Chao Cheng

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 96

Top Venues

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

International journal of cancer

Baylor College of Medicine

University of Southern California (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Baylor College of Medicine Oct 29 2018

United States

Associate Professor :: Medicine

Geisel School of Medicine at Dartmouth Aug 25 2012

United States

Assistant Professor :: Biomedical Data Science

Education History

University of Southern California Sep 01 2002 - Dec 12 2006

United States

PHD :: Computational Biology and Bioinformatics

Fudan University Sep 01 1999 - Jun 30 2002

China

MSC :: Molecualr Genetics

Publications

Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 33 (3) (2024)
Jian-Rong Li, Chao Cheng
Immune cell pair ratio captured by imaging mass cytometry has superior predictive value for prognosis of non-small cell lung cancer than cell fraction and density. Cancer communications (London, England) 44 (5) (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 33 (3) (2024)
Jia Wu, Muhammad Aminu, Lingzhi Hong, Natalie I Vokes, Stephanie Tzouanas Schmidt, Maliazurina B Saad, Bo Zhu, Xiuning Li, Cascone Tina, Ajay Sheshadri, David Jaffray, P Andrew Futreal, Jiun-Kae Jack Lee, Lauren Averett Byers, Don L Gibbons, John Victor Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Bo Wang
Joint multi-omics discriminant analysis with consistent representation learning using PANDA. Research square (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung cancer in ever- and never-smokers: findings from multi-population GWAS studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2024)
Muhammad Aminu, Bo Zhu, Natalie Vokes, Hong Chen, Lingzhi Hong, Jianrong Li, Junya Fujimoto, Yuqui Yang, Tao Wang, Bo Wang, Alissa Poteete, Monique B Nilsson, Xiuning Le, Cascone Tina, David Jaffray, Nicholas E Navin, Lauren Averett Byers, Don L Gibbons, John Victor Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Jia Wu
CoCo-ST: Comparing and Contrasting Spatial Transcriptomics data sets using graph contrastive learning. Research square (2024)
Vikram R Shaw, Angela Hudock, Baoyi Zhang, Christopher Ian Amos, Chao Cheng
Sex-Based Differences in Melanoma Survival Improvement from 2004 to 2018. Cancers 16 (7) (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Xin Hu, Bo Zhu, Natalie I Vokes, Junya Fujimoto, Frank R Rojas Alvarez, Simon Heeke, Andre L Moreira, Luisa Maren Solis Soto, Cara L Haymaker, Vamsidhar Velcheti, Daniel H Sterman, Harvey I Pass, Chao Cheng, Jiun-Kae Jack Lee, Jianhua Zhang, Zhubo Wei, Jia Wu, Xiuning Li, Edwin Justin Ostrin, Iakovos Toumazis, Don L Gibbons, Dan Su, Junya Fukuoka, Mara B Antonoff, David E Gerber, Chenyang Li, Humam Kadara, Linghua Wang, Mark M Davis, John Victor Heymach, Samir M Hanash, Ignacio Wistuba, Steven M Dubinett, Ludmil Alexandrov, Scott Lippman, Avrum Spira, P Andrew Futreal, Alexandre Reuben, Jianjun Zhang
The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. Research square (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Yupei Lin, Bryan M Burt, Hyun-Sung Lee, Thinh T Nguyen, Hee-Jin Jang, Claire Lee, Wei Hong, Robert Taylor Ripley, Christopher Ian Amos, Chao Cheng
Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. NPJ precision oncology 8 (1) (2024)
Jian-Rong Li, Shahram Arsang-Jang, Yan Cheng, Fumou Sun, Anita D Souza, Binod Dhakal, Parameswaran N Hari, Quillan Huang, Paul Auer, Yong Li, Raul Urrutia, Fenghuang Zhan, John D Shaughnessy, Siegfried Janz, Jing Dong, Chao Cheng
Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. Blood cancer journal 14 (1) (2024)
Jian-Rong Li, Shahram Arsang-Jang, Yan Cheng, Fumou Sun, Anita D Souza, Binod Dhakal, Parameswaran N Hari, Quillan Huang, Paul Auer, Yong Li, Raul Urrutia, Fenghuang Zhan, John D Shaughnessy, Siegfried Janz, Jing Dong, Chao Cheng
Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. Blood cancer journal 14 (1) (2024)
Duo-Meng Yang, Tingting Geng, Andrew G Harrison, Jason G Cahoon, Jian Xing, Baihai Jiao, Mark Wang, Chao Cheng, Robert E Hill, Huadong Wang, Anthony T Vella, Cheng Gong, Yanlin Wang, Penghua Wang
UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Nature communications 15 (1) (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Jianjun Zhang, Xin Hu, Bo Zhu, Natalie I Vokes, Junya Fukuoka, Frank Rojas Alvarez, Simon Heeke, Andre Moreira, Luisa Maren Solis Soto, Cara L Haymaker, Vamsidhar Velcheti, Daniel H Sterman, Harvey Pass, Chao Cheng, Jiun-Kae Jack Lee, Jianhua Zhang, Zhubo Wei, Jia Wu, Xiuning Li, Edwin Justin Ostrin, Iakovos Toumazis, Don L Gibbons, Dan Su, Junya Fukuoka, Mara B Antonoff, David E Gerber, Chenyang Li, Humam Kadara, Linghua Wang, Mark M Davis, John Victor Heymach, Samir M Hanash, Ignacio Wistuba, Steven M Dubinett, Ludmil Alexandrov, Scott Lippman, Avrum Spira, P Andrew Futreal, Alexandre Reuben
The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. Research square (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Yupei Lin, Bryan M Burt, Hyun-Sung Lee, Thinh T Nguyen, Hee-Jin Jang, Claire Lee, Wei Hong, Robert Taylor Ripley, Christopher Ian Amos, Chao Cheng
Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. NPJ precision oncology 8 (1) (2024)
Baoyi Zhang, Chenyang Li, Jia Wu, Jianjun Zhang, Chao Cheng
DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. International journal of cancer 154 (12) (2024)
Yupei Lin, Bryan M Burt, Hyun-Sung Lee, Thinh T Nguyen, Hee-Jin Jang, Claire Lee, Wei Hong, Robert Taylor Ripley, Christopher Ian Amos, Chao Cheng
Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. NPJ precision oncology 8 (1) (2024)
Jian-Rong Li, Chao Cheng
Immune cell pair ratio captured by imaging mass cytometry has superior predictive value for prognosis of non-small cell lung cancer than cell fraction and density. Cancer communications (London, England) (2024)
Jia Wu, Muhammad Aminu, Bo Zhu, Natalie Vokes, Hong Chen, Lingzhi Hong, Jianrong Li, Junya Fujimoto, Alissa Poteete, Monique Nilsson, Xiuning Li, Tina Cascone, David Jaffray, Nicholas E Navin, Lauren Averett Byers, Don L Gibbons, John Victor Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Yuqui Yang, Tao Wang, Bo Wang
CoCo-ST: Comparing and Contrasting Spatial Transcriptomics data sets using graph contrastive learning. Research square (2024)
Jian-Rong Li, Christiana Wang, Chao Cheng
Identifying high-risk multiple myeloma patients: A novel approach using a clonal gene signature. International journal of cancer (2024)
Duo-Meng Yang, Tingting Geng, Andrew G Harrison, Jason G Cahoon, Jian Xing, Baihai Jiao, Mark Wang, Chao Cheng, Robert E Hill, Huadong Wang, Anthony T Vella, Cheng Gong, Yanlin Wang, Penghua Wang
UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Nature communications 15 (1) (2024)
Jian-Rong Li, Abinand Krishna Parthasarathy, Aravind Singaram Kannappan, Shahram Arsang-Jang, Jing Dong, Chao Cheng
Characterization of driver mutations identifies gene signatures predictive of prognosis and treatment sensitivity in multiple myeloma. The oncologist (2024)
Chenyang Li, Wei Hong, Alexandre Reuben, Linghua Wang, Anirban Maitra, Jianjun Zhang, Chao Cheng
TimiGP-Response: the pan-cancer immune landscape associated with response to immunotherapy. bioRxiv : the preprint server for biology (2024)
Jian-Rong Li, Chao Cheng
Immune cell pair ratio captured by imaging mass cytometry has superior predictive value for prognosis of non-small cell lung cancer than cell fraction and density. Cancer communications (London, England) 44 (5) (2024)
Jian-Rong Li, Vikram R Shaw, Abi Parthasarathy, Yong Li, Christopher I Amos, Chao Cheng
Prognostic stratification in DLBCL patients with aberrant MYC gene. British journal of haematology (2024)
Baoyi Zhang, Chenyang Li, Jia Wu, Jianjun Zhang, Chao Cheng
DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. International journal of cancer 154 (12) (2024)
Yupei Lin, Bryan M Burt, Hyun-Sung Lee, Thinh T Nguyen, Hee-Jin Jang, Claire Lee, Wei Hong, Robert Taylor Ripley, Christopher Ian Amos, Chao Cheng
Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. NPJ precision oncology 8 (1) (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 33 (3) (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 33 (3) (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung cancer in ever- and never-smokers: findings from multi-population GWAS studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung cancer in ever- and never-smokers: findings from multi-population GWAS studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2024)
Chenyang Li, Wei Hong, Alexandre Reuben, Linghua Wang, Anirban Maitra, Jianjun Zhang, Chao Cheng
TimiGP-Response: the pan-cancer immune landscape associated with response to immunotherapy. bioRxiv : the preprint server for biology (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Jian-Rong Li, Shahram Arsang-Jang, Yan Cheng, Fumou Sun, Anita D Souza, Binod Dhakal, Parameswaran N Hari, Quillan Huang, Paul Auer, Yong Li, Raul Urrutia, Fenghuang Zhan, John D Shaughnessy, Siegfried Janz, Jing Dong, Chao Cheng
Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. Blood cancer journal 14 (1) (2024)
Baoyi Zhang, Chenyang Li, Jia Wu, Jianjun Zhang, Chao Cheng
DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. International journal of cancer 154 (12) (2024)
Jian-Rong Li, Chao Cheng
Immune cell pair ratio captured by imaging mass cytometry has superior predictive value for prognosis of non-small cell lung cancer than cell fraction and density. Cancer communications (London, England) 44 (5) (2024)
Xin Hu, Bo Zhu, Natalie I Vokes, Junya Fujimoto, Frank R Rojas Alvarez, Simon Heeke, Andre L Moreira, Luisa Maren Solis Soto, Cara L Haymaker, Vamsidhar Velcheti, Daniel H Sterman, Harvey I Pass, Chao Cheng, Jiun-Kae Jack Lee, Jianhua Zhang, Zhubo Wei, Jia Wu, Xiuning Li, Edwin Justin Ostrin, Iakovos Toumazis, Don L Gibbons, Dan Su, Junya Fukuoka, Mara B Antonoff, David E Gerber, Chenyang Li, Humam Kadara, Linghua Wang, Mark M Davis, John Victor Heymach, Samir M Hanash, Ignacio Wistuba, Steven M Dubinett, Ludmil Alexandrov, Scott Lippman, Avrum Spira, P Andrew Futreal, Alexandre Reuben, Jianjun Zhang
The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. Research square (2024)
Baoyi Zhang, Chenyang Li, Jia Wu, Jianjun Zhang, Chao Cheng
DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. International journal of cancer 154 (12) (2024)
Yafang Li, Xiangjun Xiao, Jian-Rong Li, Younghun Han, Chao Cheng, Gail F Fernandes, Shannon E Slewitzke, Susan M Rosenberg, Meng Zhu, Jinyoung Byun, Yohan Bosse, James D McKay, Demetrios Albanes, Stephen C Lam, Adonina Tardón, Chu Chen, Stig Egil Bojesen, Maria Teresa Landi, Mattias J Johansson, Angela Risch, Heike Bickeböller, Heinz-Erich Wichmann, David Chistopher Christiani, Gadi Rennert, Susanne M Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A L M Kiemeney, Ryan Sun, Shanbeh Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Neil C Caporaso, Angela Cox, Yun Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Kendra L Schwartz, Ivan P Gorlov, Kristen S Purrington, Ping Yang, Yanhong Liu, Richard K Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul J Brennan, Jun Xia, Hongbing Shen, Christopher Ian Amos
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 33 (3) (2024)
Muhammad Aminu, Lingzhi Hong, Natalie I Vokes, Stephanie Tzouanas Schmidt, Maliazurina Saad, Bo Zhu, Xiuning Li, Cascone Tina, Ajay Sheshadri, Bo Wang, David Jaffray, P Andrew Futreal, Jiun-Kae Jack Lee, Lauren Averett Byers, Don L Gibbons, John Victor Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Jia Wu
Joint multi-omics discriminant analysis with consistent representation learning using PANDA. Research square (2024)
Muhammad Aminu, Lingzhi Hong, Natalie I Vokes, Stephanie Tzouanas Schmidt, Maliazurina Saad, Bo Zhu, Xiuning Li, Cascone Tina, Ajay Sheshadri, Bo Wang, David Jaffray, P Andrew Futreal, Jiun-Kae Jack Lee, Lauren Averett Byers, Don L Gibbons, John Victor Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Jia Wu
Joint multi-omics discriminant analysis with consistent representation learning using PANDA. Research square (2024)
Jiefei Han, Yiting Dong, Xiuli Zhu, Alexandre Reuben, Jianjun Zhang, Jiachen Xu, Hua Bai, Jianchun Duan, Rui Wan, Jie Zhao, Jing Bai, Xuefeng Xia, Xin Yi, Chao Cheng, Jie Wang, Zhijie Wang
Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nature communications 15 (1) (2024)
Vikram R Shaw, Angela Hudock, Baoyi Zhang, Christopher Ian Amos, Chao Cheng
Sex-Based Differences in Melanoma Survival Improvement from 2004 to 2018. Cancers 16 (7) (2024)
Baoyi Zhang, Chenyang Li, Jia Wu, Jianjun Zhang, Chao Cheng
DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. International journal of cancer (2024)
Duo-Meng Yang, Tingting Geng, Andrew G Harrison, Jason G Cahoon, Jian Xing, Baihai Jiao, Mark Wang, Chao Cheng, Robert E Hill, Huadong Wang, Anthony T Vella, Cheng Gong, Yanlin Wang, Penghua Wang
UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Nature communications 15 (1) (2024)
Baoyi Zhang, Xiang Wang, Chao Cheng
The ratio of intratumour to stromal infiltrating lymphocytes better predicts prognosis in breast cancer. Clinical and translational medicine 13 (5) (2023)
Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min
Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinformatics (Oxford, England) 39 (2) (2023)
Baoyi Zhang, Jianrong Li, Mabel Tang, Chao Cheng
Reduced Racial Disparity as a Result of Survival Improvement in Prostate Cancer. Cancers 15 (15) (2023)
Yi Han, Yuqiu Yang, Yanhua Tian, Farjana J Fattah, Mitchell S von Itzstein, Yifei Hu, Minying Zhang, Xiongbin Kang, Donghan M Yang, Jialiang Liu, Yaming Xue, Chaoying Liang, Indu Raman, Chengsong Zhu, Olivia Xiao, Jonathan E Dowell, Jade Homsi, Sawsan Rashdan, Shengjie Yang, Mary E Gwin, David Hsiehchen, Yvonne Gloria-McCutchen, Ke Pan, Fangjiang Wu, Don Gibbons, Xinlei Wang, Cassian Yee, Junzhou Huang, Alexandre Reuben, Chao Cheng, Jianjun Zhang, David E Gerber, Tao Wang
pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding. bioRxiv : the preprint server for biology (2023)
Vikram R Shaw, Christopher Ian Amos, Chao Cheng
Predicting Chemotherapy Benefit across Different Races in Early-Stage Breast Cancer Patients Using the Oncotype DX Score. Cancers 15 (12) (2023)
Vikram R Shaw, Christopher Ian Amos, Chao Cheng
Predicting Chemotherapy Benefit across Different Races in Early-Stage Breast Cancer Patients Using the Oncotype DX Score. Cancers 15 (12) (2023)
Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min
Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinformatics (Oxford, England) 39 (2) (2023)
Evelien Schaafsma, Eric M Takacs, Sandeep Kaur, Chao Cheng, Manabu Kurokawa
Predicting clinical outcomes of cancer patients with a p53 deficiency gene signature. Scientific reports 12 (1) (2022)
Miao Cui, Chao Cheng, Lanjing Zhang
High-throughput proteomics: a methodological mini-review. Laboratory investigation; a journal of technical methods and pathology 102 (11) (2022)
Kevin Yao, Evelien Schaafsma, Baoyi Zhang, Chao Cheng
Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer. PLoS computational biology 18 (3) (2022)
Kevin Yao, Emily Zhou, Evelien Schaafsma, Baoyi Zhang, Chao Cheng
Immune checkpoint gene VSIR predicts patient prognosis in acute myeloid leukemia and myelodysplastic syndromes. Cancer medicine (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology 30 (1) (2022)
Thinh T Nguyen, Hyun-Sung Lee, Bryan M Burt, Jia Wu, Jianjun Zhang, Christopher I Amos, Chao Cheng
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. Genome medicine 14 (1) (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology 30 (1) (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology (2022)
Aviral Chharia, Rahul Upadhyay, Vinay Kumar, Chao Cheng, Jing Zhang, Tianyang Wang, Min Xu
Deep-Precognitive Diagnosis: Preventing Future Pandemics by Novel Disease Detection With Biologically-Inspired Conv-Fuzzy Network. IEEE access : practical innovations, open solutions 10 (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology 30 (1) (2022)
Evelien Schaafsma, Walburga Croteau, Mohamed A ElTanbouly, Elizabeth C Nowak, Nicole C Smits, Jie Deng, Aurelien Sarde, Cecilia A Webber, Dina Rabadi, Chao Cheng, Randolph J Noelle, J Louise Lines
VISTA targeting of T-cell quiescence and myeloid suppression overcomes adaptive resistance. Cancer immunology research (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology 30 (1) (2022)
Kevin Yao, Emily Zhou, Chao Cheng
A B-Raf V600E gene signature for melanoma predicts prognosis and reveals sensitivity to targeted therapies. Cancer medicine 11 (4) (2022)
Thinh T Nguyen, Hyun-Sung Lee, Bryan M Burt, Christopher Ian Amos, Chao Cheng
A combination of intrinsic and extrinsic features improves prognostic prediction in malignant pleural mesothelioma. British journal of cancer 127 (9) (2022)
Bennett K Wolf, Yanding Zhao, Andrew McCray, William H Hawk, Luke T Deary, Nicholas W Sugiarto, Ian S LaCroix, Scott A Gerber, Chao Cheng, Xiaofeng Wang
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nature structural & molecular biology (2022)
Evelien Schaafsma, Chongming Jiang, Thinh Nguyen, Kenneth Zhu, Chao Cheng
Microglia-Based Gene Expression Signature Highly Associated with Prognosis in Low-Grade Glioma. Cancers 14 (19) (2022)
Catherine H Feng, Mary L Disis, Chao Cheng, Lanjing Zhang
Multimetric feature selection for analyzing multicategory outcomes of colorectal cancer: random forest and multinomial logistic regression models. Laboratory investigation; a journal of technical methods and pathology (2021)
Evelien Schaafsma, Baoyi Zhang, Merit Schaafsma, Chun-Yip Tong, Lanjing Zhang, Chao Cheng
Impact of Oncotype DX testing on ER+ breast cancer treatment and survival in the first decade of use. Breast cancer research : BCR 23 (1) (2021)
Ming Tang, Hussein A Abbas, Marcelo Vailati Negrão, Maheshwari Ramineni, Xin Hu, Shawna Marie Hubert, Junya Fujimoto, Alexandre Reuben, Susan Varghese, Jianhua Zhang, Jun Li, Chi-Wan Chow, Xizeng Mao, Xingzhi Song, Won-Chul Lee, Jia Wu, Latasha Little, Curtis Gumbs, Carmen Behrens, Cesar A Moran, Annikka Weissferdt, Jiun-Kae Jack Lee, Boris Sepesi, Stephen G Swisher, Chao Cheng, Jonathan M Kurie, Don L Gibbons, John Victor Heymach, Ignacio I Wistuba, P Andrew Futreal, Neda Kalhor, Jianjun Zhang
The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics. Nature communications 12 (1) (2021)
Ming Chen, Runzhe Chen, Ying Jin, Jun Li, Xin Hu, Jianhua Zhang, Junya Fujimoto, Shawna Marie Hubert, Carl M Gay, Bo Zhu, Yanhua Tian, Nicholas McGranahan, Won-Chul Lee, Julie George, Xiao Hu, Yamei Chen, Meijuan Wu, Carmen Behrens, Chi-Wan Chow, Hoa H N Pham, Junya Fukuoka, Jia Wu, Edwin Roger Parra Cuentes, Latasha D Little, Curtis Gumbs, Xingzhi Song, Chang-Jiun Wu, Lixia Diao, Qi Wang, Robert Cardnell, Jianhua Zhang, Jing Wang, Xiuning Li, Don L Gibbons, John Victor Heymach, Jiun-Kae Jack Lee, William N William, Chao Cheng, Bonnie Glisson, Ignacio Wistuba, P Andrew Futreal, Roman K Thomas, Alexandre Reuben, Lauren Averett Byers, Jianjun Zhang
Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer. Nature communications 12 (1) (2021)
Xiaoyan He, Chao Qin, Yanding Zhao, Lin Zou, Hui Zhao, Chao Cheng
Gene signatures associated with genomic aberrations predict prognosis in neuroblastoma. Cancer communications (London, England) 40 (2-3) (2021)
Yanhong Liu, Jun Xia, James McKay, Spiridon Tsavachidis, Xiangjun Xiao, Margaret R Spitz, Chao Cheng, Jinyoung Byun, Wei Hong, Yafang Li, Dakai Zhu, Zhuoyi Song, Susan M Rosenberg, Michael E Scheurer, Farrah Kheradmand, Claudio W Pikielny, Christine M Lusk, Ann G Schwartz, Ignacio I Wistuba, Michael H Cho, Edwin K Silverman, Richard K Wilson, Susan M Pinney, Marshall Anderson, Elena Kupert, Colette Gaba, Diptasri Mandal, Ming You, Mariza de Andrade, Ping Yang, Triantafillos Liloglou, Michael P A Davies, Jolanta Lissowska, Beata Swiatkowska, David Zaridze, Anush Mukeria, Vladimir Janout, Ivana Holcatova, Dana Mates, Jelena Stojšić, Ghislaine Scelo, Paul J Brennan, Geoffrey Liu, John K Field, Rayjean J Hung, David Chistopher Christiani, Christopher Ian Amos
Rare deleterious germline variants and risk of lung cancer. NPJ precision oncology 5 (1) (2021)
Baoyi Zhang, Kevin Yao, Emily Zhou, Lanjing Zhang, Chao Cheng
Chr20q Amplification Defines a Distinct Molecular Subtype of Microsatellite Stable Colorectal Cancer. Cancer research 81 (8) (2021)
Evelien Schaafsma, Chloe M Fugle, Xiaofeng Wang, Chao Cheng
Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy. British journal of cancer 125 (3) (2021)
Fei Deng, Jibing Huang, Xiaoling Yuan, Chao Cheng, Lanjing Zhang
Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data. Laboratory investigation; a journal of technical methods and pathology 101 (4) (2021)
Wei Hong, Ang Li, Yanhong Liu, Xiangjun Xiao, David Chistopher Christiani, Rayjean J Hung, James McKay, John K Field, Christopher Ian Amos, Chao Cheng
Clonal Hematopoiesis Mutations in Lung Cancer Patients are Associated with Lung Cancer Risk Factors. Cancer research (2021)
Guangchun Han, Guoliang Yang, Dapeng Hao, Yang Lu, Kyaw Zin Thein, Benjamin Scott S Simpson, Jianfeng Chen, Ryan Sun, Omar Alhalabi, Ruiping Wang, Minghao Dang, Enyu Dai, Shaojun Zhang, Fengqi Nie, Shuangtao Zhao, Charles Guo, Ameer Hamza, Bogdan Czerniak, Chao Cheng, Arlene Siefker-Radtke, Krishna P Bhat, P Andrew Futreal, Guang Peng, Jennifer A Wargo, Weiyi Peng, Humam Kadara, Jaffer A Ajani, Charles Swanton, Kevin Litchfield, Jordi Rodon Ahnert, Jianjun Gao, Linghua Wang
9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy. Nature communications 12 (1) (2021)
Yanding Zhao, Evelien Schaafsma, Chao Cheng
Gene signature-based prediction of triple-negative breast cancer patient response to Neoadjuvant chemotherapy. Cancer medicine 9 (17) (2020)
Chao Cheng, Yanding Zhao, Evelien Schaafsma, Yi-Lan Weng, Christopher Amos
An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. International journal of cancer 147 (9) (2020)
Matthew Ung, Evelien Schaafsma, Daniel Mattox, George L Wang, Chao Cheng
Pan-cancer systematic identification of lncRNAs associated with cancer prognosis. PeerJ 8 (2020)
Mohamed A ElTanbouly, Yanding Zhao, Elizabeth C Nowak, Jiannan Li, Evelien Schaafsma, Isabelle Le Mercier, Sabrina Ceeraz, J Louise Lines, Changwei Peng, Catherine Carriere, Xin Huang, Maria Day, Brent H Koehn, Sam W Lee, Milagros Silva Morales, Kristin A Hogquist, Stephen C Jameson, Daniel L Mueller, Jay Rothstein, Bruce R Blazar, Chao Cheng, Randolph J Noelle
VISTA is a checkpoint regulator for naïve T cell quiescence and peripheral tolerance. Science (New York, N.Y.) 367 (6475) (2020)
Evelien Schaafsma, Yanding Zhao, Lanjing Zhang, Yong Li, Chao Cheng
MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers. Molecular cancer research : MCR 19 (3) (2020)
Jie Deng, Jiannan Li, Aurelien Sarde, J Louise Lines, Yu-Chi Lee, David C Qian, Dov A Pechenick, Richard Manivanh, Isabelle Le Mercier, Christopher H Lowrey, Frederick S Varn, Chao Cheng, David A Leib, Randolph J Noelle, Rodwell Mabaera
Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. Cancer immunology research 7 (7) (2019)
Kevin Shee, Jason D Wells, Matthew Ung, Riley A Hampsch, Nicole A Traphagen, Wei Yang, Stephanie C Liu, Megan A Zeldenrust, Liewei Wang, Krishna R Kalari, Jia Yu, Judy C Boughey, Eugene Demidenko, Arminja N Kettenbach, Chao Cheng, Matthew P Goetz, Todd W Miller
A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition. Clinical cancer research : an official journal of the American Association for Cancer Research 26 (1) (2019)
Frederick S Varn, Evelien Schaafsma, Yue Wang, Chao Cheng
Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs. Cancer research 78 (22) (2018)
Zahra Mortezaei, Jean-Baptiste Cazier, Ali Ashraf Mehrabi, Chao Cheng, Ali Masoudi-Nejad
Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. Journal of cellular biochemistry 120 (4) (2018)
Yasmin Kamal, Chao Cheng, H Robert Frost, Christopher I Amos
Predictors of disease aggressiveness influence outcome from immunotherapy treatment in renal clear cell carcinoma. Oncoimmunology 8 (1) (2018)
Yanding Zhao, Evelien Schaafsma, Ivan P Gorlov, Eva Hernando, Nancy E Thomas, Ronglai Shen, Mary Jo Turk, Marianne Berwick, Christopher I Amos, Chao Cheng
A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis. Molecular cancer research : MCR 17 (1) (2018)
Kevin Shee, Wei Yang, John W Hinds, Riley A Hampsch, Frederick S Varn, Nicole A Traphagen, Kishan Patel, Chao Cheng, Nicole P Jenkins, Arminja N Kettenbach, Eugene Demidenko, Philip Owens, Anthony C Faber, Todd R Golub, Ravid Straussman, Todd W Miller
Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. The Journal of experimental medicine 215 (3) (2018)
Frederick S Varn, Yue Wang, Chao Cheng
A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy. Oncoimmunology 8 (1) (2018)
Ai Tian, Hassina Benchabane, Zhenghan Wang, Chloe Zimmerman, Nan Xin, Jessica Perochon, Gabriela Kalna, Owen J Sansom, Chao Cheng, Julia B Cordero, Yashi Ahmed
Intestinal stem cell overproliferation resulting from inactivation of the APC tumor suppressor requires the transcription cofactors Earthbound and Erect wing. PLoS genetics 13 (7) (2017)

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Chao Cheng