Publications

2025

1. Integrating Multi-Omics Data to Uncover Prostate Tissue DNA Methylation Biomarkers and Target Genes for Prostate Cancer Risk

   Shuai Liu, Jingjing Zhu, Dylan Green, Hua Zhong, Quan Long, Chong Wu, Liang Wang, Youping Deng, and Lang Wu

   Molecular Carcinogenesis, 2025
2. Integrative Multi-Omics Approach for Improving Causal Gene Identification

   Austin King and Chong Wu

   Genetic Epidemiology, 2025
3. The Role of Double-Zero-Event Studies in Evidence Synthesis: Evaluating Robustness Using the Fragility Index

   Zelin Wang, Xing Xing, Eun-Young Mun, Chong Wu, and Lifeng Lin

   Journal of Evaluation in Clinical Practice, 2025
4. Transcriptome-Wide Association Study Identified Novel Blood Tissue Gene Biomarkers for Prostate Cancer Risk

   Yanfa Sun, Jingjing Zhu, Hua Zhong, Zichen Zhang, Fubo Wang, Akira Nakamura, Yanhui Liu, Jiawen Liu, Jie Yu, Guanghua Zeng, and 1 more author

   The Prostate, 2025

2024

1. Associations between genetically predicted plasma protein levels and Alzheimer’s disease risk: a study using genetic prediction models

   Jingjing Zhu, Shuai Liu, Keenan A Walker, Hua Zhong, Dalia H Ghoneim, Zichen Zhang, Praveen Surendran, Sarah Fahle, Adam Butterworth, Md Ashad Alam, and 1 more author

   Alzheimer’s Research & Therapy, 2024
2. A Deep Learning Approach to Nonparametric Propensity Score Estimation with Optimized Covariate Balance

   Maosen Peng, Yan Li, Chong Wu, and Liang Li

   arXiv preprint arXiv:2404.04794, 2024
3. Regional analysis to delineate intrasample heterogeneity with RegionalST

   Yue Lyu, Chong Wu, Wei Sun, and Ziyi Li

   Bioinformatics, 2024
4. SUMMIT-FA: a new resource for improved transcriptome imputation using functional annotations

   Hunter J Melton, Zichen Zhang, and Chong Wu

   Human Molecular Genetics, 2024
5. Sensitivity analysis with iterative outlier detection for systematic reviews and meta-analyses

   Zhuo Meng, Jingshen Wang, Lifeng Lin, and Chong Wu

   Statistics in Medicine, 2024
6. GigaScience

   Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

   Jingjing Zhu, Ke Wu, Shuai Liu, Alexandra Masca, Hua Zhong, Tai Yang, Dalia H Ghoneim, Praveen Surendran, Tanxin Liu, Qizhi Yao, and 1 more author

   GigaScience, 2024
7. omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass spectrometry-based omics data

   Weiqiang Lin, Jiadong Ji, Kuan-Jui Su, Chuan Qiu, Qing Tian, Lan-Juan Zhao, Zhe Luo, Chong Wu, Hui Shen, and Hongwen Deng

   NAR Genomics and Bioinformatics, 2024
8. MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations

   Hunter J Melton, Zichen Zhang, Hong-Wen Deng, Lang Wu, and Chong Wu

   Epigenetics, 2024
9. An atlas of genetic effects on the monocyte methylome across European and African populations

   Wanheng Zhang, Xiao Zhang, Chuan Qiu, Zichen Zhang, Kuan-Jui Su, Zhe Luo, Minghui Liu, Bingxin Zhao, Lang Wu, Qing Tian, and 1 more author

   medRxiv, 2024
10. Benchmarking DNA Foundation Models for Genomic Sequence Classification

    Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, and Chong Wu

    bioRxiv, 2024
11. Multi-View Integrative Approach For Imputing Short-Chain Fatty Acids and Identifying Key factors predicting Blood SCFA

    Anqi Liu, Bo Tian, Chuan Qiu, Kuan-Jui Su, Lindong Jiang, Chen Zhao, Meng Song, Yong Liu, Gang Qu, Ziyu Zhou, and 1 more author

    bioRxiv, 2024
12. Plos Med.

    Variability in performance of genetic-enhanced DXA-BMD prediction models across diverse ethnic and geographic populations: A risk prediction study

    Yong Liu, Xiang-He Meng, Chong Wu, Kuan-Jui Su, Anqi Liu, Qing Tian, Lan-Juan Zhao, Chuan Qiu, Zhe Luo, Martha I Gonzalez-Ramirez, and 1 more author

    PLoS Medicine, 2024
13. OpencanSARchem: chemistry registration and standardization pipeline for FAIR integration of bioassay data

    Rezvan Chitsazi, Phillip W Gingrich, James P Long, Chong Wu, and Bissan Al-Lazikani

    2024
14. Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data

    Chen Zhao, Kuan-Jui Su, Chong Wu, Xuewei Cao, Qiuying Sha, Wu Li, Zhe Luo, Tian Qing, Chuan Qiu, Lan Juan Zhao, and 1 more author

    Computers in Biology and Medicine, 2024
15. Diabetologia

    Identification of proteins associated with type 2 diabetes risk in diverse racial and ethnic populations

    Shuai Liu, Jingjing Zhu, Hua Zhong, Chong Wu, Haoran Xue, Burcu F Darst, Xiuqing Guo, Peter Durda, Russell P Tracy, Yongmei Liu, and 1 more author

    Diabetologia, 2024
16. Age-Related Hearing Impairment: Genome and Blood Methylome Data Integration Reveals Candidate Epigenetic Biomarkers

    Jie Yu, Jingjing Zhu, Hua Zhong, Zicheng Zhang, Jiawen Liu, Xin Lin, Guanghua Zeng, Min Zhang, Chong Wu, Youping Deng, and 1 more author

    OMICS: A Journal of Integrative Biology, 2024
17. A Zero-Inflated Hierarchical Generalized Transformation Model to Address Non-Normality in Spatially-Informed Cell-Type Deconvolution

    Hunter J Melton, Jonathan R Bradley, and Chong Wu

    bioRxiv, 2024

2023

1. Ann. Stat.

   Breaking the winner’s curse in Mendelian randomization: Rerandomized inverse variance weighted estimator

   Xinwei Ma, Jingshen Wang, and Chong Wu

   The Annals of Statistics, 2023

   PDF
2. Biometrics

   Efficient targeted learning of heterogeneous treatment effects for multiple subgroups

   Waverly Wei, Maya Petersen, Mark J Laan, Zeyu Zheng, Chong Wu, and Jingshen Wang

   Biometrics, 2023

   PDF
3. Splicing transcriptome-wide association study to identify splicing events for pancreatic cancer risk

   Duo Liu, Ye Eun Bae, Jingjing Zhu, Zichen Zhang, Yanfa Sun, Youping Deng, Chong Wu, and Lang Wu

   Carcinogenesis, 2023
4. A splicing transcriptome-wide association study identifies candidate altered splicing for prostate cancer risk

   Yanfa Sun, Ye Eun Bae, Jingjing Zhu, Zichen Zhang, Hua Zhong, Chunmei Cheng, Youping Deng, Chong Wu, and Lang Wu

   OMICS: A Journal of Integrative Biology, 2023
5. JASA

   Assessing the most vulnerable subgroup to type II diabetes associated with statin usage: Evidence from electronic health record data

   Xinzhou Guo, Waverly Wei, Molei Liu, Tianxi Cai, Chong Wu, and Jingshen Wang

   Journal of the American Statistical Association, 2023
6. A splicing transcriptome-wide association study identifies novel altered splicing for Alzheimer’s disease susceptibility

   Yanfa Sun, Ye Eun Bae, Jingjing Zhu, Zichen Zhang, Hua Zhong, Jie Yu, Chong Wu, and Lang Wu

   Neurobiology of Disease, 2023
7. The effect direction should be taken into account when assessing small-study effects

   Zhuo Meng, Chong Wu, and Lifeng Lin

   Journal of Evidence-Based Dental Practice, 2023
8. Transl. Psychiatry

   Identification of candidate DNA methylation biomarkers related to Alzheimer’s disease risk by integrating genome and blood methylome data

   Yanfa Sun, Jingjing Zhu, Yaohua Yang, Zichen Zhang, Hua Zhong, Guanghua Zeng, Dan Zhou, Richard S Nowakowski, Jirong Long, Chong Wu, and 1 more author

   Translational psychiatry, 2023
9. Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects

   Hua Zhong, Jingjing Zhu, Shuai Liu, Dalia H Ghoneim, Praveen Surendran, Tao Liu, Sarah Fahle, Adam Butterworth, Md Ashad Alam, Hong-Wen Deng, and 1 more author

   Human Molecular Genetics, 2023
10. Mediation Analysis with Mendelian Randomization and Efficient Multiple GWAS Integration

    Rita Qiuran Lyu, Chong Wu, Xinwei Ma, and Jingshen Wang

    arXiv preprint arXiv:2312.10563, 2023
11. Winner’s Curse Free Robust Mendelian Randomization with Summary Data

    Zhongming Xie, Wanheng Zhang, Jingshen Wang, and Chong Wu

    arXiv preprint arXiv:2309.04957, 2023
12. Large-scale imputation models for multi-ancestry proteome-wide association analysis

    Chong Wu, Zichen Zhang, Xiaochen Yang, and Bingxin Zhao

    bioRxiv, 2023

2022

1. Nat. Commun.

   SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification

   Zichen Zhang, Ye Eun Bae, Jonathan R Bradley, Lang Wu, and Chong Wu

   Nature Communications, 2022

   Bib PDF

   @article{zhang2022summit,
     title = {SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification},
     author = {Zhang, Zichen and Bae, Ye Eun and Bradley, Jonathan R and Wu, Lang and Wu, Chong},
     journal = {Nature Communications},
     volume = {13},
     number = {1},
     pages = {6336},
     year = {2022},
     publisher = {Nature Publishing Group UK London},
     url = {https://www.nature.com/articles/s41467-022-34016-y},
   }

2. A transcriptome-wide association study identifies novel candidate susceptibility genes for prostate cancer risk

   Duo Liu, Jingjing Zhu, Dan Zhou, Emily G Nikas, Nikos T Mitanis, Yanfa Sun, Chong Wu, Nicholas Mancuso, Nancy J Cox, Liang Wang, and 1 more author

   International Journal of Cancer, 2022
3. A transcriptome-wide association study identifies novel blood-based gene biomarker candidates for Alzheimer’s disease risk

   Yanfa Sun, Dan Zhou, Md Rezanur Rahman, Jingjing Zhu, Dalia Ghoneim, Nancy J Cox, Thomas G Beach, Chong Wu, Eric R Gamazon, and Lang Wu

   Human Molecular Genetics, 2022
4. Using R for Cell-Type Composition Imputation in Epigenome-Wide Association Studies

   Chong Wu

   In Epigenome-Wide Association Studies: Methods and Protocols, 2022
5. An autoencoder-based deep learning method for genotype imputation

   Meng Song, Jonathan Greenbaum, Joseph Luttrell IV, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan-Jui Su, Qing Tian, and 1 more author

   Frontiers in Artificial Intelligence, 2022
6. BMC Med.

   Polygenic risk score improves the accuracy of a clinical risk score for coronary artery disease

   Austin King, Lang Wu, Hong-Wen Deng, Hui Shen, and Chong Wu

   BMC medicine, 2022

   PDF

2021

1. Genet. Med.

   An integrative multiomics analysis identifies putative causal genes for COVID-19 severity

   Lang Wu, Jingjing Zhu, Duo Liu, Yanfa Sun, and Chong Wu

   Genetics in Medicine, 2021

   PDF
2. Cancer Comm.

   Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data: a multi-phased study of prostate cancer

   Chong Wu, Jingjing Zhu, Austin King, Xiaoran Tong, Qing Lu, Jong Y Park, Liang Wang, Guimin Gao, Hong-Wen Deng, Yaohua Yang, and 1 more author

   Cancer Communications, 2021

   PDF
3. Ann. Stat.

   Asymptotically independent U-statistics in high-dimensional testing

   Yinqiu He, Gongjun Xu, Chong Wu, and Wei Pan

   Annals of statistics, 2021

   PDF
4. A gene-level methylome-wide association analysis identifies novel Alzheimer’s disease genes

   Chong Wu, Jonathan Bradley, Yanming Li, Lang Wu, and Hong-Wen Deng

   Bioinformatics, 2021
5. Genome Med.

   A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes

   Yanfa Sun, Jingjing Zhu, Dan Zhou, Saranya Canchi, Chong Wu, Nancy J Cox, Robert A Rissman, Eric R Gamazon, and Lang Wu

   Genome Medicine, 2021
6. InTACT: An adaptive and powerful framework for joint-tissue transcriptome-wide association studies

   Ye Eun Bae, Lang Wu, and Chong Wu

   Genetic Epidemiology, 2021
7. Associations between genetically predicted protein levels and COVID-19 severity

   Jingjing Zhu, Chong Wu, and Lang Wu

   The Journal of Infectious Diseases, 2021
8. Nat. Comm.

   Accurate recognition of colorectal cancer with semi-supervised deep learning on pathological images

   Gang Yu, Kai Sun, Chao Xu, Xing-Hua Shi, Chong Wu, Ting Xie, Run-Qi Meng, Xiang-He Meng, Kuan-Song Wang, Hong-Mei Xiao, and 1 more author

   Nature communications, 2021
9. Systematic identification of risk factors and drug repurposing options for Alzheimer’s disease

   Chong Wu, Lang Wu, Jingshen Wang, Lifeng Lin, Yanming Li, Qing Lu, and Hong-wen Deng

   Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 2021
10. Cancer Res.

    Associations of genetically predicted blood protein biomarkers with pancreatic ductal adenocarcinoma risk: a study using comprehensive protein genetic prediction models

    Dalia Ghoneim, Jingjing Zhu, Jihwan Ha, Praveen Surendran, Qizhi Cathy Yao, Tao Liu, Sarah Fahle, Adam Butterworth, Chong Wu, and Lang Wu

    Cancer Research, 2021
11. BMC Med.

    Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

    Kuan-Song Wang, Gang Yu, Chao Xu, Xiang-He Meng, Jianhua Zhou, Changli Zheng, Zhenghao Deng, Li Shang, Ruijie Liu, Shitong Su, and 1 more author

    BMC Medicine, 2021
12. A machine-learning approach for detection of local brain networks and marginally weak signals identifies novel AD/MCI differentiating connectomic neuroimaging biomarkers

    Yanming Li, Jian Kang, Chong Wu, Ivo D Dinov, Jinxiang Hu, Prabhakar Chalise, Jonathan D Mahnken, and Alzheimer’s Disease Neuroimaging Initiative

    bioRxiv, 2021
13. Sharp inference on selected subgroups in observational studies

    Xinzhou Guo, Linqing Wei, Chong Wu, and Jingshen Wang

    arXiv preprint arXiv:2102.11338, 2021
14. Optimized intracellular staining reveals heterogeneous cytokine production ability of murine and human hematopoietic stem and progenitor cells

    Shufeng Luo, Huiling Lin, Lan Zhu, Hai-Tian Chen, Siqian Yang, Jinheng Li, Mingyu Liu, Limin Zheng, and Chong Wu

    Frontiers in Immunology, 2021

2020

1. JLMR

   A Regularization-Based Adaptive Test for High-Dimensional GLMs

   Chong Wu, Gongjun Xu, Xiaotong Shen, and Wei Pan

   Journal of Machine Learning Research, 2020

   PDF
2. Associations between genetically predicted blood protein biomarkers and pancreatic cancer risk

   Jingjing Zhu, Xiang Shu, Xingyi Guo, Duo Liu, Jiandong Bao, Roger L Milne, Graham G Giles, Chong Wu, Mengmeng Du, Emily White, and 1 more author

   Cancer Epidemiology, Biomarkers & Prevention, 2020
3. Leveraging existing GWAS summary data of genetically correlated and uncorrelated traits to improve power for a new GWAS

   Haoran Xue, Chong Wu, and Wei Pan

   Genetic Epidemiology, 2020
4. Cancer Res.

   A transcriptome-wide association study identifies candidate susceptibility genes for pancreatic cancer risk

   Duo Liu, Dan Zhou, Yanfa Sun, Jingjing Zhu, Dalia Ghoneim, Chong Wu, Qizhi Yao, Eric R Gamazon, Nancy J Cox, and Lang Wu

   Cancer Research, 2020
5. Nat. Comm.

   An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk

   Lang Wu, Yaohua Yang, Xingyi Guo, Xiao-Ou Shu, Qiuyin Cai, Xiang Shu, Bingshan Li, Ran Tao, Chong Wu, Jason B Nikas, and 1 more author

   Nature Communications, 2020
6. Integrating DNA sequencing and transcriptomic data for association analyses of low-frequency variants and lipid traits

   Tianzhong Yang, Chong Wu, Peng Wei, and Wei Pan

   Human Molecular Genetics, 2020
7. An adaptive test for meta-analysis of rare variant association studies

   Tianzhong Yang, Junghi Kim, Chong Wu, Yiding Ma, Peng Wei, and Wei Pan

   Genetic Epidemiology, 2020
8. A powerful fine-mapping method for transcriptome-wide association studies

   Chong Wu and Wei Pan

   Human Genetics, 2020
9. A review of integrative imputation for multi-omics datasets

   Meng Song, Jonathan Greenbaum, Joseph Luttrell IV, Weihua Zhou, Chong Wu, Hui Shen, Ping Gong, Chaoyang Zhang, and Hong-Wen Deng

   Frontiers in Genetics, 2020
10. Mendelian randomization analysis to characterize causal association between coronary artery disease and COVID-19

    Lang Wu, Jingjing Zhu, and Chong Wu

    medRxiv, 2020
11. Multi-trait genome-wide analyses of the brain imaging phenotypes in UK Biobank

    Chong Wu

    Genetics, 2020

2019

1. An adaptive test on high-dimensional parameters in generalized linear models

   Chong Wu, Gongjun Xu, and Wei Pan

   Statistica Sinica, 2019
2. Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes

   Chong Wu and Wei Pan

   Bioinformatics, 2019
3. Cancer Res.

   Identification of novel susceptibility loci and genes for prostate cancer risk: a transcriptome-wide association study in over 140,000 European descendants

   Lang Wu, Jifeng Wang, Qiuyin Cai, Taylor B Cavazos, Nima C Emami, Jirong Long, Xiao-Ou Shu, Yingchang Lu, Xingyi Guo, Joshua A Bauer, and 1 more author

   Cancer Research, 2019

2018

1. Genetics

   Integration of enhancer-promoter interactions with GWAS summary results identifies novel schizophrenia-associated genes and pathways

   Chong Wu and Wei Pan

   Genetics, 2018
2. Adaptive SNP-set association testing in generalized linear mixed models with application to family studies

   Jun Young Park, Chong Wu, Saonli Basu, Matt McGue, and Wei Pan

   Behavior Genetics, 2018
3. Comparison between two post-dentin bond strength measurement methods

   Laikuan Zhu, Yuping Li, Yung-Chung Chen, Carola A Carrera, Chong Wu, and Alex Fok

   Scientific Reports, 2018
4. Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia

   Chong Wu and Wei Pan

   Genetic Epidemiology, 2018
5. An adaptive gene-level association test for pedigree data

   Jun Young Park, Chong Wu, and Wei Pan

   BMC Genetics, 2018
6. An adaptive gene-based test for methylation data

   Chong Wu, Jun Young Park, Weihua Guan, and Wei Pan

   In BMC Proceedings, 2018
7. Epigenome-Wide Association Study of Moderate-Vigorous Physical Activity in Adult African Americans Identifies Loci Near HCCA2

   Steven Nguyen, Weihua Guan, Chong Wu, Megan Grove, Rui Xia, Nicholas S Roetker, Katie Holliday, Elizabeth Hibler, Yinan Zheng, Eric Whitsel, and 1 more author

   In CIRCULATION, 2018

2017

1. AOAS

   A novel and efficient algorithm for de novo discovery of mutated driver pathways in cancer

   Binghui Liu, Chong Wu, Xiaotong Shen, and Wei Pan

   The Annals of Applied Statistics, 2017
2. Neuroimage

   Imaging-wide association study: integrating imaging endophenotypes in GWAS

   Zhiyuan Xu, Chong Wu, Wei Pan, Alzheimer’s Disease Neuroimaging Initiative, and others

   Neuroimage, 2017
3. A powerful framework for integrating eQTL and GWAS summary data

   Zhiyuan Xu, Chong Wu, Peng Wei, and Wei Pan

   Genetics, 2017

2016

1. JLMR

   A new algorithm and theory for penalized regression-based clustering

   Chong Wu, Sunghoon Kwon, Xiaotong Shen, and Wei Pan

   Journal of Machine Learning Research, 2016

   PDF
2. Genome Med.

   An adaptive association test for microbiome data

   Chong Wu, Jun Chen, Junghi Kim, and Wei Pan

   Genome Medicine, 2016

   Bib PDF

   @article{wu2016adaptive,
     title = {An adaptive association test for microbiome data},
     author = {Wu, Chong and Chen, Jun and Kim, Junghi and Pan, Wei},
     journal = {Genome Medicine},
     volume = {8},
     pages = {1--12},
     year = {2016},
     publisher = {Springer},
     url = {https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0302-3},
   }

3. Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data

   Chong Wu, Ellen W Demerath, James S Pankow, Jan Bressler, Myriam Fornage, Megan L Grove, Wei Chen, and Weihua Guan

   Epigenetics, 2016

2014

1. Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk In Communities (ARIC) Study

   Maitreyee Bose, Chong Wu, James S Pankow, Ellen W Demerath, Jan Bressler, Myriam Fornage, Megan L Grove, Thomas H Mosley, Chindo Hicks, Kari North, and 1 more author

   BMC Bioinformatics, 2014