Greehey CCRI Archives
Patterns: shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning (Chen lab, et al)
February 20, 2024Li-Ju Wang 1, Michael Ning 1, Tapsya Nayak 2, Michael J. Kasper 1, Satdarshan P. Monga 3 4 5, Yufei Huang 5 6 7 8, Yidong Chen 2 9, Yu-Chiao Chiu 1 4 5 10 Show more Highlights shinyDeepDR is a web tool for predicting responses to 265 anti-cancer compou …
Nature Communications: Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset (Chen, Zheng)
February 8, 2024Yi Xu, Michael H. Nipper, Angel A. Dominguez, Zhenqing Ye, Naoki Akanuma, Kevin Lopez, Janice J. Deng, Destiny Arenas, Ava Sanchez, Francis E. Sharkey, Colin M. Court, Aatur D. Singhi, Huamin Wang, Martin E. Fernandez-Zapico, Lu-Zhe Sun, Siyuan Zheng, …
IScience: Comprehensive Characterization of Patient-Derived Xenograft Models of Pediatric Leukemia (Houghton, Grimes, Lai, Chen, Zheng, Kurmasheva, & Tomlinson Labs)
December 6, 2023Anna Rogojina 1 12, Laura, J. Klesse 2 3 4 12, Erin Butler 2 3 4 12, Jiwoong Kim 5, He Zhang 5, Xue Xiao 5, Lei Guo 5, Qinbo Zhou 5, Taylor Hartshorne 2, Dawn Garcia 1, Korri Weldon 1, Trevor Holland 1, Abhik Bandyopadhyay 1, Luz Perez Prado 1, Shidan …
Cold Spring Harbor, Spatial-Live: A lightweight and versatile tool for single cell spatial-omics data visualization (Chen, Zheng, Lai)
December 5, 2023Zhenqing Ye, Zhao Lai, Siyuan Zheng, Yidong Chen Abstract Single-cell spatial-omics data visualization plays a pivotal role in unraveling the intricate spatial organization and heterogeneity of cellular systems. Although various software tools and pack …
Nature Communications: Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer (Zheng, Grimes, Lai, Chen, Wang, Tomlinson, Houghton, & Kurmasheva Labs)
November 27, 2023Funan He, Abhik M. Bandyopadhyay, Laura J. Klesse, Anna Rogojina, Sang H. Chun, Erin Butler, Taylor Hartshorne, Trevor Holland, Dawn Garcia, Korri Weldon, Luz-Nereida Perez Prado, Anne-Marie Langevin, Allison C. Grimes, Aaron Sugalski, Shafqat Shah, Ch …
Embro Reports: Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping (Chen)
September 5, 2023Abstract Bromodomain-containing protein 4 (BRD4) is overexpressed and functionally implicated in various myeloid malignancies. However, the role of BRD4 in normal hematopoiesis remains largely unknown. Here, utilizing an inducible Brd4 knockout mouse m …
Science Reports: Sex-dependent differences in the genomic profile of lingual sensory neurons in naïve and tongue-tumor bearing mice (Chen, Lai)
August 14, 2023Tarek Ibrahim, Ping Wu, Li-Ju Wang, Chang Fang-Mei, Josue Murillo, Jaclyn Merlo, Sergey S. Shein, Alexei V. Tumanov, Zhao Lai, Korri Weldon, Yidong Chen & Shivani Ruparel Abstract Mechanisms of sex-dependent orofacial pain are widely understudied. …
Bioinformatics Advances: DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer (Zheng, Houghton, & Chen Labs)
June 27, 2023Tapsya Nayak, Li-Ju Wang, Michael Ning, Gabriela Rubannelsonkumar, Eric Jin, Siyuan Zheng, Peter J Houghton, Yufei Huang, Yu-Chiao Chiu, Yidong Chen Abstract Motivation Large-scale genetic and pharmacologic dependency maps are generated to reveal genet …
ELife: Defining function of wild-type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma (Ignatius Lab, Houghton Lab, Libich Lab, Chen, Tomlinson)
June 2, 2023Jiangfei Chen Kunal Baxi Amanda E Lipsitt Nicole Rae Hensch Long Wang Prethish Sreenivas Paulomi Modi Xiang Ru Zhao Antoine Baudin Daniel G Robledo Abhik Bandyopadhyay Aaron Sugalski Anil K Challa Dias Kurmashev Andrea R Gilbert Gail E Tomlinson Peter …
Clinical Cancer Research: Phase II Investigation of TVB-2640 (Denifanstat)with Bevacizumabin Patients with First Relapse High-Grade Astrocytoma (Chen)
May 24, 2023William Kelly 1, Adolfo Enrique Diaz Duque 1,Joel Michalek 2, Brandon Konkel 3,L aura Caflisch 3, Yidong Chen 2,Sarath Chand Pathuri 1,Vinu Madhusudanannair-Kunnuparampil 4, John Floyd II 5,and Andrew Brenner 1 ABSTRACT Purpose: Glioblastoma represents …
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