Zobrazeno 1 - 10
of 65
pro vyhledávání: '"Alan J. Simmons"'
Autor:
Jia Li, Alan J. Simmons, Caroline V. Hawkins, Sophie Chiron, Marisol A. Ramirez-Solano, Naila Tasneem, Harsimran Kaur, Yanwen Xu, Frank Revetta, Paige N. Vega, Shunxing Bao, Can Cui, Regina N. Tyree, Larry W. Raber, Anna N. Conner, Jennifer M. Pilat, Justin Jacobse, Kara M. McNamara, Margaret M. Allaman, Gabriella A. Raffa, Alain P. Gobert, Mohammad Asim, Jeremy A. Goettel, Yash A. Choksi, Dawn B. Beaulieu, Robin L. Dalal, Sara N. Horst, Baldeep S. Pabla, Yuankai Huo, Bennett A. Landman, Joseph T. Roland, Elizabeth A. Scoville, David A. Schwartz, M. Kay Washington, Yu Shyr, Keith T. Wilson, Lori A. Coburn, Ken S. Lau, Qi Liu
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-19 (2024)
Abstract Crohn’s disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identify a di
Externí odkaz:
https://doaj.org/article/0ba81d63e38741479e8c66302f19cf18
Autor:
Ela W. Contreras-Panta, Su-Hyung Lee, Yoonkyung Won, Allison E. Norlander, Alan J. Simmons, R. Stokes Peebles, Jr., Ken S. Lau, Eunyoung Choi, James R. Goldenring
Publikováno v:
Cellular and Molecular Gastroenterology and Hepatology, Vol 18, Iss 3, Pp 101366- (2024)
Background & Aims: Type 2 innate lymphoid cells (ILC2s) and interleukin-13 (IL-13) promote the onset of spasmolytic polypeptide-expressing metaplasia (SPEM) cells. However, little is known about molecular effects of IL-13 in SPEM cells. We now sought
Externí odkaz:
https://doaj.org/article/3f940af3bdcd40e5b822af7b7b0a90b6
Autor:
Deronisha Arceneaux, Zhengyi Chen, Alan J. Simmons, Cody N. Heiser, Austin N. Southard-Smith, Michael J. Brenan, Yilin Yang, Bob Chen, Yanwen Xu, Eunyoung Choi, Joshua D. Campbell, Qi Liu, Ken S. Lau
Publikováno v:
iScience, Vol 26, Iss 7, Pp 107242- (2023)
Summary: Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused by nucleic acid material released by dead and dying cells. This material is mixed into the buffer and is co-encapsulated with cells, leading to a
Externí odkaz:
https://doaj.org/article/023e2b611ee743e9a29a87c90b558a38
Autor:
Alan J. Simmons, Ken S. Lau
Publikováno v:
STAR Protocols, Vol 3, Iss 3, Pp 101570- (2022)
Summary: In droplet-based single-cell RNA-sequencing (scRNA-seq) experiments, cells, along with some of their surrounding buffer and ambient material, are encapsulated into droplets for mRNA capture and barcoding. This protocol details the steps for
Externí odkaz:
https://doaj.org/article/8c683301736c427195744722e5bb196a
Autor:
Paige N. Vega, Avlant Nilsson, Manu P. Kumar, Hiroaki Niitsu, Alan J. Simmons, James Ro, Jiawei Wang, Zhengyi Chen, Brian A. Joughin, Wei Li, Eliot T. McKinley, Qi Liu, Joseph T. Roland, M. Kay Washington, Robert J. Coffey, Douglas A. Lauffenburger, Ken S. Lau
Publikováno v:
Frontiers in Oncology, Vol 12 (2022)
The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for r
Externí odkaz:
https://doaj.org/article/6217fa8676db45dfb3ac2e1f123faa26
Autor:
Austin N. Southard-Smith, Alan J. Simmons, Bob Chen, Angela L. Jones, Marisol A. Ramirez Solano, Paige N. Vega, Cherie’ R. Scurrah, Yue Zhao, Michael J. Brenan, Jiekun Xuan, Martha J. Shrubsole, Ely B. Porter, Xi Chen, Colin J. H. Brenan, Qi Liu, Lauren N. M. Quigley, Ken S. Lau
Publikováno v:
BMC Genomics, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract Background The increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data quality. New high-throughpu
Externí odkaz:
https://doaj.org/article/85d9c14a13754f6b9a913a50e3805c93
Autor:
Jimin Min, Paige N. Vega, Amy C. Engevik, Janice A. Williams, Qing Yang, Loraine M. Patterson, Alan J. Simmons, R. Jarrett Bliton, Joshua W. Betts, Ken S. Lau, Scott T. Magness, James R. Goldenring, Eunyoung Choi
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)
How a precancerous form (dysplasia) becomes gastric cancer is unclear. Here, the authors assess the role of Kras activation in heterogenous dysplastic cells in murine stomach corpus organoids, identifying two dysplastic stem cell populations and show
Externí odkaz:
https://doaj.org/article/b7f6044c24154289a8aced09b8c59729
Autor:
Alan J. Simmons, Ken S. Lau
Publikováno v:
Molecular & Cellular Oncology, Vol 4, Iss 1 (2017)
An impediment to the understanding of cancer is the heterogeneous nature of cell populations within a tumor microenvironment. We reported a method to query protein signaling in single epithelial cells from formalin-fixed paraffin-embedded (FFPE) colo
Externí odkaz:
https://doaj.org/article/e79f073d67bf4bf39bd295505708817a
Autor:
Cody N. Heiser, Alan J. Simmons, Frank Revetta, Eliot T. McKinley, Marisol A. Ramirez-Solano, Jiawei Wang, Justin Shao, Gregory D. Ayers, Yu Wang, Sarah E. Glass, Harsimran Kaur, Andrea Rolong, Bob Chen, Paige N. Vega, Julia L. Drewes, Nabil Saleh, Simon Vandekar, Angela L. Jones, M. Kay Washington, Joseph T. Roland, Cynthia L. Sears, Qi Liu, Martha J. Shrubsole, Robert J. Coffey, Ken S. Lau
Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Leveraging spatial molecular information to construct a phylogeographic map of tumor evolution can reveal individualize
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f125eec2cdb2d01b8f5b8cc75194818e
https://doi.org/10.1101/2023.03.09.530832
https://doi.org/10.1101/2023.03.09.530832
Autor:
Qi Liu, Charles A Herring, Quanhu Sheng, Jie Ping, Alan J Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J Coffey, Yu Shyr, Ken S Lau
Publikováno v:
PLoS Biology, Vol 16, Iss 10, p e2006687 (2018)
Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for the systematic investigation of cellular diversity. As a number of computational tools have been developed to identify and visualize cell populations within a single scRNA-seq data
Externí odkaz:
https://doaj.org/article/4532c001b272488bbf12f068b3538c09