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Journal Articles

The Lung Cancer Autochthonous Model Gene Expression Database Enables Cross-Study Comparisons of the Transcriptomic Landscapes Across Mouse Models

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Ling Cai, Fangjiang Wu, Qinbo Zhou, Ying Gao, Bo Yao, Ralph J. DeBerardinis, George K. Acquaah-Mensah, Vassilis Aidinis, Jennifer E. Beane, Shyam Biswal, Ting Chen, Carla P. Concepcion-Crisol, Barbara M. Grüner, Deshui Jia, Robert A. Jones, Jonathan M. Kurie, Min Gyu Lee, Per Lindahl, Yonathan Lissanu, Corina Lorz, David MacPherson, Rosanna Martinelli, Pawel K. Mazur, Sarah A. Mazzilli, Shinji Mii, Herwig P. Moll, Roger A. Moorehead, Edward E. Morrisey, Sheng Rong Ng, Matthew G. Oser, Arun R. Pandiri, Charles A. Powell, Giorgio Ramadori, Mirentxu Santos, Eric L. Snyder, Rocio Sotillo, Kang-Yi Su, Tetsuro Taki, Kekoa Taparra, Phuoc T. Tran, Yifeng Xia, J. Edward van Veen, Monte M. Winslow, Guanghua Xiao, Charles M. Rudin, Trudy G. Oliver, Yang Xie, John D. Minna
Journal: Cancer Research
Cancer Res (2025) 85 (10): 1769–1783.
https://doi.org/10.1158/0008-5472.CAN-24-1607
Published: 15 May 2025
View articletitled, The Lung Cancer Autochthonous Model Gene Expression Database Enables Cross-Study Comparisons of the Transcriptomic Landscapes Across Mouse Models
Open the PDF for The Lung Cancer Autochthonous Model Gene Expression Database Enables Cross-Study Comparisons of the Transcriptomic Landscapes Across Mouse Models in another window
Includes: Supplementary data
Journal Articles

Abstract 6297: Mapping cellular interactions from spatially resolved transcriptomics data

Free
James Zhu, Yunguan Wang, Woo Yong Chang, Alicia Malewska, Fabiana Napolitano, Jeffrey C. Gahan, Nisha Unni, Min Zhao, Rongqing Yuan, Fangjiang Wu, Lauren Yue, Lei Guo, Zhuo Zhao, Danny Chen, Raquibul Hannan, Siyuan Zhang, Guanghua Xiao, Ping Mu, Ariella B. Hanker, Douglas Strand, Carlos L. Arteaga, Neil Desai, Xinlei Wang, Yang Xie, Tao Wang
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 6297.
https://doi.org/10.1158/1538-7445.AM2025-6297
Published: 21 April 2025
View articletitled, Abstract 6297: Mapping cellular interactions from spatially resolved transcriptomics data
Journal Articles

A Pan-Cancer Patient-Derived Xenograft Histology Image Repository with Genomic and Pathologic Annotations Enables Deep Learning Analysis

Open Access
Brian S. White, Xing Yi Woo, Soner Koc, Todd Sheridan, Steven B. Neuhauser, Shidan Wang, Yvonne A. Evrard, Li Chen, Ali Foroughi pour, John D. Landua, R. Jay Mashl, Sherri R. Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W. Evans, Matthew H. Bailey, Yeqing Chen, Min Xiao, Jill C. Rubinstein, Brian J. Sanderson, Michael W. Lloyd, Sergii Domanskyi, Lacey E. Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C. Fields, Jacqueline L. Mudd, Xiaowei Xu, Melinda G. Hollingshead, Shahanawaz Jiwani, Saul Acevedo, PDXNet Consortium, Brandi N. Davis-Dusenbery, Peter N. Robinson, Jeffrey A. Moscow, James H. Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Luis G. Carvajal-Carmona, Alana L. Welm, Bryan E. Welm, Ramaswamy Govindan, Shunqiang Li, Michael A. Davies, Jack A. Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T. Lewis, Carol J. Bult, Dennis A. Dean, II, Jeffrey H. Chuang
Journal: Cancer Research
Cancer Res (2024) 84 (13): 2060–2072.
https://doi.org/10.1158/0008-5472.CAN-23-1349
Published: 02 July 2024
View articletitled, A Pan-Cancer Patient-Derived Xenograft Histology Image Repository with Genomic and Pathologic Annotations Enables Deep Learning Analysis
Open the PDF for A Pan-Cancer Patient-Derived Xenograft Histology Image Repository with Genomic and Pathologic Annotations Enables Deep Learning Analysis in another window
Includes: Supplementary data
Journal Articles

Abstract 5407: A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis

Free
Brian S. White, Xing Yi Woo, Soner Koc, Todd Sheridan, Steven B. Neuhauser, Shidan Wang, Yvonne A. Evrard, John David Landua, R Jay Mashl, Sherri R. Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W. Evans, Matthew H. Bailey, Yeqing Chen, Min Xiao, Jill Rubinstein, Ali Foroughi pour, Lacey Elizabeth Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C. Fields, Jacqueline L. Mudd, Xiaowei Xu, Melinda G. Hollingshead, Shahanawaz Jiwani, PDXNet consortium, Tiffany A. Wallace, Jeffrey A. Moscow, James H. Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S. Chen, Luis G. Carvajal-Carmona, Alana L. Welm, Bryan E. Welm, Ramaswamy Govindan, Shunqiang Li, Michael A. Davies, Jack A. Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T. Lewis, Carol J. Bolt, Dennis A. Dean, Jeffrey H. Chuang
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5407.
https://doi.org/10.1158/1538-7445.AM2023-5407
Published: 04 April 2023
View articletitled, Abstract 5407: A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis
Journal Articles

Abstract 6572: A lung cancer cell line explorer

Free
Ling Cai, Luc Girard, Ralph DeBerardinis, Guanghua Xiao, John Minna, Yang Xie
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6572.
https://doi.org/10.1158/1538-7445.AM2023-6572
Published: 04 April 2023
View articletitled, Abstract 6572: A lung cancer cell line explorer
Journal Articles

Abstract 1202: A repository of PDX histology images for exploring spatial heterogeneity and cancer dynamics

Free
Brian S. White, Xingyi Woo, Soner Koc, Todd Sheridan, Steven B. Neuhauser, Akshat M. Savaliya, Lacey E. Dobrolecki, John D. Landua, Matthew H. Bailey, Maihi Fujita, Kurt W. Evans, Bingliang Fang, Junya Fujimoto, Maria Gabriela Raso, Shidan Wang, Guanghua Xiao, Yang Xie, Sherri R. Davies, Ryan C. Fields, R Jay Mashl, Jacqueline L. Mudd, Yeqing Chen, Min Xiao, Xiaowei Xu, Melinda G. Hollingshead, Shahanawaz Jiwani, PDXNet Consortium, Yvonne A. Evrard, Tiffany A. Wallace, Jeffrey A. Moscow, James H. Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S. Chen, Luis G. Carvajal-Carmona, Alana L. Welm, Bryan E. Welm, Michael T. Lewis, Ramaswamy Govindan, Li Ding, Shunqiang Li, Meenhard Herlyn, Michael A. Davies, Jack A. Roth, Funda Meric-Bernstam, Carol J. Bult, Brandi Davis-Dusenbery, Dennis A. Dean, Jeffrey H. Chuang
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1202.
https://doi.org/10.1158/1538-7445.AM2022-1202
Published: 15 June 2022
View articletitled, Abstract 1202: A repository of PDX histology images for exploring spatial heterogeneity and cancer dynamics
Journal Articles

Abstract 1208: Denoising spatial expression profiling data based on in situ position and image information

Free
Yunguan Wang, Bing Song, Shidan Wang, Mengyi Chen, Yang Xie, Guanghua Xiao, Li Wang, Tao Wang
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1208.
https://doi.org/10.1158/1538-7445.AM2022-1208
Published: 15 June 2022
View articletitled, Abstract 1208: Denoising spatial expression profiling data based on in situ position and image information
Journal Articles

Abstract 871: KYNU expression is a prognostic factor in KEAP1/STK11 co-mutated lung adenocarcinoma

Free
Ling Cai, Thomas J. Rogers, Huiyu Li, Jiyeon Kim, Yang Xie, Guanghua Xiao, John Minna, Ralph J. DeBerardinis
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 871.
https://doi.org/10.1158/1538-7445.AM2021-871
Published: 01 July 2021
View articletitled, Abstract 871: KYNU expression is a prognostic factor in KEAP1/STK11 co-mutated lung adenocarcinoma
Journal Articles

Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer

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Shidan Wang, Ruichen Rong, Donghan M. Yang, Junya Fujimoto, Shirley Yan, Ling Cai, Lin Yang, Danni Luo, Carmen Behrens, Edwin R. Parra, Bo Yao, Lin Xu, Tao Wang, Xiaowei Zhan, Ignacio I. Wistuba, John Minna, Yang Xie, Guanghua Xiao
Journal: Cancer Research
Cancer Res (2020) 80 (10): 2056–2066.
https://doi.org/10.1158/0008-5472.CAN-19-1629
Published: 15 May 2020
View articletitled, Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer
Open the PDF for Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer in another window
Includes: Supplementary data
Journal Articles

Abstract 5715: Gene body methylation and expression of SHOX2 gene are potent prognostic markers for survival in intermediate grade gliomas and renal cancers

Free
Yu-An Zhang, Yunyun Zhou, Xin Luo, Guanghua Xiao, Adi F. Gazdar
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 5715.
https://doi.org/10.1158/1538-7445.AM2017-5715
Published: 01 July 2017
View articletitled, Abstract 5715: Gene body methylation and expression of SHOX2 gene are potent prognostic markers for survival in intermediate grade gliomas and renal cancers
Journal Articles

Abstract 2965: Identification of SMARCA4/BRG1 mutation types in NSCLC cell lines and tumors

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Wei Zhang, Yibing Yao, Yunyun Zhou, Xiaotu Ma, Jingsheng Yan, Tao Wang, Luc Girard, John Minna, Guanghua Xiao, Yang Xie, Adi Gazdar
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 2965.
https://doi.org/10.1158/1538-7445.AM2015-2965
Published: 01 August 2015
View articletitled, Abstract 2965: Identification of SMARCA4/BRG1 mutation types in NSCLC cell lines and tumors
Journal Articles

Abstract 5589: Molecular signatures of in vitro drug response in lung cancer.

Free
Luc Girard, Michael Peyton, Ignacio Wistuba, Yang Xie, Rachel Greer, Milind B. Suraokar, Carmen Behrens, Guanghua Xiao, John Heymach, David A. Wheeler, Caleb F. Davis, Kenneth Huffman, David S. Shames, Kevin R. Coombes, Adi F. Gazdar, David CL Lam, David G. Beer, John D. Minna
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 5589.
https://doi.org/10.1158/1538-7445.AM2013-5589
Published: 15 April 2013
View articletitled, Abstract 5589: Molecular signatures of in vitro drug response in lung cancer.
Journal Articles

Abstract 354: Nuclear receptor expression atlas: A theragnostic targets for lung cancer patients

Free
Yangsik Jeong, Yang Xie, Guanghua Xiao, Luc Girard, Woochang Lee, Carmen Behrens, Ignacio I. Wistuba, John D. Minna, David J. Mangelsdorf
Journal: Cancer Research
Cancer Res (2011) 71 (8_Supplement): 354.
https://doi.org/10.1158/1538-7445.AM2011-354
Published: 15 April 2011
View articletitled, Abstract 354: Nuclear receptor expression atlas: A theragnostic targets for lung cancer patients
Journal Articles

The Receptor Interacting Protein 1 Inhibits p53 Induction through NF-κB Activation and Confers a Worse Prognosis in Glioblastoma

Free
Seongmi Park, Kimmo J. Hatanpaa, Yang Xie, Bruce E. Mickey, Christopher J. Madden, Jack M. Raisanen, Deepti B. Ramnarain, Guanghua Xiao, Debabrata Saha, David A. Boothman, Dawen Zhao, Robert M. Bachoo, Russell O. Pieper, Amyn A. Habib
Journal: Cancer Research
Cancer Res (2009) 69 (7): 2809–2816.
https://doi.org/10.1158/0008-5472.CAN-08-4079
Published: 01 April 2009
View articletitled, The Receptor Interacting Protein 1 Inhibits p53 Induction through NF-κB Activation and Confers a Worse Prognosis in Glioblastoma
Open the PDF for The Receptor Interacting Protein 1 Inhibits p53 Induction through NF-κB Activation and Confers a Worse Prognosis in Glioblastoma in another window
Includes: Supplementary data