Mapping genome-wide transcription-factor binding sites using DAP-seq

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

(2012) Sunil K. Raghav et al.   MOLECULAR CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Yuchun Guo et al.   PLoS Computational Biology

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Protein production and purification

(2008) Susanne Gräslund et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY