The University of Queensland

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. (2023). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e1. doi: 10.1016/j.devcel.2023.11.012

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

ADVANCES IN POLYGENIC SCORE METHODS AND APPLICATIONS IN PSYCHIATRIC GENETICS

Vilhjalmsson, Bjarni, Zeng, Jian and Wray, Naomi (2023). ADVANCES IN POLYGENIC SCORE METHODS AND APPLICATIONS IN PSYCHIATRIC GENETICS. European Neuropsychopharmacology, 75, S29. doi: 10.1016/j.euroneuro.2023.08.062

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

Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes

Wu, Yang, Qi, Ting, Wray, Naomi R., Visscher, Peter M., Zeng, Jian and Yang, Jian (2023). Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes. Cell Genomics, 3 (8) 100344, 100344. doi: 10.1016/j.xgen.2023.100344

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

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

Li, Ang, Liu, Shouye, Bakshi, Andrew, Jiang, Longda, Chen, Wenhan, Zheng, Zhili, Sullivan, Patrick F., Visscher, Peter M., Wray, Naomi R., Yang, Jian and Zeng, Jian (2023). mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data. American Journal of Human Genetics, 110 (1), 30-43. doi: 10.1016/j.ajhg.2022.12.006

Dynamic Robust Particle Swarm Optimization Algorithm Based on Hybrid Strategy

Zeng, Jian, Yu, Xiaoyong, Yang, Guoyan and Gui, Haitao (2023). Dynamic Robust Particle Swarm Optimization Algorithm Based on Hybrid Strategy. International Journal of Swarm Intelligence Research, 14 (1). doi: 10.4018/IJSIR.325006

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

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

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

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

Widespread signatures of natural selection across human complex traits and functional genomic categories

Zeng, Jian, Xue, Angli, Jiang, Longda, Lloyd-Jones, Luke R., Wu, Yang, Wang, Huanwei, Zheng, Zhili, Yengo, Loic, Kemper, Kathryn E., Goddard, Michael E., Wray, Naomi R., Visscher, Peter M. and Yang, Jian (2021). Widespread signatures of natural selection across human complex traits and functional genomic categories. Nature Communications, 12 (1) 1164, 1-12. doi: 10.1038/s41467-021-21446-3

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

Correction: 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). Correction: Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes. Nature Communications, 12 (1) 988, 988. doi: 10.1038/s41467-021-21294-1

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

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

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

Improved polygenic prediction by Bayesian multiple regression on summary statistics

Lloyd-Jones, Luke R., Zeng, Jian, Sidorenko, Julia, Yengo, Loïc, Moser, Gerhard, Kemper, Kathryn E., Wang, Huanwei, Zheng, Zhili, Magi, Reedik, Esko, Tõnu, Metspalu, Andres, Wray, Naomi R., Goddard, Michael E., Yang, Jian and Visscher, Peter M. (2019). Improved polygenic prediction by Bayesian multiple regression on summary statistics. Nature Communications, 10 (1) 5086, 1-10. doi: 10.1038/s41467-019-12653-0

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

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

Minimally invasive lobectomy with neoadjuvant targeted therapy: the Zhejiang Cancer Hospital experience

Luo, Taobo and Zeng, Jian (2019). Minimally invasive lobectomy with neoadjuvant targeted therapy: the Zhejiang Cancer Hospital experience. Journal of Thoracic Disease, 11 (1), 266-269. doi: 10.21037/jtd.2018.12.100

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

Xue, Angli, Wu, Yang, Zhu, Zhihong, Zhang, Futao, Kemper, Kathryn E., Zheng, Zhili, Yengo, Loic, Lloyd-Jones, Luke R., Sidorenko, Julia, Wu, Yeda, eQTLGen Consortium, McRae, Allan F., Visscher, Peter M., Zeng, Jian and Yang, Jian (2018). Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes. Nature Communications, 9 (1) 2941, 2941. doi: 10.1038/s41467-018-04951-w

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

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

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. Nature Genetics, 50 (5), 746-753. doi: 10.1038/s41588-018-0101-4

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

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

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits

