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

67 works between 2011 and 2026
All (67) Journal Article (58) Other Outputs (2) Conference Publication (7)

41 - 60 of 67 works

2023

Journal Article

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Sullivan, Patrick F., Meadows, Jennifer R. S., Gazal, Steven, Phan, BaDoi N., Li, Xue, Genereux, Diane P., Dong, Michael X., Bianchi, Matteo, Andrews, Gregory, Sakthikumar, Sharadha, Nordin, Jessika, Roy, Ananya, Christmas, Matthew J., Marinescu, Voichita D., Wang, Chao, Wallerman, Ola, Xue, James, Yao, Shuyang, Sun, Quan, Szatkiewicz, Jin, Wen, Jia, Huckins, Laura M., Lawler, Alyssa, Keough, Kathleen C., Zheng, Zhili, Zeng, Jian, Wray, Naomi R., Li, Yun, Johnson, Jessica ... Zoonomia Consortium§ (2023). Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science, 380 (6643) eabn2937, 1-12. doi: 10.1126/science.abn2937

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

2022

Journal Article

Genetic control of RNA splicing and its distinct role in complex trait variation

Qi, Ting, Wu, Yang, Fang, Hailing, Zhang, Futao, Liu, Shouye, Zeng, Jian and Yang, Jian (2022). Genetic control of RNA splicing and its distinct role in complex trait variation. Nature Genetics, 54 (9), 1355-1363. doi: 10.1038/s41588-022-01154-4

Genetic control of RNA splicing and its distinct role in complex trait variation

2022

Journal Article

Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data

Zhao, Tianjing, Zeng, Jian and Cheng, Hao (2022). Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data. Genetics, 221 (1) iyac034. doi: 10.1093/genetics/iyac034

Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data

2022

Journal Article

Comparative analysis reveals novel changes in plasma metabolites and metabolomic networks of infants with retinopathy of prematurity

Yang, Yuhang, Yang, Qian, Luo, Sisi, Zhang, Yinsheng, Lian, Chaohui, He, Honghui, Zeng, Jian and Zhang, Guoming (2022). Comparative analysis reveals novel changes in plasma metabolites and metabolomic networks of infants with retinopathy of prematurity. Investigative Ophthalmology and Visual Science, 63 (1) 28. doi: 10.1167/iovs.63.1.28

Comparative analysis reveals novel changes in plasma metabolites and metabolomic networks of infants with retinopathy of prematurity

2021

Journal Article

A comparison of ten polygenic score methods for psychiatric disorders applied across multiple cohorts

Ni, Guiyan, Zeng, Jian, Revez, Joana A., Wang, Ying, Zheng, Zhili, Ge, Tian, Restuadi, Restuadi, Kiewa, Jacqueline, Nyholt, Dale R., Coleman, Jonathan R.I., Smoller, Jordan W., Yang, Jian, Visscher, Peter M. and Wray, Naomi R. (2021). A comparison of ten polygenic score methods for psychiatric disorders applied across multiple cohorts. Biological Psychiatry, 90 (9), 611-620. doi: 10.1016/j.biopsych.2021.04.018

A comparison of ten polygenic score methods for psychiatric disorders applied across multiple cohorts

2021

Journal Article

Tumor mutational burden is polygenic and genetically associated with complex traits and diseases

Sun, Xiwei, Xue, Angli, Qi, Ting, Chen, Dan, Shi, Dandan, Wu, Yang, Zheng, Zhili, Zeng, Jian and Yang, Jian (2021). Tumor mutational burden is polygenic and genetically associated with complex traits and diseases. Cancer Research, 81 (5) canres.3459.2020, 12230-1239. doi: 10.1158/0008-5472.can-20-3459

Tumor mutational burden is polygenic and genetically associated with complex traits and diseases

2021

Journal Article

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

Yap, Chloe X., Alvares, Gail A., Henders, Anjali K., Lin, Tian, Wallace, Leanne, Farrelly, Alaina, McLaren, Tiana, Berry, Jolene, Vinkhuyzen, Anna A. E., Trzaskowski, Maciej, Zeng, Jian, Yang, Yuanhao, Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren, Leslie, Jodie, Levis Frenk, Mira, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Visscher, Peter M., Dawson, Paul A., Dissanayake, Cheryl ... Gratten, Jacob (2021). Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank. Molecular Autism, 12 (1) 12, 12. doi: 10.1186/s13229-020-00407-5

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

2021

Journal Article

Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes

Xue, Angli, Jiang, Longda, Zhu, Zhihong, Wray, Naomi R., Visscher, Peter M., Zeng, Jian and Yang, Jian (2021). Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes. Nature Communications, 12 (1) 6450, 6450. doi: 10.1038/s41467-020-20237-6

Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes

2020

Journal Article

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

Wu, Yang, Qi, Ting, Wang, Huanwei, Zhang, Futao, Zheng, Zhili, Phillips-Cremins, Jennifer E., Deary, Ian J., McRae, Allan F., Wray, Naomi R., Zeng, Jian and Yang, Jian (2020). Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data. Nature Communications, 11 (1) 2061, 1-12. doi: 10.1038/s41467-020-15587-0

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

2020

Journal Article

Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration

Revez, Joana A., Lin, Tian, Qiao, Zhen, Xue, Angli, Holtz, Yan, Zhu, Zhihong, Zeng, Jian, Wang, Huanwei, Sidorenko, Julia, Kemper, Kathryn E., Vinkhuyzen, Anna A. E., Frater, Julanne, Eyles, Darryl, Burne, Thomas H. J., Mitchell, Brittany, Martin, Nicholas G., Zhu, Gu, Visscher, Peter M., Yang, Jian, Wray, Naomi R. and McGrath, John J. (2020). Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration. Nature Communications, 11 (1) 1647, 1-12. doi: 10.1038/s41467-020-15421-7

Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration

2019

Journal Article

Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank

Wang, Huanwei, Zhang, Futao, Zeng, Jian, Wu, Yang, Kemper, Kathryn E., Xue, Angli, Zhang, Min, Powell, Joseph E., Goddard, Michael E., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2019). Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank. Science Advances, 5 (8) eaaw3538, 1-12. doi: 10.1126/sciadv.aaw3538

Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank

2019

Journal Article

The effect of X-linked dosage compensation on complex trait variation

Sidorenko, Julia, Kassam, Irfahan, Kemper, Kathryn E., Zeng, Jian, Lloyd-Jones, Luke R., Montgomery, Grant W., Gibson, Greg, Metspalu, Andres, Esko, Tonu, Yang, Jian, McRae, Allan F. and Visscher, Peter M. (2019). The effect of X-linked dosage compensation on complex trait variation. Nature Communications, 10 (1) 3009, 3009. doi: 10.1038/s41467-019-10598-y

The effect of X-linked dosage compensation on complex trait variation

2018

Journal Article

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

Qi, Ting, Wu, Yang, Zeng, Jian, Zhang, Futao, Xue, Angli, Jiang, Longda, Zhu, Zhihong, Kemper, Kathryn, Yengo, Loic, Zheng, Zhili, eQTLGen Consortium, Marioni, Riccardo E., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018). Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. Nature Communications, 9 (1) 2282, 2282. doi: 10.1038/s41467-018-04558-1

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

2018

Journal Article

Global genetic differentiation of complex traits shaped by natural selection in humans

Guo, Jing, Wu, Yang, Zhu, Zhihong, Zheng, Zhili, Trzaskowski, Maciej, Zeng, Jian, Robinson, Matthew R., Visscher, Peter M. and Yang, Jian (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications, 9 (1) 1865, 1865. doi: 10.1038/s41467-018-04191-y

Global genetic differentiation of complex traits shaped by natural selection in humans

2018

Journal Article

A nested mixture model for genomic prediction using whole-genome SNP genotypes

Zeng, Jian, Garrick, Dorian, Dekkers, Jack and Fernando, Rohan (2018). A nested mixture model for genomic prediction using whole-genome SNP genotypes. PloS one, 13 (3) e0194683, e0194683. doi: 10.1371/journal.pone.0194683

A nested mixture model for genomic prediction using whole-genome SNP genotypes

2018

Journal Article

Genomic prediction from multiple-trait bayesian regression methods using mixture priors

Cheng, Hao, Kizilkaya, Kadir, Zeng, Jian, Garrick, Dorian and Fernando, Rohan (2018). Genomic prediction from multiple-trait bayesian regression methods using mixture priors. Genetics, 209 (1), 89-103. doi: 10.1534/genetics.118.300650

Genomic prediction from multiple-trait bayesian regression methods using mixture priors

2018

Conference Publication

Signatures of negative selection in the genetic architecture of human complex traits

Zeng, Jian, de Vlaming, Ronald, Wu, Yang, Robinson, Matthew R., Lloyd-Jones, Luke R., Yengo, Loic, Yap, Chloe X., Xue, Angli, Sidorenko, Julia, Mcrae, Allan F., Powell, Joseph E., Montgomery, Grant W., Metspalu, Andres, Esko, Tonu, Gibson, Greg, Wray, Naomi R., Visscher, Peter M. and Yang, Jian (2018). Signatures of negative selection in the genetic architecture of human complex traits. 48th Annual Meeting of the Behavior-Genetics-Association (BGA), Boston MA, United States, 20-23 June 2018. New York, NY United States: Springer New York.

Signatures of negative selection in the genetic architecture of human complex traits

2017

Journal Article

Concepts, estimation and interpretation of SNP-based heritability

Yang, Jian, Zeng, Jian, Goddard, Michael E., Wray, Naomi R. and Visscher, Peter M. (2017). Concepts, estimation and interpretation of SNP-based heritability. Nature Genetics, 49 (9), 1304-1310. doi: 10.1038/ng.3941

Concepts, estimation and interpretation of SNP-based heritability

2017

Journal Article

Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models

Lloyd-Jones, Luke R., Robinson, Matthew R., Moser, Gerhard, Zeng, Jian, Beleza, Sandra, Barsh, Gregory S., Tang, Hua and Visscher, Peter M. (2017). Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics, 206 (2), 1113-1126. doi: 10.1534/genetics.116.193383

Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models

2016

Journal Article

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers

Heidaritabar, M., Wolc, A., Arango, J., Zeng, J., Settar, P., Fulton, J. E., O'Sullivan, N. P., Bastiaansen, J. W. M., Fernando, R. L., Garrick, D. J. and Dekkers, J. C. M. (2016). Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers. Journal of Animal Breeding and Genetics, 133 (5), 334-346. doi: 10.1111/jbg.12225

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers

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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