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Xiaoqing Yu
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Journal Articles

spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis

Oscar E. Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Y. Tsai, Joseph Markowitz, Mariam L. Khaled, Ethan Vallebuona, Anders E. Berglund, Steven A. Eschrich, Xiaoqing Yu, Brooke L. Fridley
Journal: Cancer Research
Cancer Res (2025) 85 (5): 848–858.
https://doi.org/10.1158/0008-5472.CAN-24-2346
Published: 03 March 2025
View article titled, spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis
Open the PDF for spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis in another window
Includes: Supplementary data
Journal Articles

Abstract 876: spatialGE: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics

Oscar Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Tsai, Joseph Markowitz, Anders Berglund, Xiaoqing Yu, Brooke L. Fridley
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 876.
https://doi.org/10.1158/1538-7445.AM2024-876
Published: 22 March 2024
View article titled, Abstract 876: <em>spatialGE</em>: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics
Journal Articles

Abstract 3886: Analysis of clonal heterogeneity within paired primary and metastatic tumor samples of patients with solid tumors and implications for neoantigen-based personalized cancer vaccines

Alyssa Obermayer, Timothy Shaw, Darwin Chang, Joshua Davis, Jamie K. Teer, Xiaoqing Yu, Xuefeng Wang, Dale Hedges, Aik Choon Tan, Robert Rounbehler, Abdul Rafeh Naqash, Margaret Gatti-Mays, Aakrosh Ratan, Martin McCarter, Howard Colman, Igor Puzanov, Susanne Arnold, Michelle Churchman, Patrick Hwu, William Dalton, George Weiner, Jose Conejo-Garcia, Paulo C. Rodriguez, Bodour Salhia, Ahmad A. Tarhini
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 3886.
https://doi.org/10.1158/1538-7445.AM2024-3886
Published: 22 March 2024
View article titled, Abstract 3886: Analysis of clonal heterogeneity within paired primary and metastatic tumor samples of patients with solid tumors and implications for neoantigen-based personalized cancer vaccines
Journal Articles

Abstract 6245: Missed opportunity at the subcellular level: Enhancing the utility of cellular imaging modality in spatial transcriptomic profiling of tumor tissues

Xiaofei Song, Xiaoqing Yu, Carlos M. Moran-Segura, G Daniel Grass, Roger Li, Xuefeng Wang
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 6245.
https://doi.org/10.1158/1538-7445.AM2024-6245
Published: 22 March 2024
View article titled, Abstract 6245: Missed opportunity at the subcellular level: Enhancing the utility of cellular imaging modality in spatial transcriptomic profiling of tumor tissues
Journal Articles

Abstract 3557: A pancancer gamma delta T cell repertoire atlas

Xiaoqing Yu, Song Li, Ling Cen, Xuefeng Wang
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 3557.
https://doi.org/10.1158/1538-7445.AM2024-3557
Published: 22 March 2024
View article titled, Abstract 3557: A pancancer gamma delta T cell repertoire atlas
Journal Articles

Abstract A004: Patterns of lncRNA-regulated gene expression in high-grade serous ovarian carcinomas

Brett M. Reid, Ann Chen, Zhihua Chen, Florian A. Karreth, Peter Kanetsky, Jennifer B. Permuth, Ozlen Saglam, Jamie K. Teer, Xiaoqing Yu, Simon Gayther, Ellen Goode, Paul Pharoah, Thomas A. Sellers, Kate Lawrenson, Jonathan Tyrer
Journal: Cancer Research
Cancer Res (2024) 84 (5_Supplement_2): A004.
https://doi.org/10.1158/1538-7445.OVARIAN23-A004
Published: 04 March 2024
View article titled, Abstract A004: Patterns of lncRNA-regulated gene expression in high-grade serous ovarian carcinomas
Journal Articles

Abstract CT103: A phase 1 first-in-human study of MEM-288 oncolytic virus in solid tumors including non-small cell lung cancer (NSCLC): impact on tumor and systemic T cell immunity

