Motivation: High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.
Results: Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology.
Availability And Implementation: The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247943 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/bty430 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The basic helix-loop-helix transcription factor PpeUNE12 regulates peach ripening by promoting polyamine catabolism and anthocyanin synthesis.
Plant Physiol Biochem
January 2025
College of Horticulture, Henan Agricultural University, 218 Pingan Road, 450046, Zhengzhou, China; Henan Engineering and Technology Center for Peach Germplasm Innovation and Utilization, Zhengzhou, 450046, China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Agricultural University, Zhengzhou, 450046, China. Electronic address:
The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in various plant developmental and biological processes. However, the precise mechanisms by which bHLH TFs regulate fruit ripening warrant further investigation. Polyamine oxidase (PAO) is crucial for polyamine (PA) catabolism and plays crucial roles in fruit ripening.
View Article and Find Full Text PDFPitch-based correspondences related to abstract concepts.
Acta Psychol (Amst)
January 2025
Phonetics and speech synthesis research group, Department of Digital Humanities, Faculty of Arts, University of Helsinki, Unioninkatu 38, Helsinki, Finland. Electronic address:
Previous investigations have shown pitch-based correspondences with various perceptual and conceptual attributes. The present study reveals two novel pitch-based correspondences with highly abstract concepts. Three experiments with varying levels of implicitness of the association task showed that the concepts of future and in are associated with high-pitch sounds, while past and out are associated with low-pitch sounds.
View Article and Find Full Text PDFMelatonin protects aged oocytes from depalmitoylation-mediated quality reduction by promoting PPT1 degradation and antioxidation.
Redox Biol
January 2025
Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China; State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China; Department of Reproductive Medicine, Affiliated Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210002, China. Electronic address:
Oocyte aging is closely related to a decline in female fertility, accompanied by increased reactive oxygen species levels and changes in protein posttranslational modifications. However, the role of protein palmitoylation in oocyte aging has not been investigated. In the present study, a new association between redox and palmitoylation in aging oocytes was found.
View Article and Find Full Text PDFThe Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway.
Cell Rep
January 2025
Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:
Mutation or deletion of the deubiquitinase USP7 causes Hao-Fountain syndrome (HAFOUS), which is characterized by speech delay, intellectual disability, and aggressive behavior and highlights important unknown roles of USP7 in the nervous system. Here, we conditionally delete USP7 in glutamatergic neurons in the mouse forebrain, triggering disease-relevant phenotypes, including sensorimotor deficits, impaired cognition, and aggressive behavior. Although USP7 deletion induces p53-dependent neuronal apoptosis, most behavioral abnormalities in USP7 conditional knockout mice persist following p53 loss.
View Article and Find Full Text PDFOptimized inner ear organoids for efficient hair cell generation and ototoxicity response modeling.
Sci China Life Sci
January 2025
Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Hair cells in the mammalian cochlea are highly vulnerable to damage from drug toxicity, noise exposure, aging, and genetic mutations, with no capacity for regeneration. Progress in hair cell protection research has been limited by the scarcity of cochlear tissue and suitable in vitro models. Here, we present a novel one-step, self-organizing inner ear organoid system optimized with small molecules, which bypasses the need for multi-step expansion and forced differentiation protocols.
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!