Copy number variations (CNV) and allelic imbalance in tumor tissue can show strong segmentation. Their graphical presentation can be enhanced by appropriate smoothing. Existing signal and scatterplot smoothers do not respect segmentation well. We present novel algorithms that use a penalty on the L(0) norm of differences of neighboring values. Visualization is our main goal, but we compare classification performance to that of VEGA.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367998 | PMC |
| http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038230 | PLOS |
Publication Analysis
Top Keywords
Similar Publications
Development and evaluation of patient-centred polygenic risk score reports for glaucoma screening.
BMC Med Genomics
January 2025
Department of Ophthalmology, Flinders Medical and Health Research Institute, Flinders University, Adelaide, SA, Australia.
Background: Polygenic risk scores (PRS), which provide an individual probabilistic estimate of genetic susceptibility to develop a disease, have shown effective risk stratification for glaucoma onset. However, there is limited best practice evidence for reporting PRS and patient-friendly reports for communicating PRS effectively are lacking. Here we developed patient-centred PRS reports for glaucoma screening based on the literature, and evaluated them with participants using a qualitative research approach.
View Article and Find Full Text PDFLonger recreational screen time contributes to the risk of age-related macular degeneration: a UK Biobank cohort study and two-sample Mendelian randomisation.
J Glob Health
January 2025
Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Background: Recreational screen time (RST) has been found to be associated with cognitive decline and neurodegenerative diseases. However, the association between RST and age-related macular degeneration (AMD), an ocular neurodegenerative disease, is still unclear. We aimed to elucidate the association between RST and AMD.
View Article and Find Full Text PDFAutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment.
PLoS One
January 2025
Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy.
Plant viruses pose a significant threat to global agriculture and require efficient tools for their timely detection. We present AutoPVPrimer, an innovative pipeline that integrates artificial intelligence (AI) and machine learning to accelerate the development of plant virus primers. The pipeline uses Biopython to automatically retrieve different genomic sequences from the NCBI database to increase the robustness of the subsequent primer design.
View Article and Find Full Text PDFABCA4 Deep Intronic Variants Contributed to Nearly Half of Unsolved Stargardt Cases With a Milder Phenotype.
Invest Ophthalmol Vis Sci
January 2025
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Purpose: The purpose of this study was to investigate the contribution and natural progression of ABCA4 deep intronic variants (DIVs) among a Chinese Stargardt disease (STGD) cohort.
Methods: For unsolved STGD probands, DIVs in ABCA4 were detected by next-generation sequencing, and splicing effects were evaluated by in silico tools and validated through minigene experiments. Comprehensive ocular examinations, especially fundus changes, were carried out and analyzed.
Exploring the plant lipidome: techniques, challenges, and prospects.
Adv Biotechnol (Singap)
March 2024
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
Plant lipids are a diverse group of biomolecules that play essential roles in plant architecture, physiology, and signaling. To advance our understanding of plant biology and facilitate innovations in plant-based product development, we must have precise methods for the comprehensive analysis of plant lipids. Here, we present a comprehensive overview of current research investigating plant lipids, including their structures, metabolism, and functions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!