a Marker of Neuroblastoma Outcome

(2009) Sidong Huang et al.   CANCER CELL

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

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

Expression of the Multiple Sclerosis-Associated MHC Class II Allele HLA-DRB1*1501 Is Regulated by Vitamin D

(2009) Sreeram V. Ramagopalan et al.   PLoS Genetics

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Bayes factors for genome-wide association studies: comparison withP-values

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY