Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes

Promoter CpG Island Methylation of Genes in Key Cancer Pathways Associates with Clinical Outcome in High-Grade Serous Ovarian Cancer

(2013) W. Dai et al.   CLINICAL CANCER RESEARCH

Diverse Mechanisms of AKT Pathway Activation in Human Malignancy

(2013) Mitchell Cheung et al.   CURRENT CANCER DRUG TARGETS

Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage

(2013) Mirang Kim et al.   HUMAN MOLECULAR GENETICS

Towards Sustained Silencing of HER2/neu in Cancer By Epigenetic Editing

(2013) F. Falahi et al.   MOLECULAR CANCER RESEARCH

Comprehensive analysis of the functional microRNA–mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression

(2013) Yongsheng Li et al.   NUCLEIC ACIDS RESEARCH

Signaling Network Assessment of Mutations and Copy Number Variations Predict Breast Cancer Subtype-Specific Drug Targets

(2013) Naif Zaman et al.   Cell Reports

Chromatin Modifications Sequentially Enhance ErbB2 Expression in ErbB2-Positive Breast Cancers

(2013) Sathish Kumar Mungamuri et al.   Cell Reports

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

(2012) C. L. Plaisier et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Ectopic expression of RhoBTB2 inhibits migration and invasion of human breast cancer cells

(2011) Li-Jun Ling et al.   CANCER BIOLOGY & THERAPY

Hallmarks of Cancer: The Next Generation

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DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

Cell type-specific DNA methylation at intragenic CpG islands in the immune system

(2011) A. M. Deaton et al.   GENOME RESEARCH

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing

(2011) Zhifu Sun et al.   PLoS One

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome profiling of ERBB2-amplified breast cancers

(2010) Fabrice Sircoulomb et al.   BMC CANCER

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Global Histone Modifications in Breast Cancer Correlate with Tumor Phenotypes, Prognostic Factors, and Patient Outcome

(2009) S. E. Elsheikh et al.   CANCER RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

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

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery

(2009) Jessica Kao et al.   PLoS One

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

Inhibition of histone deacetylase suppresses EGF signaling pathways by destabilizing EGFR mRNA in ER-negative human breast cancer cells

(2008) Qun Zhou et al.   BREAST CANCER RESEARCH AND TREATMENT

Inferring causal relationships among different histone modifications and gene expression

(2008) H. Yu et al.   GENOME RESEARCH

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS