ArticleBMC genomics2012
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers, 1 of them a synthesis that pooled it.
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Who cites it
181 citing papers in PubMed, 1 synthesis or guideline pooled it, 345 citations in OpenAlex.
- Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition.Cell · 2021Pooled it
- Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations.Genome medicine · 2018Trial
- Development of an homologous recombination deficiency scoring algorithm for unmatched ovarian tumor sample based on next-generation sequencing.Journal of gynecologic oncology · 2026Article
- GREB1-rearranged uterine tumour shares a common DNA methylation signature with ESR1-rearranged UTROSCT.Histopathology · 2026Article
- Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.Scientific reports · 2026Article
- Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types.Nature genetics · 2026Article
- PARP1 Suppression Drives ROS Resistance in Aneuploid Cancer Cells.bioRxiv : the preprint server for biology · 2026Article
- Negative Selection Maintains Grossly Altered but Broadly Stable Karyotypes in Metastatic Colorectal Cancer.Cancer discovery · 2026Article
- Analyses of the Coexpression of Lactate Metabolism- and Ferroptosis-Related Genes in Hepatocellular Carcinoma.Journal of hepatocellular carcinoma · 2026Article
- ctDNA detectability and representativeness in seven body liquids from patients with metastatic breast cancer.Nature communications · 2025Article
- CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.BMC bioinformatics · 2025Article
- Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data.Nucleic acids research · 2025Article
- RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organization.Developmental cell · 2025Article
- Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm.Cancer research · 2025Article
- Stratified Medicine Pediatrics: Cell-Free DNA and Serial Tumor Sequencing Identifies Subtype-Specific Cancer Evolution and Epigenetic States.Cancer discovery · 2025Article
- Extensive epigenomic dysregulation is a hallmark of homologous recombination deficiency in triple-negative breast cancer.International journal of cancer · 2025Article
- BCMA: An integrative and versatile database for multi-scale and multi-omics molecular atlas of breast cancer.Computational and structural biotechnology journal · 2025Article
- Article
- Uterine mesenchymal tumours harboring the KAT6B/A::KANSL1 gene fusion represent a distinct type of uterine sarcoma based on DNA methylation profiles.Virchows Archiv : an international journal of pathology · 2024Article
- CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma.NPJ genomic medicine · 2024Article
121 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number.
resultsA comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented.
conclusionsThe R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.