MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

(2019) Gregory J. Fonseca et al.   Nature Communications

QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants

(2019) Vincentius Martin et al.   NUCLEIC ACIDS RESEARCH

RUNX transcription factors: orchestrators of development

(2019) Renaud Mevel et al.   DEVELOPMENT

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Developing in 3D: the role of CTCF in cell differentiation

(2018) Rodrigo G. Arzate-Mejía et al.   DEVELOPMENT

MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements

(2018) Verena M Link et al.   NUCLEIC ACIDS RESEARCH

Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation

(2018) Zhe Ji et al.   Nature Communications

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Systematic dissection of genomic features determining transcription factor binding and enhancer function

(2017) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating tools for transcription factor binding site prediction

(2016) Narayan Jayaram et al.   BMC BIOINFORMATICS

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

(2016) Matthias Siebert et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

(2016) Valentina Boeva   Frontiers in Genetics

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The selection and function of cell type-specific enhancers

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

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Mechanisms and consequences of constitutive NF-κB activation in B-cell lymphoid malignancies

(2014) D Nagel et al.   ONCOGENE

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

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

(2012) Jacob F. Degner et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

Measuring reproducibility of high-throughput experiments

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

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF- B p50

(2011) C. S. Cheng et al.   Science Signaling

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL