S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

Evolution of hemoglobin loci and their regulatory elements

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Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points

(2018) Elisabeth F. Heuston et al.   Epigenetics & Chromatin

Between form and function: the complexity of genome folding

(2017) A. Marieke Oudelaar et al.   HUMAN MOLECULAR GENETICS

DeepChrome: deep-learning for predicting gene expression from histone modifications

(2016) Ritambhara Singh et al.   BIOINFORMATICS

A semi-parametric statistical model for integrating gene expression profiles across different platforms

(2016) Yafei Lyu et al.   BMC BIOINFORMATICS

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Jointly characterizing epigenetic dynamics across multiple human cell types

(2016) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Normalization of ChIP-seq data with control

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

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An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries

(2012) Nishanth Ulhas Nair et al.   PLoS One

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

(2012) Aaron Diaz et al.   GENOME BIOLOGY

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

A Statistical Framework for the Analysis of ChIP-Seq Data

(2011) Pei Fen Kuan et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative study on ChIP-seq data: normalization and binding pattern characterization

(2009) Cenny Taslim et al.   BIOINFORMATICS

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries

(2009) Vinsensius B. Vega et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME 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