Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Unraveling the 3D genome: genomics tools for multiscale exploration

(2015) Viviana I. Risca et al.   TRENDS IN GENETICS

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

(2015) Julieta L Mateos et al.   GENOME BIOLOGY

M3D: a kernel-based test for spatially correlated changes in methylation profiles

(2014) Tom R. Mayo et al.   BIOINFORMATICS

Relationship between genome and epigenome - challenges and requirements for future research

(2014) Geneviève Almouzni et al.   BMC GENOMICS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs

(2014) Tao Wu et al.   Cell Stem Cell

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

A defining decade in DNA sequencing

(2014) John D McPherson   NATURE METHODS

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

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

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

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

(2014) Hao Wu et al.   PLoS One

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Global Quantitative Modeling of Chromatin Factor Interactions

(2014) Jian Zhou et al.   PLoS Computational Biology

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

(2014) Alice Pajoro et al.   GENOME BIOLOGY

Computational and experimental methods to decipher the epigenetic code

(2014) Stefano de Pretis et al.   Frontiers in Genetics

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

(2013) Gabriele Schweikert et al.   BMC GENOMICS

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution

(2013) Marco-Antonio Mendoza-Parra et al.   BMC GENOMICS

Applications of functional data analysis: A systematic review

(2013) Shahid Ullah et al.   BMC Medical Research Methodology

Shape information from glucose curves: Functional data analysis compared with traditional summary measures

(2013) Kathrine Frey Frøslie et al.   BMC Medical Research Methodology

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

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

(2013) Julia Lasserre et al.   PLoS Computational Biology

Human Genome Replication Proceeds through Four Chromatin States

(2013) Hanna Julienne et al.   PLoS Computational Biology

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

(2012) Jian Xu et al.   DEVELOPMENTAL CELL

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

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Integrative annotation of chromatin elements from ENCODE data

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

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

(2011) Ho Sung Rhee et al.   CELL

Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage

(2011) Michał J. Okoniewski et al.   NUCLEIC ACIDS RESEARCH

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

(2011) Schraga Schwartz et al.   PLoS One

Emerging patterns of epigenomic variation

(2011) Aleksandar Milosavljevic   TRENDS IN GENETICS

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Tackling the epigenome: challenges and opportunities for collaboration

(2010) John S Satterlee et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Histones: Annotating Chromatin

(2008) Eric I. Campos et al.   Annual Review of Genetics

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology