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Articles by D. Branch
Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells
Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells Tan-Yun Cheng, T. Praveena, Srinath Govindarajan, +8 , Catarina F. Almeida https://orcid.org/0000-0002-3393-4411, Daniel G. Pellicci, Wellington C. Arkins https://orcid.org/0009-0009-3511-7149, Ildiko Van Rhijn https://orcid.org/0000-0002-1446-5701, Koen Venken https://orcid.org/0000-0002-4950-386X, Dirk Elewaut https://orcid.org/0000-0002-7468-974X, Dale I.
Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics - Nature Biotechnology
Abstract As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes, such as clinical phenotypes. Current statistical approaches typically map cells to clusters and then assess differences in cluster abundance. Here we present co-varying neighborhood analysis (CNA), an unbiased method to identify associated cell populations with greater flexibility than cluster-based approaches.
Efficient and precise single-cell reference atlas mapping with Symphony - Nature Communications
Abstract Recent advances in single-cell technologies and integration algorithms make it possible to construct comprehensive reference atlases encompassing many donors, studies, disease states, and sequencing platforms. Much like mapping sequencing reads to a reference genome, it is essential to be able to map query cells onto complex, multimillion-cell reference atlases to rapidly identify relevant cell states and phenotypes.
CD1a selectively captures endogenous cellular lipids that broadly block T cell response
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CD1b-mycolic acid tetramers demonstrate T- cell fine specificity for mycobacterial lipid tails
Mycobacterium tuberculosis synthesizes a thick cell wall comprised of mycolic acids (MA), which are foreign antigens for human T cells. T-cell clones from multiple donors were used to determine the fine-specificity of MA recognition by human ?? T cells. Most CD1-presented lipid antigens contain large hydrophilic head groups comprised of carbohydrates or peptides that dominate patterns of T-cell specificity. MA diverges from the consensus antigen motif in that it lacks a head group.
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