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Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.
We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concertedExpand
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Subtype and pathway specific responses to anticancer compounds in breast cancer
Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many ofExpand
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Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists, and clinicians. These dataExpand
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Serotonin autoreceptor function and antidepressant drug action
This article briefly summarizes, within the context of a brief review of the relevant literature, the outcome of our recent rat microdialysis studies on (1) the relative importance of serotoninExpand
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DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences,Expand
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Estimation and assessment of raw copy numbers at the single locus level
We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays using a multichip probe-level model. Expand
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Type I Collagen α1 Sp1 Polymorphism and the Risk of Cruciate Ligament Ruptures or Shoulder Dislocations
Background Cruciate ligament ruptures and shoulder dislocations are often caused by trauma, but predisposing intrinsic factors might also influence the risk. These injuries are more common in thoseExpand
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aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory
Summary: We have developed a cross-platform open-source framework for analyzing Affymetrix data sets consisting of 1 to 1,000s of arrays. By working directly with CDF and CEL files (standardExpand
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Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
MOTIVATION High-throughput techniques facilitate the simultaneous measurement of DNA copy number at hundreds of thousands of sites on a genome. Expand
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Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1
Significance Identifying the drivers of tumorigenesis provides insight into mechanisms of transformation and can suggest novel therapeutic targets. IDH1 mutations in gliomas are one such promisingExpand
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