• Publications
  • Influence
Orchestrating high-throughput genomic analysis with Bioconductor
TLDR
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology with 934 interoperable packages contributed by a large, diverse community of scientists. Expand
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Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutationalExpand
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A framework for oligonucleotide microarray preprocessing
MOTIVATION The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for theseExpand
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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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Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis
Cancer genome sequencing studies have identified numerous driver genes, but the relative timing of mutations in carcinogenesis remains unclear. The gradual progression from premalignant Barrett'sExpand
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Comprehensive high-throughput arrays for relative methylation (CHARM).
This study was originally conceived to test in a rigorous way the specificity of three major approaches to high-throughput array-based DNA methylation analysis: (1) MeDIP, or methylated DNAExpand
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Estimation and assessment of raw copy numbers at the single locus level
TLDR
We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays using a multichip probe-level model. Expand
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Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
TLDR
We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. Expand
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Genome‐wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays
SNP arrays offer the opportunity to get a genome‐wide view on copy number alterations and are increasingly used in oncology. DNA from formalin‐fixed paraffin‐embedded material (FFPE) is partiallyExpand
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Quantifying uncertainty in genotype calls
TLDR
MOTIVATION Genome-wide association studies (GWAS) are used to discover genes underlying complex, heritable disorders for which less powerful study designs have failed in the past. Expand
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