AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

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

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

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Inferring direct DNA binding from ChIP-seq

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

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Functional autonomy of distant-acting human enhancers

(2009) Axel Visel et al.   GENOMICS

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

NestedMICA as an ab initio protein motif discovery tool

(2008) Mutlu Doğruel et al.   BMC BIOINFORMATICS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY