Dr Jian Zeng
Dr

Jian Zeng

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Background

Dr Jian Zeng is a statistical geneticist, NHMRC Emerging Leadership Fellow and Group Leader at the Institute for Molecular Bioscience, The University of Queensland. His research uses large-scale genomic data to understand the genetic basis of complex traits and diseases, improve polygenic risk prediction, and identify the genes, cell types and biological processes through which genetic risk acts.

His group develops statistical methods and software tools across four interconnected areas:

  • genetic architecture and evolutionary signatures of complex traits;
  • polygenic prediction within and across diverse populations;
  • fine-mapping of causal genetic variants and genes;
  • integration of human genetics with functional and single-cell genomics.

This work addresses major challenges in statistical genetics and precision medicine, including the analysis of whole-genome sequencing data, the reduced accuracy of genetic prediction in underrepresented populations, and the biological interpretation of disease-associated variants. His methods are translated into accessible software used by researchers internationally and are applied to psychiatric, neurological, metabolic and other complex diseases.

Dr Zeng received the IMB Impact Award for Enabling Technology and Method Development in 2021 and the UQ Foundation Research Excellence Award in 2025.

Availability

Dr Jian Zeng is:
Available for supervision

Fields of research

Bioinformatics and computational biology Biological Sciences Epigenetics (incl. genome methylation and epigenomics) Gene mapping Genetics Genetics not elsewhere classified Genomics Statistical and quantitative genetics

Qualifications

  • Doctor of Philosophy, University of Iowa

Research interests

  • Understanding genetic architecture and evolution of complex traits

  • Prediction of polygenic scores of complex traits and diseases

  • Mapping causal variants, genes and regulatory elements using multi-omics data

  • Integration of population genetics with single-cell genomics

Research impacts

Dr Jian Zeng’s research translates advances in statistical genetics into freely available software that helps researchers worldwide analyse genomic data, improve disease-risk prediction, and identify likely causal variants, genes and cell types. His work supports more accurate and equitable precision medicine by enabling earlier identification of disease risk and a deeper understanding of the biological mechanisms that could guide prevention and therapeutic discovery.

Search Professor Jian Zeng’s works on UQ eSpace

70 works between 2011 and 2026
All (70) Journal Article (59) Other Outputs (2) Conference Publication (9)

21 - 40 of 70 works

2026

Journal Article

Progress in understanding the biological basis of polygenic disorders

Wray, Naomi R., Lin, Tian, Li, A., de Almeida, Valéria Correia, Ziller, Michael Johannes and Zeng, Jian (2026). Progress in understanding the biological basis of polygenic disorders. Current Opinion in Genetics and Development, 97 102433, 102433. doi: 10.1016/j.gde.2025.102433

Progress in understanding the biological basis of polygenic disorders

2026

Journal Article

Author Correction: Genome-wide fine-mapping improves identification of causal variants (Nature Genetics, (2026), 58, 4, (940-951), 10.1038/s41588-026-02549-3)

Wu, Yang, Zheng, Zhili, Thibaut, Loic, Lin, Tian, Feng, Qian, Cheng, Hao, Yengo, Loic, Goddard, Michael E., Wray, Naomi R., Visscher, Peter M. and Zeng, Jian (2026). Author Correction: Genome-wide fine-mapping improves identification of causal variants (Nature Genetics, (2026), 58, 4, (940-951), 10.1038/s41588-026-02549-3). Nature Genetics, 58 (6), 1446-1446. doi: 10.1038/s41588-026-02627-6

Author Correction: Genome-wide fine-mapping improves identification of causal variants (Nature Genetics, (2026), 58, 4, (940-951), 10.1038/s41588-026-02549-3)

