Department of Medical Genetics
Wenjian Bi
Wenjian Bi
Contact Information
Email: wenjianb@pku.edu.cn
Research Direction
With the advances in genotyping technologies and electronic health records (EHRs), large biobanks have been great resources to identify novel genetic associations and gene-environment interactions on a genome-wide and even a phenome-wide scale. Our researches focus on big data analysis, statistical genetics, and systems biology.
Personal Profile
WenJian Bi is a Principal Investigator and tenure-track Assistant Professor at the Department of Medical Genetics, Peking University School of Basic Medical Sciences. He received his bachelor's degree from the School of Mathematics at Sichuan University in 2010, and his Ph.D. from the Academy of Mathematics and Systems Science, Chinese Academy of Sciences in 2015. He carried out postdoctoral research at St. Jude Children's Research Hospital in the United States from 2015 to 2018 and at the University of Michigan from 2018 to 2021. In June 2021, he joined the School of Basic Medical Sciences at Peking University.
His main research interests include statistical genetics, biostatistics and systems biology, and bioinformatics. He has developed multiple fast and accurate analytical algorithms for gene-environment interaction, survival data, and multiclass phenotypic data, which have been applied to real data from large biobanks such as the UK Biobank. He has published as first or corresponding author in journals including Nature Genetics (2022), Nature Computational Science (2025), American Journal of Human Genetics (2019, 2020, 2021, 2023), Cell Reports Medicine (2025), Nature Communications (2025a, 2025b, 2025c), Genome Biology (2025), PLOS Genetics , Genetics , and Biostatistics . He has led several research projects.
Representative works (last five years)
2025
1. Ying Li, Yuzhuo Ma, He Xu, Yaoyao Sun*, Min Zhu, Weihua Yue, Wei Zhou*, Wenjian Bi*, Applying weighted Cox regression to genome-wide association studies of time-to-event phenotypes. Nature Computational Science , 2025.
2. Yuzhuo Ma, Yanlong Zhao, Ji-Feng Zhang, Wenjian Bi*, Efficient and accurate framework for genome-wide gene-environment interaction analysis in large-scale biobanks. Nature Communications , 2025, 16: 3064. (中国科学院1区top)
3. He Xu, Yuzhuo Ma, Lin-lin Xu, Yin Li, Yufei Liu, Ying Li, Xu-jie Zhou,Wei Zhou, Seunggeun Lee, Peipei Zhang*, Weihua Yue*, Wenjian Bi*, SPAGRM: effectively controlling for sample relatedness in large-scale genome-wide association studies of longitudinal traits. Nature Communications , 2025, 16: 1413. (中科院1区top)
4. Yaoyao Sun, Yundan Liao, Yuyanan Zhang, Zhe Lu, Yuzhuo Ma, Zhewei Kang, Xiaoyang Feng, Guorui Zhao, Junyuan Sun, Yunqing Zhu, Rui Yuan, Yang Yang, Liangkun Guo, Xiao Zhang, Dai Zhang, Runsen Chen*, Wenjian Bi*, Weihua Yue*, Genome-wide interaction association analysis identifies interactive effects of childhood maltreatment and kynurenine pathway on depression. Nature Communications , 2025, 16: 1748. (中科院1区top)
5. Yuzhuo Ma, He Xu, Ying Li, Hyesung Kim, Lin-lin Xu, Lin Miao, Peng Xu, Fengbiao Mao, Xu-jie Zhou, Wei Zhou, Seunggeun Lee, Ji-Feng Zhang*, Peipei Zhang*, Wenjian Bi*, SPAmix: a scalable, accurate, and universal analysis framework for large‑scale genetic association studies in admixed populations. Genome Biology , 2025, https://doi.org/10.1186/s13059-025-03827-9.
6. Yaoyao Sun#, Guorui Zhao#, Yuyanan Zhang, Zhe Lu, Zhewei Kang, Junyuan Sun, Xiaoyang Feng, Jing Guo, Yundan Liao, Liangkun Guo, Yang Yang, Dai Zhang, Wenjian Bi*, Runsen Chen*, Weihua Yue*, Multitrait GWAS of non-suicidal self-injury and the polygenetic effects on child psychopathology and brain structures, Cell Reports Medicine , 2025, 6(5): 102119. (中科院1区top)
2024
7. Wenjian Bi*, Zhiyu Xu*, Feng Liu, Zhi Xie, Hao Liu, Xiaotian Zhu, Wenge Zhong, Peipei Zhang#, Xing Tang#, Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer type, PLOS Genetics , 2024, 1: e1011134. (中科院2区top, 遗传学)
2023
8. Wenjian Bi#*, Wei Zhou*, Peipei Zhang, Yaoyao Sun, Weihua Yue, Seunggeun Lee#. Scalable mixed model methods for set-based association studies on large-scale categorical data analysis and its application to exome sequencing data in UK Biobank, American Journal of Human Genetics , 2023, 110(5): 762-773. (中科院1区top, 遗传学)
9. Yaoyao Sun, Yuyanan Zhang, Zhe Lu, Hao Yan, Liangkun Guo, Yundan Liao, Tianlan Lu, Lifang Wang, Jun Li, Wenqiang Li, Yongfeng Yang, Hao Yu, Luxian Lv, Dai Zhang, Wenjian Bi#, Weihua Yue#, Longitudinal Network Analysis Reveals Interactive Change of Schizophrenia Symptoms During Acute Antipsychotic Treatment. Schizophrenia Bulletin , 2023, 49(1): 208-217.
2022
10. Wei Zhou#* Wenjian Bi#*, Zhangchen Zhao*, Kushal K. Dey, Karthik A. Jagadeesh, Konrad J. Karczewski, Mark J. Daly, Benjamin M. Neale, Seunggeun Lee#, Set-based rare variant association tests for biobank scale sequencing data sets. Nature Genetics , 2022, 54 (10), 1466-1469. (中科院1区top, 遗传学)
11. Yongwen Zhuang, Brooke N Wolford, Kisung Nam, Wenjian Bi, Wei Zhou, Cristen J Willer, Bhramar Mukherjee, Seunggeun Lee. Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies. Bioinformatics . 2022. 38(18): 4337-4343.
12. Xiaohui Shi, Huajing Teng, Leisheng Shi, Wenjian Bi, Wenqing Wei, Fengbiao Mao#, and Zhongsheng Sun#. Comprehensive evaluation of computational methods for predicting cancer driver genes. Briefings in Bioinformatics, 2022. (中科院1区, 生化研究方法)
13. Xiaolu Zhao*, Leisheng Shi*, Shasha Ruan*, Wenjian Bi, Yifan Chen, Lin Chen, Yifan Liu, Mingkun Li, Jie Qiao#, and Fengbiao Mao#. CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic A cids Research , 2022, 50 (D1): D72-D82. (中科院1区, 生化与分子生物学)
2021
14. Wenjian Bi#, Wei Zhou, Rounak Dey, Bhramar Mukherjee, Joshua N Sampson, Seunggeun Lee# (2021), Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes. A merican Journal of Human Genetics , 108(5), 825-839. (中科院1区top, 遗传学)
15. Wenjian Bi#, Seunggeun Lee# (2021), Scalable and robust regression methods for phenome-wide association analysis on large-scale biobank data. Frontiers in Genetics , 12, 960.
16. Peng Xu, Daniel C. Scott, Beisi Xu, Yu Yao, Ruopeng Feng, Li Cheng, Kalin Mayberry, Yong-Dong Wang, Wenjian Bi, Lance E. Palmer, Moeko T. King, Hong Wang, Yuxin Li, Yiping Fan, Arno F. Alpi, Chunliang Li, Junmin Peng, James Papizan, Shondra M. Pruett-Miller, Ria Spallek, Florian Bassermann, Yong Cheng, Brenda A. Schulman, Mitchell J. Weiss (2021), FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. Blood , 137(2), 155–167.
2020
17. Wenjian Bi, Lars G. Fritsche, Bhramar Mukherjee, Sehee Kim, Seunggeun Lee (2020), A fast and accurate method for genome-wide time-to-event data analysis and its application to UK-Biobank. A merican Journal of Human Genetics , 107(2), 222-233. (中科院1区top, 遗传学)
18. Wenjian Bi, Yun Li, Matthew P. Smeltzer, Guimin Gao, Shengli Zhao, Guolian Kang (2020), STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing. Biostatistics , 21(1), 33-49. (中科院1区top, 数学与计算生物学)
19. Hang Zhang*, Wenjian Bi*, Yuehua Cui, Honglei Chen, Jinbo Chen, Yanlong Zhao, Guolian Kang (2020), Extreme-value sampling design is cost-benefit only with valid statistical approach for exposure-secondary outcome association analyses. Statistical Methods in Medical Research , 29 (2), 466-480. (中科院2区, 数学与计算生物学)
20. Wei Zhou, Zhangchen Zhao, Jonas B Nielsen, Lars G Fritsche, Jonathon LeFaive, Sarah A Gagliano Taliun, Wenjian Bi, Maiken E Gabrielsen, Mark J Daly, Benjamin M Neale, Kristian Hveem, Goncalo R Abecasis, Cristen J Willer, Seunggeun Lee (2020), Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts. Nature Genetics . 52, 634-639. (中科院1区top, 遗传学)
21. Zhangchen Zhao, Wenjian Bi, Wei Zhou, Peter VandeHaar, Lars G Fritsche, Seunggeun Lee (2020), UK-Biobank whole exome sequence binary phenome analysis with robust region-based rare variant test. American Journal of Human Genetics , 106(1), 3-12. (中科院1区top, 遗传学)
22. Bing Bai, Xusheng Wang, Yuxin Li, Ping-Chung Chen, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutx, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn A. Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu, Junmin Peng (2020), Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression. Neuron , 105 (6), 975-991. (中科院1区top, 神经科学)