Zobrazeno 1 - 10
of 50
pro vyhledávání: '"Wenpin, Hou"'
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-21 (2023)
Abstract Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal tra
Externí odkaz:
https://doaj.org/article/16c2bac5be1b45d4a1d754a571ed624c
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-24 (2023)
Abstract When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We develo
Externí odkaz:
https://doaj.org/article/92e33beeab964fcd9a96437448ba8c77
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-30 (2020)
Abstract Background The rapid development of single-cell RNA-sequencing (scRNA-seq) technologies has led to the emergence of many methods for removing systematic technical noises, including imputation methods, which aim to address the increased spars
Externí odkaz:
https://doaj.org/article/33348cd27b4b452ea163d6f1b74a1b05
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-36 (2020)
Abstract Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing
Externí odkaz:
https://doaj.org/article/44bdb7b9b5f84dbdbd387b2d2115e42a
Autor:
Zhicheng Ji, Wenpin Hou
Publikováno v:
bioRxiv
Cell type annotation is an essential step in single-cell RNA-seq analysis. However, it is a time-consuming process that often requires expertise in collecting canonical marker genes and manually annotating cell types. Automated cell type annotation m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea29b6f3e8e763140a936eab1d76c055
https://doi.org/10.21203/rs.3.rs-2824971/v1
https://doi.org/10.21203/rs.3.rs-2824971/v1
Autor:
Richard Xu, Xiumei Hong, Christine Ladd-Acosta, Jessie P. Buckley, Giehae Choi, Guoying Wang, Wenpin Hou, Xiaobin Wang, Liming Liang, Hongkai Ji
Publikováno v:
The Journal of Nutrition.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9d771050d8caeae9e92f9e19c87b4be1
https://doi.org/10.1016/j.tjnut.2023.05.002
https://doi.org/10.1016/j.tjnut.2023.05.002
Autor:
Christina Jackson, Christopher Cherry, Sadhana Bom, Arbor G. Dykema, Elizabeth Thompson, Ming Zheng, Zhicheng Ji, Wenpin Hou, Runzhe Li, Hao Zhang, John Choi, Fausto Rodriguez, Jon Weingart, Srinivasan Yegnasubramanian, Michael Lim, Chetan Bettegowda, Jonathan Powell, Jennifer Eliesseff, Hongkai Ji, Drew Pardoll
Publikováno v:
bioRxiv
The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fc43b44ea289394d4b8ee04cedf69e34
https://europepmc.org/articles/PMC10081225/
https://europepmc.org/articles/PMC10081225/
When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We developed a dee
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a31ca4715c9dff4c35074efe7e78476e
https://doi.org/10.1101/2022.12.13.520283
https://doi.org/10.1101/2022.12.13.520283
Autor:
Arbor G. Dykema, Jiajia Zhang, Boyang Zhang, Laurene S. Cheung, Zhen Zeng, Christopher M. Cherry, Taibo Li, Justina X. Caushi, Marni Nishimoto, Sydney Connor, Zhicheng Ji, Andrew J. Munoz, Wenpin Hou, Wentao Zhan, Dipika Singh, Rufiaat Rashid, Marisa Mitchell-Flack, Sadhana Bom, Ada Tam, Nick Ionta, Yi Wang, Camille A. Sawosik, Lauren E. Tirado, Luke M. Tomasovic, Derek VanDyke, Jamie B. Spangler, Valsamo Anagnostou, Stephen Yang, Jonathan Spicer, Roni Rayes, Janis Taube, Julie R. Brahmer, Patrick M. Forde, Srinivasan Yegnasubramanian, Hongkai Ji, Drew M. Pardoll, Kellie N. Smith
Regulatory T cells (Treg) are conventionally viewed to suppress endogenous and therapyinduced anti-tumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RN
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ce42b39bf2f7a64cbf23b41e33e0bda2
https://doi.org/10.1101/2022.12.13.520329
https://doi.org/10.1101/2022.12.13.520329
Autor:
Wenpin Hou, Zhicheng Ji
Spatial transcriptomics provides a unique opportunity to study continuous biological processes in a spatial context. We developed Paella, a computational method to decompose a cell trajectory into multiple spatial sub-trajectories and identify genes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::18c1eedff375701161fed1a5caf25970
https://doi.org/10.1101/2022.09.05.506682
https://doi.org/10.1101/2022.09.05.506682