ArticlebioRxiv : the preprint server for biology2025
A knowledge-guided approach to recovering important rare signals from high-dimensional single-cell data.
Zhenghao Zhang, Jiamin Chen, Haoran Wu, Kelly Yichen Li, Peter D Adams, Pamela Itkin-Ansari, Kevin Y Yip
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
7 authors.
Zhenghao ZhangDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.ORCID 0000-0001-7866-1106 Jiamin ChenDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Haoran WuSchool of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Kelly Yichen LiCenter for Data Science and Artificial Intelligence, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.ORCID 0000-0001-7377-5729 Peter D AdamsCancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-0684-1770 Pamela Itkin-AnsariDevelopment, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Kevin Y YipDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.ORCID 0000-0001-5516-9944 Funding
Tumor Microenvironment and Cancer ImmunologyP30CA030199 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Michael Jackson · 1985 to 2026
$107.2MSpatial Mapping Senescent Cells Across the Mouse Lifespan by Multiplex Transcriptomics and EpigenomicsU54AG079758 · NIA · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI PETER D. ADAMS · 2022 to 2026
$12.1MRewiring T cell exhaustion with immune checkpoint blockade therapyR01CA287114 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Linda Mac Pherson Bradley · 2024 to 2026
$3.4MNovel Neuroprotective Roles for the Alzheimer's Disease Risk Gene SORLA in Tau Pathology and PathogenesisR01AG085498 · NIA · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Timothy Yikai Huang · 2024 to 2026
$2.6MA knowledge-guided analysis approach to recovering rare signals from single-cell transcriptomic dataR21GM159319 · NIGMS · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI YIP, YUK-LAP KEVIN · 2025 to 2025
$536kNCI NIH HHS P30 CA030199NCI NIH HHS R01 CA287114NIA NIH HHS R01 AG085498NIA NIH HHS U54 AG079758NIGMS NIH HHS R21 GM159319
6 · The paper itselfAbstract
Single-cell transcriptomic data are high-dimensional, with many genes profiled in each cell. Dimensionality reduction is routinely applied to improve interpretability, remove noise and redundancy, and enable visualization. Most existing methods aim at preserving the most prominent data properties, which can lead to omission of rare but important signals. Here we propose a novel framework that uses knowledge-derived genes of interest to guide dimensionality reduction, which can help cluster rare cells and separate highly similar cell sub-populations. We demonstrate the utility of our framework in identifying endocrine cell subtypes in the pancreatic islet, highly similar hematopoietic sub-populations, and rare senescent cells.
Identifiers
PMID41256547
PMCPMC12621906
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