Related references
Note: Only part of the references are listed.Evolution of hemoglobin loci and their regulatory elements
Sjaak Philipsen et al.
BLOOD CELLS MOLECULES AND DISEASES (2018)
Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points
Elisabeth F. Heuston et al.
EPIGENETICS & CHROMATIN (2018)
Between form and function: the complexity of genome folding
A. Marieke Oudelaar et al.
HUMAN MOLECULAR GENETICS (2017)
An introduction to computational tools for differential binding analysis with ChIP-seq data
Shiqi Tu et al.
QUANTITATIVE BIOLOGY (2017)
DeepChrome: deep-learning for predicting gene expression from histone modifications
Ritambhara Singh et al.
BIOINFORMATICS (2016)
A semi-parametric statistical model for integrating gene expression profiles across different platforms
Yafei Lyu et al.
BMC BIOINFORMATICS (2016)
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
Hendrik G. Stunnenberg et al.
CELL (2016)
CTCF: making the right connections
Rodolfo Ghirlando et al.
GENES & DEVELOPMENT (2016)
Jointly characterizing epigenetic dynamics across multiple human cell types
Yu Zhang et al.
NUCLEIC ACIDS RESEARCH (2016)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
UpSet: Visualization of Intersecting Sets
Alexander Lex et al.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2014)
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
Clifford A. Meyer et al.
NATURE REVIEWS GENETICS (2014)
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
Anthony Mathelier et al.
NUCLEIC ACIDS RESEARCH (2014)
BLUEPRINT: mapping human blood cell epigenomes
Joost H. A. Martens et al.
HAEMATOLOGICA (2013)
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
Jason D. Buenrostro et al.
NATURE METHODS (2013)
Integrative annotation of chromatin elements from ENCODE data
Michael M. Hoffman et al.
NUCLEIC ACIDS RESEARCH (2013)
A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
Hirotaka Nakahashi et al.
CELL REPORTS (2013)
Normalization of ChIP-seq data with control
Kun Liang et al.
BMC BIOINFORMATICS (2012)
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt et al.
GENOME RESEARCH (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Michael M. Hoffman et al.
NATURE METHODS (2012)
ChromHMM: automating chromatin-state discovery and characterization
Jason Ernst et al.
NATURE METHODS (2012)
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Peter A. Jones
NATURE REVIEWS GENETICS (2012)
ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries
Nishanth Ulhas Nair et al.
PLOS ONE (2012)
CHANCE: comprehensive software for quality control and validation of ChIP-seq data
Aaron Diaz et al.
GENOME BIOLOGY (2012)
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
Zhen Shao et al.
GENOME BIOLOGY (2012)
Modeling gene expression using chromatin features in various cellular contexts
Xianjun Dong et al.
GENOME BIOLOGY (2012)
Synthetic spike-in standards for RNA-seq experiments
Lichun Jiang et al.
GENOME RESEARCH (2011)
A Statistical Framework for the Analysis of ChIP-Seq Data
Pei Fen Kuan et al.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2011)
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
Sam John et al.
NATURE GENETICS (2011)
ChIP-Seq: technical considerations for obtaining high-quality data
Benjamin L. Kidder et al.
NATURE IMMUNOLOGY (2011)
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Naim U. Rashid et al.
GENOME BIOLOGY (2011)
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
MOLECULAR CELL (2010)
GREAT improves functional interpretation of cis-regulatory regions
Cory Y. McLean et al.
NATURE BIOTECHNOLOGY (2010)
The NIH Roadmap Epigenomics Mapping Consortium
Bradley E. Bernstein et al.
NATURE BIOTECHNOLOGY (2010)
Histone modification levels are predictive for gene expression
Rosa Karlic et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Comparative study on ChIP-seq data: normalization and binding pattern characterization
Cenny Taslim et al.
BIOINFORMATICS (2009)
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Joel Rozowsky et al.
NATURE BIOTECHNOLOGY (2009)
Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries
Vinsensius B. Vega et al.
PLOS ONE (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
F-Seq: a feature density estimator for high-throughput sequence tags
Alan P. Boyle et al.
BIOINFORMATICS (2008)
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
John C. Marioni et al.
GENOME RESEARCH (2008)
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
Juliane C. Dohm et al.
NUCLEIC ACIDS RESEARCH (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
BM Bolstad et al.
BIOINFORMATICS (2003)
Normalization of cDNA microarray data
GK Smyth et al.
METHODS (2003)