Publications by authors named "Guanghua Xiao"

139 Publications

Evaluating short-term forecasting of COVID-19 cases among different epidemiological models under a Bayesian framework.

Authors:
Qiwei Li Tejasv Bedi Christoph U Lehmann Guanghua Xiao Yang Xie

Gigascience 2021 02;10(2)

Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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February 2021

MB-GAN: Microbiome Simulation via Generative Adversarial Network.

Authors:
Ruichen Rong Shuang Jiang Lin Xu Guanghua Xiao Yang Xie Dajiang J Liu Qiwei Li Xiaowei Zhan

Gigascience 2021 Feb;10(2)

University of Texas Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.

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February 2021

A deep learning-based model for screening and staging pneumoconiosis.

Authors:
Liuzhuo Zhang Ruichen Rong Qiwei Li Donghan M Yang Bo Yao Danni Luo Xiong Zhang Xianfeng Zhu Jun Luo Yongquan Liu Xinyue Yang Xiang Ji Zhidong Liu Yang Xie Yan Sha Zhimin Li Guanghua Xiao

Sci Rep 2021 Jan 26;11(1):2201. Epub 2021 Jan 26.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

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January 2021

Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherin.

Authors:
Tobias Wijshake Zhongju Zou Beibei Chen Lin Zhong Guanghua Xiao Yang Xie John G Doench Lynda Bennett Beth Levine

Proc Natl Acad Sci U S A 2021 Feb;118(5)

Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390.

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February 2021

Sorting nexin 5 mediates virus-induced autophagy and immunity.

Authors:
Xiaonan Dong Yuting Yang Zhongju Zou Yuting Zhao Bo Ci Lin Zhong Madhura Bhave Liwei Wang Yi-Chun Kuo Xiao Zang Rui Zhong Elizabeth R Aguilera R Blake Richardson Boris Simonetti John W Schoggins Julie K Pfeiffer Li Yu Xuewu Zhang Yang Xie Sandra L Schmid Guanghua Xiao Paul A Gleeson Nicholas T Ktistakis Peter J Cullen Ramnik J Xavier Beth Levine

Nature 2021 01 16;589(7842):456-461. Epub 2020 Dec 16.

Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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January 2021

eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer.

Authors:
Shruthy Suresh BeiBei Chen Jingfei Zhu Ryan J Golden Changzheng Lu Bret M Evers Nicole Novaresi Bethany Smith Xiaowei Zhan Vanessa Schmid Sojeong Jun Chelsea M Karacz Michael Peyton Lin Zhong Zhuoyu Wen Adwait Amod Sathe Chao Xing Carmen Behrens Ignacio I Wistuba Guanghua Xiao Yang Xie Yang-Xin Fu John D Minna Joshua T Mendell Kathryn A O'Donnell

Nat Cancer 2020 May 20;1(5):533-545. Epub 2020 Apr 20.

Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX.

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May 2020

Molecular differences across invasive lung adenocarcinoma morphological subgroups.

Authors:
Bo Ci Donghan M Yang Ling Cai Lin Yang Luc Girard Junya Fujimoto Ignacio I Wistuba Yang Xie John D Minna William Travis Guanghua Xiao

Transl Lung Cancer Res 2020 Aug;9(4):1029-1040

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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August 2020

The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2.

Authors:
James Zhu Jiwoong Kim Xue Xiao Yunguan Wang Danni Luo Shuang Jiang Ran Chen Lin Xu He Zhang Lenny Moise Andres H Gutierrez Anne S De Groot Guanghua Xiao John W Schoggins Xiaowei Zhan Tao Wang Yang Xie

bioRxiv 2020 Sep 4. Epub 2020 Sep 4.

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September 2020

Spatial molecular profiling: platforms, applications and analysis tools.

Authors:
Minzhe Zhang Thomas Sheffield Xiaowei Zhan Qiwei Li Donghan M Yang Yunguan Wang Shidan Wang Yang Xie Tao Wang Guanghua Xiao

Brief Bioinform 2020 Aug 6. Epub 2020 Aug 6.

Department of Population and Data Sciences at University of Texas Southwestern Medical Center.

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August 2020

HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity.

Authors:
Shuang Jiang Guanghua Xiao Andrew Y Koh Yingfei Chen Bo Yao Qiwei Li Xiaowei Zhan

Front Genet 2020 3;11:445. Epub 2020 Jun 3.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States.

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June 2020

Development of a Data Model and Data Commons for Germ Cell Tumors.

Authors:
Bo Ci Donghan M Yang Mark Krailo Caihong Xia Bo Yao Danni Luo Qinbo Zhou Guanghua Xiao Lin Xu Stephen X Skapek Matthew M Murray James F Amatruda Lindsay Klosterkemper Furqan Shaikh Cecile Faure-Conter Brice Fresneau Samuel L Volchenboum Sara Stoneham Luiz Fernando Lopes James Nicholson A Lindsay Frazier Yang Xie

JCO Clin Cancer Inform 2020 06;4:555-566

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX.

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June 2020

Bayesian multiple instance regression for modeling immunogenic neoantigens.

Authors:
Seongoh Park Xinlei Wang Johan Lim Guanghua Xiao Tianshi Lu Tao Wang

Stat Methods Med Res 2020 10 13;29(10):3032-3047. Epub 2020 May 13.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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October 2020

TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise.

Authors:
Yang Liu Phong T Nguyen Xun Wang Yuting Zhao Corbin E Meacham Zhongju Zou Bogdan Bordieanu Manuel Johanns Didier Vertommen Tobias Wijshake Herman May Guanghua Xiao Sanae Shoji-Kawata Mark H Rider Sean J Morrison Prashant Mishra Beth Levine

Nature 2020 02 12;578(7796):605-609. Epub 2020 Feb 12.

Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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February 2020

Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury.

Authors:
Yu-Hsuan Lin Shuyuan Zhang Min Zhu Tianshi Lu Kenian Chen Zhuoyu Wen Shidan Wang Guanghua Xiao Danni Luo Yuemeng Jia Lin Li Malcolm MacConmara Yujin Hoshida Amit G Singal Adam Yopp Tao Wang Hao Zhu

Gastroenterology 2020 05 20;158(6):1698-1712.e14. Epub 2020 Jan 20.

Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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May 2020

Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets.

Authors:
Minzhe Zhang Tao Wang Guanghua Xiao Yang Xie

Genes (Basel) 2020 01 3;11(1). Epub 2020 Jan 3.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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January 2020

Interaction between the autophagy protein Beclin 1 and Na+,K+-ATPase during starvation, exercise, and ischemia.

Authors:
Álvaro F Fernández Yang Liu Vanessa Ginet Mingjun Shi Jihoon Nah Zhongju Zou Anwu Zhou Bruce A Posner Guanghua Xiao Marion Tanguy Valérie Paradis Junichi Sadoshima Pierre-Emmanuel Rautou Julien Puyal Ming Chang Hu Beth Levine

JCI Insight 2020 01 16;5(1). Epub 2020 Jan 16.

Center for Autophagy Research.

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January 2020

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.

Authors:
Jiwoong Kim David E Greenberg Reed Pifer Shuang Jiang Guanghua Xiao Samuel A Shelburne Andrew Koh Yang Xie Xiaowei Zhan

PLoS Comput Biol 2020 01 13;16(1):e1007511. Epub 2020 Jan 13.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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January 2020

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

Authors:
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

Cancer Res 2020 05 8;80(10):2056-2066. Epub 2020 Jan 8.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.

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May 2020

A Bayesian zero-inflated negative binomial regression model for the integrative analysis of microbiome data.

Authors:
Shuang Jiang Guanghua Xiao Andrew Y Koh Jiwoong Kim Qiwei Li Xiaowei Zhan

Biostatistics 2019 Dec 17. Epub 2019 Dec 17.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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December 2019

Integrating germline and somatic genetics to identify genes associated with lung cancer.

Authors:
Jack Pattee Xiaowei Zhan Guanghua Xiao Wei Pan

Genet Epidemiol 2020 04 10;44(3):233-247. Epub 2019 Dec 10.

Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota.

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April 2020

ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network.

Authors:
Shidan Wang Tao Wang Lin Yang Donghan M Yang Junya Fujimoto Faliu Yi Xin Luo Yikun Yang Bo Yao ShinYi Lin Cesar Moran Neda Kalhor Annikka Weissferdt John Minna Yang Xie Ignacio I Wistuba Yousheng Mao Guanghua Xiao

EBioMedicine 2019 Dec 22;50:103-110. Epub 2019 Nov 22.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX. Electronic address:

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December 2019

ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network.

Authors:
Shidan Wang Tao Wang Lin Yang Donghan M Yang Junya Fujimoto Faliu Yi Xin Luo Yikun Yang Bo Yao ShinYi Lin Cesar Moran Neda Kalhor Annikka Weissferdt John Minna Yang Xie Ignacio I Wistuba Yousheng Mao Guanghua Xiao

EBioMedicine 2019 Dec 22;50:103-110. Epub 2019 Nov 22.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX. Electronic address:

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December 2019

Artificial Intelligence in Lung Cancer Pathology Image Analysis.

Authors:
Shidan Wang Donghan M Yang Ruichen Rong Xiaowei Zhan Junya Fujimoto Hongyu Liu John Minna Ignacio Ivan Wistuba Yang Xie Guanghua Xiao

Cancers (Basel) 2019 Oct 28;11(11). Epub 2019 Oct 28.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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October 2019

Histone lysine demethylase KDM4B regulates the alternative splicing of the androgen receptor in response to androgen deprivation.

Authors:
Lingling Duan Zhenhua Chen Jun Lu Yanping Liang Ming Wang Carlos M Roggero Qing-Jun Zhang Jason Gao Yong Fang Jiazheng Cao Jian Lu Hongwei Zhao Andrew Dang Rey-Chen Pong Elizabeth Hernandez Chun-Mien Chang David T Hoang Jung-Mo Ahn Guanghua Xiao Rui-Tao Wang Kai-Jiang Yu Payal Kapur Josep Rizo Jer-Tsong Hsieh Junhang Luo Zhi-Ping Liu

Nucleic Acids Res 2019 12;47(22):11623-11636

Department of Internal Medicine-Cardiology Division, UT Southwestern Medical Center, Dallas, TX 75390, USA.

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December 2019

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.

Authors:
Pei-Hsuan Chen Ling Cai Kenneth Huffman Chendong Yang Jiyeon Kim Brandon Faubert Lindsey Boroughs Bookyung Ko Jessica Sudderth Elizabeth A McMillan Luc Girard Dong Chen Michael Peyton Misty D Shields Bo Yao David S Shames Hyun Seok Kim Brenda Timmons Ikuo Sekine Rebecca Britt Stephanie Weber Lauren A Byers John V Heymach Jing Chen Michael A White John D Minna Guanghua Xiao Ralph J DeBerardinis

Mol Cell 2019 12 26;76(5):838-851.e5. Epub 2019 Sep 26.

Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA. Electronic address:

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December 2019

Type and case volume of health care facility influences survival and surgery selection in cases with early-stage non-small cell lung cancer.

Authors:
Shidan Wang Sunny Lai Mitchell S von Itzstein Lin Yang Donghan M Yang Xiaowei Zhan Guanghua Xiao Ethan A Halm David E Gerber Yang Xie

Cancer 2019 12 10;125(23):4252-4259. Epub 2019 Sep 10.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.

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December 2019

Correction: LCE: an open web portal to explore gene expression and clinical associations in lung cancer.

Authors:
Ling Cai ShinYi Lin Luc Girard Yunyun Zhou Lin Yang Bo Ci Qinbo Zhou Danni Luo Bo Yao Hao Tang Jeffrey Allen Kenneth Huffman Adi Gazdar John Heymach Ignacio Wistuba Guanghua Xiao John Minna Yang Xie

Oncogene 2020 Jan;39(3):718-719

Quantitative Biomedical Research Center, Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.

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January 2020

Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of and .

Authors:
Ling Cai Danni Luo Bo Yao Donghan M Yang ShinYi Lin Luc Girard Ralph J DeBerardinis John D Minna Yang Xie Guanghua Xiao

Cancers (Basel) 2019 Jun 25;11(6). Epub 2019 Jun 25.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.

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June 2019

Pathology Image Analysis Using Segmentation Deep Learning Algorithms.

Authors:
Shidan Wang Donghan M Yang Ruichen Rong Xiaowei Zhan Guanghua Xiao

Am J Pathol 2019 09 11;189(9):1686-1698. Epub 2019 Jun 11.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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September 2019

Development and Validation of a Nomogram Prognostic Model for Patients With Advanced Non-Small-Cell Lung Cancer.

Authors:
Tao Wang Rong Lu Sunny Lai Joan H Schiller Fang Liz Zhou Bo Ci Stacy Wang Xiaohan Gao Bo Yao David E Gerber David H Johnson Guanghua Xiao Yang Xie

Cancer Inform 2019 5;18:1176935119837547. Epub 2019 Apr 5.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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April 2019