Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion

(2015) Arvind Shakya et al.   MOLECULAR AND CELLULAR BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas

(2014) Hideo Watanabe et al.   JOURNAL OF CLINICAL INVESTIGATION

The Myc 3' Wnt-Responsive Element Suppresses Colonic Tumorigenesis

(2014) W. M. Konsavage et al.   MOLECULAR AND CELLULAR BIOLOGY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interpreting 4C-Seq data: how far can we go?

(2014) Ramya Raviram et al.   Epigenomics

Functional annotation of colon cancer risk SNPs

(2014) Lijing Yao et al.   Nature Communications

MORC1 represses transposable elements in the mouse male germline

(2014) William A. Pastor et al.   Nature Communications

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

(2014) Dong-Sung Lee et al.   Nature Communications

DNA Methylation of Transcriptional Enhancers and Cancer Predisposition

(2013) Dvir Aran et al.   CELL

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Cross-talk between Site-specific Transcription Factors and DNA Methylation States

(2013) Adam Blattler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

High expression ofZNF703independent of amplification indicates worse prognosis in patients with luminal B breast cancer

(2013) Inga Reynisdottir et al.   Cancer Medicine

Cys2His2 zinc finger protein family: Classification, functions, and major members

(2012) S. V. Razin et al.   BIOCHEMISTRY-MOSCOW

A Blueprint for an International Cancer Epigenome Consortium. A Report from the AACR Cancer Epigenome Task Force

(2012) S. Beck et al.   CANCER RESEARCH

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies

(2012) Ross C. Hardison   JOURNAL OF BIOLOGICAL CHEMISTRY

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

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

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

(2012) I. K. Sur et al.   SCIENCE

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

(2012) Seth Frietze et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

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

(2011) Jason Ernst et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

(2011) Adam J Bass et al.   NATURE GENETICS

General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells

(2010) C. Gebhard et al.   CANCER RESEARCH

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

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

(2010) Guillaume J. Filion et al.   CELL

GATA3 Inhibits Breast Cancer Metastasis through the Reversal of Epithelial-Mesenchymal Transition

(2010) Wei Yan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GATA Switches as Developmental Drivers

(2010) Emery H. Bresnick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

c-Jun N-terminal phosphorylation antagonises recruitment of the Mbd3/NuRD repressor complex

(2010) Cristina Aguilera et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GATA3 in development and cancer differentiation: Cells GATA have it!

(2009) Jonathan Chou et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy

(2009) Tohru Fujiwara et al.   MOLECULAR CELL

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

GATA-3 Links Tumor Differentiation and Dissemination in a Luminal Breast Cancer Model

(2008) Hosein Kouros-Mehr et al.   CANCER CELL

GATA-3 and the regulation of the mammary luminal cell fate

(2008) Hosein Kouros-Mehr et al.   CURRENT OPINION IN CELL BIOLOGY

A Genome-Wide Screen for  -Catenin Binding Sites Identifies a Downstream Enhancer Element That Controls c-Myc Gene Expression

(2008) G. S. Yochum et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of the hTERT promoter activity by MSH2, the hnRNPs K and D and GRHL2 in human oral squamous cell carcinoma cells

(2008) X Kang et al.   ONCOGENE