HiCoP, a simple and robust method for detecting interactions of regulatory regions

[1]  Sandy L. Klemm,et al.  Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.

[2]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[3]  Kairong Cui,et al.  Trac-looping measures genome structure and chromatin accessibility , 2018, Nature Methods.

[4]  Tingting Li,et al.  OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks , 2018, Genome Biology.

[5]  Howard Y. Chang,et al.  Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements , 2017, Nature Genetics.

[6]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[7]  Michael Q. Zhang,et al.  In Situ Capture of Chromatin Interactions by Biotinylated dCas9 , 2017, Cell.

[8]  M. Tolstorukov,et al.  Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. , 2017, Genes & development.

[9]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[10]  Peter J. Park,et al.  MNase titration reveals differences between nucleosome occupancy and chromatin accessibility , 2016, Nature Communications.

[11]  L. Mirny,et al.  The 3D Genome as Moderator of Chromosomal Communication , 2016, Cell.

[12]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[13]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[14]  Nir Friedman,et al.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C , 2015, Cell.

[15]  Philip A. Ewels,et al.  Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C , 2015, Nature Genetics.

[16]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[17]  M. Buck,et al.  Chromatin accessibility: a window into the genome , 2014, Epigenetics & Chromatin.

[18]  William Stafford Noble,et al.  Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes , 2014, Nature Methods.

[19]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[20]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[21]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[22]  E. Liu,et al.  Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. , 2009, Genome research.

[23]  William Stafford Noble,et al.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.

[24]  Darrell N. Kotton,et al.  Figure 3 , 2008 .

[25]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[26]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[27]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[28]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[29]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[30]  Patrick O. Brown,et al.  Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[31]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[32]  Elzo de Wit,et al.  A decade of 3C technologies: insights into nuclear organization. , 2012, Genes & development.

[33]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..