DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data

PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

(2013) Masashi Yamaji et al.   Cell Stem Cell

Importance of Polη for Damage-Induced Cohesion Reveals Differential Regulation of Cohesion Establishment at the Break Site and Genome-Wide

(2013) Elin Enervald et al.   PLoS Genetics

Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast

(2012) A. Tazumi et al.   GENES & DEVELOPMENT

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

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

Replisome Stability at Defective DNA Replication Forks Is Independent of S Phase Checkpoint Kinases

(2012) Giacomo De Piccoli et al.   MOLECULAR CELL

HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle

(2012) Matthew A. Deardorff et al.   NATURE

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Measuring reproducibility of high-throughput experiments

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

An integrated ChIP-seq analysis platform with customizable workflows

(2011) Eugenia G Giannopoulou et al.   BMC BIOINFORMATICS

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

(2011) Ho Sung Rhee et al.   CELL

Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing

(2011) Seiji Tanaka et al.   CURRENT BIOLOGY

Chromosome length influences replication-induced topological stress

(2011) Andreas Kegel et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

Q&A: ChIP-seq technologies and the study of gene regulation

(2010) Edison T Liu et al.   BMC BIOLOGY

Both Interaction Surfaces within Cohesin's Hinge Domain Are Essential for Its Stable Chromosomal Association

(2010) Ajay Mishra et al.   CURRENT BIOLOGY

ATP Hydrolysis Is Required for Relocating Cohesin from Sites Occupied by Its Scc2/4 Loading Complex

(2010) Bin Hu et al.   CURRENT BIOLOGY

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

(2010) Alexander Kurze et al.   EMBO JOURNAL

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY