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Articles by Yiing Lin
Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) - Nature Cell Biology
Correction to: Nature Cell Biology https://doi.org/10.1038/s41556-023-01194-w. Published online 19 July 2023. In the version of this article originally published, the name of Tianyang Xu was misspelled as Tiangyang Xu. The name has been corrected in the HTML and PDF versions of the article. About this article Jain, S., Pei, L., Spraggins, J.M. et al. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol (2024).
Organization of the human intestine at single-cell resolution - Nature
Abstract The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function.
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) - Nature Cell Biology
Data types, organs and technologies Since the second quarter of 2023, HuBMAP datasets using 18 different analytical technologies or assay types have been publicly available (Figs. 1a and 2). These encompass 1,672 publicly available datasets from regions with no histopathologic abnormality from 14 organs across 180 donors. Protocols were optimized to minimize the ischaemia time of healthy donors. All published data are freely available via the HuBMAP portal (https://portal.hubmapconsortium.org).
Segmentation of human functional tissue units in support of a Human Reference Atlas - Communications Biology
Data preparation For the “HuBMAP – Hacking the Kidney” Kaggle competition, a dataset was compiled comprising 30 Periodic acid-Schiff (PAS) stain whole slide images (WSIs) with 7102 segmented renal glomeruli (see Supplementary Table 3 and “Methods”). To determine if algorithms generalize to other FTU types, a second dataset was compiled comprising seven colon hematoxylin and eosin (H&E) stain WSIs with 395 segmented colonic crypts (see Supplementary Table 4 and “Methods”).
Circulating exosomes from brain death and cardiac death donors have distinct molecular and immunologic properties: A pilot study
ORIGINAL ARTICLE Ranjithkumar Ravichandran and Yoshihiro Itabashi contributed equally. Thalachallour Mohanakumar and William C. Chapman are co-senior authors. Abstract Background and aims Comparison of donation after brain death (DBD) and donation after cardiac death (DCD) lung tissue before transplantation have demonstrated activation of pro-inflammatory cytokine pathway in DBD donors.
Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer - Nature Communications
Abstract Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools (www.regtools.org), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing.
Mitochondrial Autophagy in Ischemic Aged Livers
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Cutting Edge: Human CD49e− NK Cells Are Tissue Resident in the Liver
Cutting Edge: Human CD49e? NK Cells Are Tissue Resident in the Liver Han Xian Aw Yeang, Sytse J. Piersma, Yiing Lin, Liping Yang, Olga N. Malkova, Cathrine Miner, Alexander S. Krupnick, William C. Chapman, Wayne M. Yokoyama The Journal of Immunology February 15, 2017, 198 (4) 1417-1422; DOI: 10.4049/jimmunol.1601818
Cutting Edge: Human CD49e− NK Cells Are Tissue Resident in the Liver
Cutting Edge: Human CD49e? NK Cells Are Tissue Resident in the Liver Han Xian Aw Yeang, Sytse J. Piersma, Yiing Lin, Liping Yang, Olga N. Malkova, Cathrine Miner, Alexander S. Krupnick, William C. Chapman, Wayne M. Yokoyama The Journal of Immunology January 16, 2017, 1601818; DOI: 10.4049/jimmunol.1601818
Human liver contains two populations of NK cells based on CD49e expression
Natural killer cells are a subset of innate immune lymphocytes that can kill transformed and infected cells, and produce cytokines that modulate the host immune response. Previous studies on human NK cells have primarily characterized NK cells isolated from peripheral blood. However, studies in mice from our lab and others indicate an additional tissue-resident NK (trNK) population that does not re-circulate in contrast to conventional NK (cNK).
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