Andreas N. Saltos, Christy Arrowood, Georgia Beasley, James Ronald, Ghassan El-Haddad, Uzma Khan, Luiziane Guerra-Guevara, Steven Wolf, Lin Gu, Xiaofei F. Wang, Dana Foresman, Xiaoqing Yu, Mark J. Cantwell, Scott J. Antonia, Amer A. Beg, Neal E. Ready
Journal: Cancer Research
Cancer Res (2023) 83 (8_Supplement): CT103.
https://doi.org/10.1158/1538-7445.AM2023-CT103
Published: 14 April 2023
View article titled, Abstract CT103: A phase 1 first-in-human study of MEM-288 oncolytic virus in solid tumors including non-small cell lung cancer (NSCLC): impact on tumor and systemic T cell immunity
Journal Articles

Abstract 3264: Sotorasib, a selective G12C K-RAS inhibitor, modulates the tumor microenvironment to promote TNFα and IFNγ signaling and augment immunotherapy response

Mohammed L. Ibrahim, Dana Foresman, Hong Zheng, Eric B. Haura, Daniel Abate-Daga, Xiaoqing Yu, Amer A. Beg
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3264.
https://doi.org/10.1158/1538-7445.AM2023-3264
Published: 04 April 2023
View article titled, Abstract 3264: Sotorasib, a selective G12C K-RAS inhibitor, modulates the tumor microenvironment to promote TNFα and IFNγ signaling and augment immunotherapy response
Journal Articles

Abstract 3312: Comparison of risk factors to molecular risk stratification in Chinese early-stage non-squamous non-small cell lung cancer patients

Naixin Liang, Jianchao Xue, Ming Zhao, Bowen Li, Yadong Wang, Zhicheng Huang, Yankai Xia, Ruirui Li, Zhongxing Bing, Zhibo Zheng, Jianpeng Zhang, Bin Wang, Zhe Feng, Xinyu Liu, Haochen Li, Xiaoqing Yu, Yang Song
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3312.
https://doi.org/10.1158/1538-7445.AM2023-3312
Published: 04 April 2023
View article titled, Abstract 3312: Comparison of risk factors to molecular risk stratification in Chinese early-stage non-squamous non-small cell lung cancer patients
Journal Articles

Abstract 621: Aging dampens lymphoma-provoked phenotypic and epigenomic changes to the adaptive immune system

Rebecca S. Hesterberg, Chia-Ho Cheng, Jiqiang Yao, Xiaofei Song, Xiaoqing Yu, John L. Cleveland
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 621.
https://doi.org/10.1158/1538-7445.AM2023-621
Published: 04 April 2023
View article titled, Abstract 621: Aging dampens lymphoma-provoked phenotypic and epigenomic changes to the adaptive immune system
Journal Articles

Abstract 6065: Patterns of dysregulated coding and noncoding gene expression in high-grade serous ovarian carcinomas

Brett M. Reid, Ann Chen, Zhihua Chen, Florian A. Karreth, Peter Kanetsky, Jennifer B. Permuth, Ozlen Saglam, Jamie Teer, Xiaoqing Yu, Simon Gayther, Ellen Goode, Paul Pharoah, Thomas A. Sellers, Kate Lawrenson
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6065.
https://doi.org/10.1158/1538-7445.AM2023-6065
Published: 04 April 2023
View article titled, Abstract 6065: Patterns of dysregulated coding and noncoding gene expression in high-grade serous ovarian carcinomas
Journal Articles

Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis

Xiaonan Xu, Kaizhen Wang, Olga Vera, Akanksha Verma, Neel Jasani, Ilah Bok, Olivier Elemento, Dongliang Du, Xiaoqing Yu, Florian A. Karreth
Journal: Cancer Research
Cancer Res (2022) 82 (17): 3016–3031.
https://doi.org/10.1158/0008-5472.CAN-22-0283
Published: 02 September 2022
View article titled, Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis
Open the PDF for Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis in another window
Includes: Supplementary data
Journal Articles

Abstract 3542: Oncolytic adenovirus encoding transgenes for IFN-beta and recombinant CD40 ligand promotes conventional dendritic cell activation and trafficking with enhanced tumor infiltrating lymphocytes for effective cancer immunotherapy

Hong Zheng, Scott Antonia, Mark J. Cantwell, Xiaoqing Yu, Amer A. Beg
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 3542.
https://doi.org/10.1158/1538-7445.AM2022-3542
Published: 15 June 2022
View article titled, Abstract 3542: Oncolytic adenovirus encoding transgenes for IFN-beta and recombinant CD40 ligand promotes conventional dendritic cell activation and trafficking with enhanced tumor infiltrating lymphocytes for effective cancer immunotherapy
Journal Articles

Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures

Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy I. Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Journal: Cancer Research
Cancer Res (2022) 82 (9): 1724–1735.
https://doi.org/10.1158/0008-5472.CAN-21-3113
Published: 03 May 2022
View article titled, Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures
Open the PDF for Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures in another window
Includes: Supplementary data
Journal Articles

IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer

Gunjan Mandal, Subir Biswas, Carmen M. Anadon, Xiaoqing Yu, Chandler D. Gatenbee, Sandhya Prabhakaran, Kyle K. Payne, Ricardo A. Chaurio, Alexandra Martin, Patrick Innamarato, Carlos Moran, John J. Powers, Carly M. Harro, Jessica A. Mine, Kimberly B. Sprenger, Kristen E. Rigolizzo, Xuefeng Wang, Tyler J. Curiel, Paulo C. Rodriguez, Alexander R. Anderson, Ozlen Saglam, Jose R. Conejo-Garcia
Journal: Cancer Research
Cancer Res (2022) 82 (5): 859–871.
https://doi.org/10.1158/0008-5472.CAN-21-2376
Published: 03 March 2022
View article titled, IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer
Open the PDF for IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer in another window
Includes: Supplementary data
Journal Articles

Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer

Asmaa El-Kenawi, William Dominguez-Viqueira, Min Liu, Shivanshu Awasthi, Julieta Abraham-Miranda, Aysenur Keske, KayLee K. Steiner, Leenil Noel, Amparo N. Serna, Jasreman Dhillon, Robert J. Gillies, Xiaoqing Yu, John M. Koomen, Kosj Yamoah, Robert A. Gatenby, Brian Ruffell
Journal: Cancer Research
Cancer Res (2021) 81 (21): 5477–5490.
https://doi.org/10.1158/0008-5472.CAN-20-4028
Published: 01 November 2021
View article titled, Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer
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Includes: Supplementary data
Journal Articles

Abstract 734: Macrophage tumor cell metabolic interactions induce therapeutic resistance in prostate cancer

Asmaa El-Kenawi, William Dominguez Viqueira, Min Liu, Shivanshu Awasthi, Jasreman Dhillon, Kosj Yamoah, Xiaoqing Yu, John Koomen, Robert Gatenby, Brian Ruffell
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 734.
https://doi.org/10.1158/1538-7445.AM2021-734
Published: 01 July 2021
View article titled, Abstract 734: Macrophage tumor cell metabolic interactions induce therapeutic resistance in prostate cancer
Journal Articles

Abstract 4974: Germline prognostic SNPs and tumor-immunity-specific expression QTL (tis-eQTL) in cancer

Xiaoqing Yu, Xuefeng Wang
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 4974.
https://doi.org/10.1158/1538-7445.AM2019-4974
Published: 01 July 2019
View article titled, Abstract 4974: Germline prognostic SNPs and tumor-immunity-specific expression QTL (tis-eQTL) in cancer
Journal Articles

Targeting LUNX Inhibits Non–Small Cell Lung Cancer Growth and Metastasis

Xiaohu Zheng, Min Cheng, Binqing Fu, Xiaolei Fan, Qing Wang, Xiaoqing Yu, Rui Sun, Zhigang Tian, Haiming Wei
Journal: Cancer Research
Cancer Res (2015) 75 (6): 1080–1090.
https://doi.org/10.1158/0008-5472.CAN-14-1831
Published: 12 March 2015
View article titled, Targeting LUNX Inhibits Non–Small Cell Lung Cancer Growth and Metastasis
Open the PDF for Targeting LUNX Inhibits Non–Small Cell Lung Cancer Growth and Metastasis in another window
Includes: Supplementary data
Journal Articles

Expression of c-Jun oncoprotein in androgen depletion independent prostate cancer

Guangzhou Han, Xiaoqing Yu, Brent W. Sutherland, Norman M. Greenberg
Journal: Cancer Research
Cancer Res (2006) 66 (8_Supplement): 23.
Published: 15 April 2006
View article titled, Expression of c-Jun oncoprotein in androgen depletion independent prostate cancer