Zobrazeno 1 - 10
of 153
pro vyhledávání: '"Joshua D, Campbell"'
Autor:
Irzam Sarfraz, Yichen Wang, Amulya Shastry, Wei Kheng Teh, Artem Sokolov, Brian R. Herb, Heather H. Creasy, Isaac Virshup, Ruben Dries, Kylee Degatano, Anup Mahurkar, Daniel J. Schnell, Pedro Madrigal, Jason Hilton, Nils Gehlenborg, Timothy Tickle, Joshua D. Campbell
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-15 (2024)
Abstract Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen and experimental information is often captured, detailed metadata standards related to data matr
Externí odkaz:
https://doaj.org/article/878df33f65034434a42db96816edbe92
Autor:
Nicholas K. O’Neill, Thor D. Stein, Junming Hu, Habbiburr Rehman, Joshua D. Campbell, Masanao Yajima, Xiaoling Zhang, Lindsay A. Farrer
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-16 (2023)
Abstract Background Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequen
Externí odkaz:
https://doaj.org/article/5a782d5b442d41b5ab02fe13b0f301c3
Autor:
Ana B. Pavel, Carly Garrison, Lingqi Luo, Gang Liu, Daniel Taub, Ji Xiao, Brenda Juan-Guardela, John Tedrow, Yuriy O. Alekseyev, Ivana V. Yang, Mark W. Geraci, Frank Sciurba, David A. Schwartz, Naftali Kaminski, Jennifer Beane, Avrum Spira, Marc E. Lenburg, Joshua D. Campbell
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-14 (2023)
Abstract Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miR
Externí odkaz:
https://doaj.org/article/3ab462eb96c1423b8efb64bcedd52c26
Autor:
Ke Xu, Xingyi Shi, Christopher Husted, Rui Hong, Yichen Wang, Boting Ning, Travis B. Sullivan, Kimberly M. Rieger-Christ, Fenghai Duan, Helga Marques, Adam C. Gower, Xiaohui Xiao, Hanqiao Liu, Gang Liu, Grant Duclos, Michael Platt, Avrum E. Spira, Sarah A. Mazzilli, Ehab Billatos, Marc E. Lenburg, Joshua D. Campbell, Jennifer E. Beane
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-11 (2022)
Abstract SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compa
Externí odkaz:
https://doaj.org/article/ba234dab333940e49f16b1217758cc45
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:
Marc A. Vittoria, Nathan Kingston, Kristyna Kotynkova, Eric Xia, Rui Hong, Lee Huang, Shayna McDonald, Andrew Tilston-Lunel, Revati Darp, Joshua D. Campbell, Deborah Lang, Xiaowei Xu, Craig J. Ceol, Xaralabos Varelas, Neil J. Ganem
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-17 (2022)
Activating mutations of BRAF alone are inadequate to drive melanoma formation. Here the authors show that activation of Hippo signalling by oncogenic BRAF represents an additional safeguard to limit BRAF-dependent human melanocyte growth and melanoma
Externí odkaz:
https://doaj.org/article/f742ba331c9e4c36a7f1fe1c4bdef362
Autor:
Kim Vanuytsel, Carlos Villacorta-Martin, Jonathan Lindstrom-Vautrin, Zhe Wang, Wilfredo F. Garcia-Beltran, Vladimir Vrbanac, Dylan Parsons, Evan C. Lam, Taylor M. Matte, Todd W. Dowrey, Sara S. Kumar, Mengze Li, Feiya Wang, Anthony K. Yeung, Gustavo Mostoslavsky, Ruben Dries, Joshua D. Campbell, Anna C. Belkina, Alejandro B. Balazs, George J. Murphy
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-13 (2022)
During human embryonic development, haematopoietic stem cells of the foetal liver undergo expansion, while retaining engraftment capacity. Here the authors apply CITE-seq to profile single cells from a human foetal liver, identifying a molecular sign
Externí odkaz:
https://doaj.org/article/cac11a57fa10405ca22f6fddb6df2365
Autor:
Rui Hong, Yusuke Koga, Shruthi Bandyadka, Anastasia Leshchyk, Yichen Wang, Vidya Akavoor, Xinyun Cao, Irzam Sarfraz, Zhe Wang, Salam Alabdullatif, Frederick Jansen, Masanao Yajima, W. Evan Johnson, Joshua D. Campbell
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-9 (2022)
Quality control (QC) is a crucial step in single-cell RNA-seq data analysis. Here, the authors present the SCTK-QC pipeline which generates and visualizes a comprehensive set of QC metrics to streamline the process of detecting and removing poor qual
Externí odkaz:
https://doaj.org/article/3b9c0a0a78f74f97957e4f3059d88d39
Autor:
Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, Joshua D. Campbell
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross
Externí odkaz:
https://doaj.org/article/eb723902385c482f96dc28348751ae7c
Autor:
Gang Liu, Asaf Maoz, Christopher Stevenson, Mary E Reid, Avrum Spira, Marc E Lenburg, Joshua D Campbell, Carter Merenstein, Yusuke Koga, Austin Potter, Adam C Gower, Sherry Zhang, Hanqiao Liu, Sarah A Mazzilli, Jennifer Beane
Publikováno v:
Journal for ImmunoTherapy of Cancer, Vol 9, Iss 9 (2021)
Externí odkaz:
https://doaj.org/article/1a370bde366f4973b623356a8d390ced