Circular binary segmentation for the analysis of array-based DNA copy number data.

By Adam B. Olshen, E. Venkatraman, R. Lucito, M. Wigler. Biostatistics, 2004

2,352 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/874cc3d7f38afed3543f961b49511aead2c91457

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Citations in the corpus

Optimal detection of changepoints with a linear computational cost (2011, background): “Consider, for example, recent work in genomics, looking at detecting changes in gene copy numbers or in the compositional structure of the genome (Braun, Braun, and Muller 2000; Olshen et al. 2004; Picard et al. 2005); and in finance where, for example, interest lies in detecting changes in the vola”
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. (2017, neutral): “…RRID:SCR_001802; https://support.illumina.com/ sequencing/sequencing_software/bcl2fastqconversion-software.html Circular Binary Segmentation (CBS) Olshen et al., 2004 PMID:15475419 ConsensusClusterPlus Wilkerson and Hayes, 2010…”
A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose (2009, methodology): “. The resultant genomic copy number profiles were then segmented using Circular Binary Segmentation”
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers (2011, methodology): “The first step, accurately defining the copy-number profile of each cancer sample, has been addressed by multiple previous studies [28-35] and is not discussed in detail here.”
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis (2009, methodology): “The copy number data were segmented using the CBS algorithm (Olshen et al., 2004; Venkatraman et al., 2007).”
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, background): “Essentially, the algorithm recursively localizes the breakpoints by changing genomic positions until the chromosomes are divided into segments with equal copy numbers that are significantly different from the copy numbers from their adjacent genomic regions [37].”
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma (2017, neutral): “…Dobin et al., 2013 PMID: 23104886 Copy number estimation - Birdseed Korn et al., 2008 PMID: 18776909 Copy number analysis – Circular Binary Segmentation Olshen et al., 2004 PMID: 15475419 Significant focal copy number change – GISTIC 2.0 Mermel et al., 2011 PMID: 21527027 Purity, ploidy, genome…”
A SIMPLE BAYESIAN APPROACH TO MULTIPLE CHANGE-POINTS (2011, methodology): “Zhang and Siegmund (2006) propose to approximate ln(k) by using the circular binary segmentation procedure of Olshen et al. (2004) to determine the maximizer (t1, . . . tk) in (4.6).”
A simple new approach to variable selection in regression, with application to genetic fine mapping (2018, methodology): “Software packages in R that can be used for detecting change points include changepoint (Killick and Eckley, 2014), DNAcopy (Seshan and Olshen, 2018; Olshen et al., 2004), bcp (Erdman and Emerson, 2007) and genlasso (Tibshirani, 2014; Arnold and Tibshirani, 2016); see Killick and Eckley (2014) for a”
A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets (2012, methodology): “Step 2) Segmentation: Copy number segmentation data was produced using the Circular Binary Segmentation (CBS) algorithm using the R package DNAcopy [1] for both tumor and normal gastric samples.”