The association between copy number aberration, DNA methylation and gene expression in tumor samples

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

(2017) Nipun Verma et al.   NATURE GENETICS

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

(2017) Bin Zhu et al.   Scientific Reports

DNA Methylation in Cancer and Aging

(2016) M. Klutstein et al.   CANCER RESEARCH

Statistical Methods in Integrative Genomics

(2016) Sylvia Richardson et al.   Annual Review of Statistics and Its Application

Predicting tumor purity from methylation microarray data

(2015) Naiqian Zhang et al.   BIOINFORMATICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Pancancer analysis of DNA methylation-driven genes using MethylMix

(2015) Olivier Gevaert et al.   GENOME BIOLOGY

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

(2015) Mihaela Angelova et al.   GENOME BIOLOGY

On the presence and role of human gene-body DNA methylation

(2015) Daudi Jjingo et al.   Oncotarget

Convergence of sample eigenvalues, eigenvectors, and principal component scores for ultra-high dimensional data

(2014) S. Lee et al.   BIOMETRIKA

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes

(2014) Huiping Zhang et al.   HUMAN GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data

(2012) Wenting Wang et al.   BIOINFORMATICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

(2012) Jesse D. Ziebarth et al.   NUCLEIC ACIDS RESEARCH

Oxidative Damage Targets Complexes Containing DNA Methyltransferases, SIRT1, and Polycomb Members to Promoter CpG Islands

(2011) Heather M. O'Hagan et al.   CANCER CELL

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

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY