*Corresponding Author  #Co-first author

1. 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.

2. 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.

3. 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. 

4. 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, 2022, https://doi.org/10.1093/schbul/sbac131.

5. Wenjian Bi^*, Wei Zhou, Rounak Dey, Bhramar Mukherjee, Joshua N. Sampson, Seunggeun Lee^*, Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes. American Journal of Human Genetics, 2021, 108(5): 825-839.

6. Wenjian Bi, Lars G. Fritsche, Bhramar Mukherjee, Sehee Kim, Seunggeun Lee^*, A fast and accurate method for genome-wide time-to-event data analysis and its application to UK-Biobank. American Journal of Human Genetics, 2020, 107(2): 222-233.

7. Wenjian Bi, Zhangchen Zhao, Rounak Dey, Lars G Fritsche, Bhramar Mukherjee, Seunggeun Lee^*, A fast and accurate method for genome-wide scale phenome-wide G×E analysis and its application to UK Biobank. American Journal of Human Genetics, 2019, 105(6): 1182-1192.

8. Wenjian Bi, Yun Li, Matthew P. Smeltzer, Guimin Gao, Shengli Zhao, Guolian Kang^*, STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing. Biostatistics, 2020, 21(1): 33-49.

9. Guolian Kang^#*, Wenjian Bi^#, Hang Zhang, Stanley Pounds, Cheng Cheng, Sanjay Shete, Fei Zou, Yanlong Zhao, Ji-Feng Zhang, Weihua Yue^*, A robust and powerful set-valued approach to rare variant association analyses of secondary traits in case-control sequencing studies. Genetics, 2017, 205(3): 1049-1062.

10. 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.

11. 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.

12. 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 acids research, 2022, 50(D1): D72-D82.

13. Hang Zhang^#, Wenjian Bi^#, Yuehua Cui, Honglei Chen, Jinbo Chen, Yanlong Zhao*, Guolian Kang*, Extreme-value sampling design is cost-benefit only with valid statistical approach for exposure-secondary outcome association analyses. Statistical Methods in Medical Research, 2020, 29 (2): 466-480.

14. Guolian Kang^#*, Wenjian Bi^#, Yanlong Zhao^*, Ji-Feng Zhang, Jun J. Yang, Heng Xu, Mignon L. Loh, Stephen P. Hunger, Mary V. Relling, Stanley Pounds and Cheng Cheng, A system identification approach to identifying genetic variants in sequencing studies for a binary phenotype, Human Heredity, 2014, 78: 104-116.

15. Wenjian Bi^#, Guolian Kang^#*, Yanlong Zhao, Yuehua Cui, Yun Li, Christine M Hartford, Wing Leung and Ji-Feng Zhang^*, SVSI: A fast and powerful set-valued system identification approach to identifying rare variants in sequencing studies for ordered categorical traits, Annals of Human Genetics, 2015, 79: 294-309.

16. Wenjian Bi, Yanlong Zhao*, Iterative parameter estimate with batched binary-valued observations: convergence with an exponential rate, IFAC2014, 2014, 47(3): 3220-3225.

17. Hang Zhang, Wenjian Bi^*, Yanlong Zhao^*, Long Cheng, Set-valued system identification methods in retrospective cohort study and applications to GWAS, IFAC2017, 2017, 50(1): 1583-1588.

18. Hao Yu^#, Wenjian Bi^#, Chenxing Liu, Yanlong Zhao, Ji-Feng Zhang, Dai Zhang^* and Weihua Yue^*, Protein-interaction-network-based analysis for genome-wide association analysis of schizophrenia in Han Chinese population, Journal of Psychiatric Research, 2014, 50: 73-78. 

19. Hao Yu^#, Wenjian Bi^#, Chenxing Liu, Yanlong Zhao, Dai Zhang and Weihua Yue^*, A hypothesis-driven pathway analysis reveals Myelin-related pathways that contribute to the risk of schizophrenia and bipolar disorder, Progress in Neuro-Psychopharmacology & Biological Psychiatry, 2014, 51: 140-145. 

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^*, Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts. Nature Genetics. 2020, 52: 634-639.

21. Zhangchen Zhao, Wenjian Bi, Wei Zhou, Peter VandeHaar, Lars G Fritsche, Seunggeun Lee^*, UK-Biobank whole exome sequence binary phenome analysis with robust region-based rare variant test. American Journal of Human Genetics, 2020, 106(1): 3-12.

22. Yanlong Zhao*, Ting Wang, Wenjian Bi, Consensus protocol for multiagent systems with undirected topologies and binary-valued communications, IEEE Transactions on Automatic Control, 2019, 64(1): 206-221.

23. Yanlong Zhao^*, Wenjian Bi and Ting Wang, Iterative parameter estimate with batched binary-valued observations. Science China Information Sciences, 2016, 59: 052201.

24. 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, 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^*, Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression. Neuron, 2020, 105 (6): 975-991.

25. Peng Xu, Daniel C. Scott, Beisi Xu, Yu Yao, Ruopeng Feng, Li Cheng, Kalin Mayberry, 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^*, FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. Blood, 2020, 137 (2): 155-167.

26. Miguel Ganuza, Trent Hall, David Finkelstein, Yong-Dong Wang, Ashley Chabot, Guolian Kang, Wenjian Bi, Gang Wu, Shannon McKinney-Freeman^*, The global clonal complexity of the murine blood system declines throughout life and after serial transplantation. Blood, 2019, 133(18): 1927-1942.

27. Miguel Ganuza, Ashley Chabot, Xing Tang, Wenjian Bi, Sivaraman Natarajan, Robert Carter, Charles Gawad, Guolian Kang, Yong Cheng, Shannon McKinney-Freeman^*, Murine hematopoietic stem cell activity is derived from pre-circulation embryos but not yolk sacs. Nature Communications, 2018, 9: 5405.

28. Mingming Niu, Ji-Hoon Cho, Kiran Kodali, Vishwajeeth Pagala, Anthony A. High, Hong Wang, Zhiping Wu, Yuxin Li, Wenjian Bi, Hui Zhang, Xusheng Wang, Wei Zou, Junmin Peng^*, Extensive peptide fractionation and y₁ ion-based interference detection enable accurate quantification by isobaric labeling mass spectrometry. Analytical Chemistry, 2017, 89(5): 2956-2963.

29. Latika Puri, Jonathan M Flanagan, Guolian Kang, Juan Ding, Wenjian Bi, Beth M McCarville, Ralf B Loeffler, Aaryani Tipirneni-Sajja, Martha Villavicencio, Kristine R Crews, Claudia M Hillenbrand, Jane S Hankins^*, GSTM1 and liver iron content in children with sickle cell anemia and iron overload. Journal of Clinical Medicine, 2019, 8(11): 1878.