2025

Journal Article

Estimation and mapping of the missing heritability of human phenotypes

Wainschtein, Pierrick, Zhang, Yuanxiang, Schwartzentruber, Jeremy, Kassam, Irfahan, Sidorenko, Julia, Fiziev, Petko P., Wang, Huanwei, McRae, Jeremy, Border, Richard, Zaitlen, Noah, Sankararaman, Sriram, Goddard, Michael E., Zeng, Jian, Visscher, Peter M., Farh, Kyle Kai-How and Yengo, Loic (2025). Estimation and mapping of the missing heritability of human phenotypes. Nature, 649 (8099), 1219-1227. doi: 10.1038/s41586-025-09720-6

Estimation and mapping of the missing heritability of human phenotypes

2025

Journal Article

Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease

Sinniah, Enakshi, Mizikovsky, Dalia, Shim, Woo Jun, Chow, Chris Siu Yeung, Souilmi, Yassine, Cheng, Fei-Fei, Zeng, Zhili, Laurie, Jordan, Foster, Matthew, Shah, Sonia, Bodén, Mikael, Zeng, Jian, Llamas, Bastien and Palpant, Nathan J. (2025). Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease. Nucleic Acids Research, 53 (20) gkaf971, 1-23. doi: 10.1093/nar/gkaf971

Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease

2025

Conference Publication

A mixture model approach for correcting systematic measurement errors in sitting height data from UK biobank

Ge, Jieyu, Zeng, Jian, Yengo, Loic and Visscher, Peter (2025). A mixture model approach for correcting systematic measurement errors in sitting height data from UK biobank. 2025 Annual Meeting of the International Genetic Epidemiology Society, Cologne, Germany, 1 - 2 September 2025. Hoboken, NJ, United States: John Wiley & Sons. doi: 10.1002/gepi.70017

A mixture model approach for correcting systematic measurement errors in sitting height data from UK biobank

2025

Journal Article

Brain–heart–eye axis revealed by multi-organ imaging genetics and proteomics

Zeng, Jian, Aisen, Paul, Rafii, Michael S., Bai, Wenjia, Ferrucci, Luigi, Tian, Ye Ella, Zalesky, Andrew, Boquet-Pujadas, Aleix, Anagnostakis, Filippos, Duggan, Michael R., Joynes, Cassandra M., Toga, Arthur W., Yang, Zhijian, Walker, Keenan A., Davatzikos, Christos and Wen, Junhao (2025). Brain–heart–eye axis revealed by multi-organ imaging genetics and proteomics. Nature Biomedical Engineering, 10 (6), 1171-1193. doi: 10.1038/s41551-025-01506-5

Brain–heart–eye axis revealed by multi-organ imaging genetics and proteomics

2025

Journal Article

Harnessing functional annotation to improve the accuracy and transferability of polygenic scores

Zeng, Jian and Visscher, Peter M. (2025). Harnessing functional annotation to improve the accuracy and transferability of polygenic scores. Nature Reviews Genetics, 26 (12), 1-2. doi: 10.1038/s41576-025-00893-4

Harnessing functional annotation to improve the accuracy and transferability of polygenic scores

2025

Journal Article

MUTATE: a human genetic atlas of multiorgan artificial intelligence endophenotypes using genome-wide association summary statistics

Boquet-Pujadas, Aleix, Zeng, Jian, Tian, Ye Ella, Yang, Zhijian, Shen, Li, Zalesky, Andrew, Davatzikos, Christos and Wen, Junhao (2025). MUTATE: a human genetic atlas of multiorgan artificial intelligence endophenotypes using genome-wide association summary statistics. Briefings in Bioinformatics, 26 (2) bbaf125, 1-16. doi: 10.1093/bib/bbaf125

MUTATE: a human genetic atlas of multiorgan artificial intelligence endophenotypes using genome-wide association summary statistics

2025

Journal Article

Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies

Adams, Mark J., Streit, Fabian, Meng, Xiangrui, Awasthi, Swapnil, Adey, Brett N., Choi, Karmel W., Chundru, V. Kartik, Coleman, Jonathan R.I., Ferwerda, Bart, Foo, Jerome C., Gerring, Zachary F., Giannakopoulou, Olga, Gupta, Priya, Hall, Alisha S.M., Harder, Arvid, Howard, David M., Hübel, Christopher, Kwong, Alex S.F., Levey, Daniel F., Mitchell, Brittany L. (Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium member), Ni, Guiyan, Ota, Vanessa K., Pain, Oliver, Pathak, Gita A., Schulte, Eva C., Shen, Xueyi, Thorp, Jackson G., Walker, Alicia, Yao, Shuyang ... McIntosh, Andrew M. (2025). Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies. Cell, 188 (3), 640-652.e9. doi: 10.1016/j.cell.2024.12.002

Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies

2025

Journal Article

Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity

Yao, Shuyang, Harder, Arvid, Darki, Fahimeh, Chang, Yu-Wei, Li, Ang, Nikouei, Kasra, Volpe, Giovanni, Lundström, Johan N., Zeng, Jian, Wray, Naomi R., Lu, Yi, Sullivan, Patrick F. and Hjerling-Leffler, Jens (2025). Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity. Nature Communications, 16 (1) 395, 1-18. doi: 10.1038/s41467-024-55611-1

Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity

2025

Journal Article

Tracing human trait evolution through integrative genomics and temporal annotations

Zeng, Jian (2025). Tracing human trait evolution through integrative genomics and temporal annotations. Cell Genomics, 5 (2) 100767, 100767-2. doi: 10.1016/j.xgen.2025.100767

Tracing human trait evolution through integrative genomics and temporal annotations

2024

Journal Article

DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits

Hwang, Liang-Dar, Cuellar-Partida, Gabriel, Yengo, Loic, Zeng, Jian, Toivonen, Jarkko, Arvas, Mikko, Beaumont, Robin N., Freathy, Rachel M., Moen, Gunn-Helen, Warrington, Nicole M. and Evans, David M. (2024). DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits. Nature Communications, 15 (1) 9255, 1-14. doi: 10.1038/s41467-024-53495-9

DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits

2024

Conference Publication

Genome-wide Fine-mapping Improves Identification Of Causal Variants

Zeng, Jian, Wu, Yang, Zheng, Zhili, Thibaut, Loic, Goddard, Michael, Wray, Naomi and Visscher, Peter (2024). Genome-wide Fine-mapping Improves Identification Of Causal Variants. World Congress of Psychiatric Genetics WCPG 2024, Singapore, 15-19 October 2024. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.euroneuro.2024.08.037

Genome-wide Fine-mapping Improves Identification Of Causal Variants

2024

Journal Article

Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics

Yap, Chloe X., Vo, Daniel D., Heffel, Matthew G., Bhattacharya, Arjun, Wen, Cindy, Yang, Yuanhao, Kemper, Kathryn E., Zeng, Jian, Zheng, Zhili, Zhu, Zhihong, Hannon, Eilis, Vellame, Dorothea Seiler, Franklin, Alice, Caggiano, Christa, Wamsley, Brie, Geschwind, Daniel H., Zaitlen, Noah, Gusev, Alexander, Pasaniuc, Bogdan, Mill, Jonathan, Luo, Chongyuan and Gandal, Michael J. (2024). Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics. Science Advances, 10 (21) adn7655, eadn7655. doi: 10.1126/sciadv.adn7655

Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics

2024

Journal Article

Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits

Keaton, Jacob M., Kamali, Zoha, Xie, Tian, Vaez, Ahmad, Williams, Ariel, Goleva, Slavina B., Ani, Alireza, Evangelou, Evangelos, Hellwege, Jacklyn N., Yengo, Loic, Young, William J., Traylor, Matthew, Giri, Ayush, Zheng, Zhili, Zeng, Jian, Chasman, Daniel I., Morris, Andrew P., Caulfield, Mark J., Hwang, Shih-Jen, Kooner, Jaspal S., Conen, David, Attia, John R., Morrison, Alanna C., Loos, Ruth J. F., Kristiansson, Kati, Schmidt, Reinhold, Hicks, Andrew A., Pramstaller, Peter P., Nelson, Christopher P. ... ICBP Consortium (2024). Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits. Nature Genetics, 56 (5), 1-14. doi: 10.1038/s41588-024-01714-w

Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits

2024

Journal Article

Unravelling the complex causal effects of substance use behaviours on common diseases

Xue, Angli, Zhu, Zhihong, Wang, Huanwei, Jiang, Longda, Visscher, Peter M., Zeng, Jian and Yang, Jian (2024). Unravelling the complex causal effects of substance use behaviours on common diseases. Communications Medicine, 4 (1) 43, 1-13. doi: 10.1038/s43856-024-00473-3

Unravelling the complex causal effects of substance use behaviours on common diseases

2024

Journal Article

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

Friedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and Palpant, Nathan J. (2024). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e6. doi: 10.1016/j.devcel.2023.11.012

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

2023

Journal Article

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

Costilla, R., Zeng, J., Al Kalaldeh, M., Swaminathan, M., Gibson, J.P., Ducrocq, V. and Hayes, B.J. (2023). Developing flexible models for genetic evaluations in smallholder crossbred dairy farms. Journal of Dairy Science, 106 (12), 9125-9135. doi: 10.3168/jds.2022-23135

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

2023

Journal Article

Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits

Li, Jinghui, Zhao, Tianjing, Guan, Dailu, Pan, Zhangyuan, Bai, Zhonghao, Teng, Jinyan, Zhang, Zhe, Zheng, Zhili, Zeng, Jian, Zhou, Huaijun, Fang, Lingzhao and Cheng, Hao (2023). Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits. Cell Genomics, 3 (10) 100390, 100390. doi: 10.1016/j.xgen.2023.100390

Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits

2023

Conference Publication

IDENTIFICATION OF CELL TYPES AND CELLULAR DYNAMICS GENETICALLY ASSOCIATED WITH BRAIN DISORDERS AND COGNITIVE TRAITS

Yao, Shuyang, Harder, Arvid, Darki, Fahimeh, Li, Ang, Zeng, Jian, Nikouei, Kasra, Lundstrom, Johan, Wray, Naomi, Lu, Yi, Sullivan, Patrick and Hjerling-Leffler, Jens (2023). IDENTIFICATION OF CELL TYPES AND CELLULAR DYNAMICS GENETICALLY ASSOCIATED WITH BRAIN DISORDERS AND COGNITIVE TRAITS. World Congress of Psychiatric Genetics (WCPG), Montreal Canada, Oct 10-14, 2023. AMSTERDAM: ELSEVIER. doi: 10.1016/j.euroneuro.2023.08.160

IDENTIFICATION OF CELL TYPES AND CELLULAR DYNAMICS GENETICALLY ASSOCIATED WITH BRAIN DISORDERS AND COGNITIVE TRAITS

Current funding

  • 2026 - 2028
    The Claustrum as a Vulnerability Node: Linking Psychiatric Disease Risk to Circuit Architecture
    The Hebrew University of Jerusalem
    Open grant
  • 2026 - 2029
    Developing and Applying Novel Polygenic Score Approaches in ALS for Risk Prediction, Stratification, and Precision Medicine
    FightMND Discovery Grant
    Open grant
  • 2026 - 2028
    Identification of causal variants for complex traits (ARC Discovery Project administered by the University of Melbourne)
    University of Melbourne
    Open grant
  • 2026
    Integrating individual genotypes and phenotypes with single-cell transcriptomic data to enhance disease risk prediction
    UQ Foundation Research Excellence Awards
    Open grant
  • 2026 - 2030
    Integrating single-cell omics with genetics: Novel statistical methods to enhance biological understanding and risk prediction of common diseases
    NHMRC Investigator Grants
    Open grant
  • 2022 - 2026
    Genetic architecture and evolution of complex traits across populations
    ARC Discovery Projects
    Open grant

Past funding

  • 2020 - 2025
    Statistical methods and tools to integrate genetic and non-genetic data for risk prediction of common diseases
    NHMRC Investigator Grants
    Open grant

Availability

Dr Jian Zeng is:
Available for supervision

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Supervision history

Current supervision

Completed supervision

Enquiries

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