ArticleJournal of bioinformatics and systems biology : Open access2023
NMF Clustering: Accessible NMF-based Clustering Utilizing GPU Acceleration.
Article in Journal of bioinformatics and systems biology : Open access, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed.
- From paradox to target: IFN-β hijacks MEK signaling to drive a cell death-evading dormant phenotype in colorectal cancer.Journal of experimental & clinical cancer research : CR · 2026Article
- Molecular classification of primary Sjögren's syndrome based on salivary gland omics.Arthritis research & therapy · 2026Article
- Machine learning assists regulated cell death crucial biomarker selection in adenocarcinoma of the lung: biological data testing and cell assay determination.Discover oncology · 2025Article
- Multiple machine learning algorithms identify 13 types of cell death-critical genes in large and multiple non-alcoholic steatohepatitis cohorts.Lipids in health and disease · 2025Article
- Regulation of Inflammation, Lipid Metabolism, and Liver Fibrosis by Core Genes of M1 Macrophages in NASH.Journal of inflammation research · 2024Article
- COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Non-negative Matrix Factorization (NMF) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using CuPy, a GPU backed python library, and the Message Passing Interface (MPI). This reduces the computation time by up to three orders of magnitude and makes the NMF Clustering analysis of large RNA-Seq and scRNA-seq datasets practical. We have made the method freely available through the GenePattern gateway, which provides free public access to hundreds of tools for the analysis and visualization of multiple 'omic data types. Its web-based interface gives easy access to these tools and allows the creation of multi-step analysis pipelines on high performance computing (HPC) clusters that enable reproducible
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What OpenQuestion holds
Registered trials
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.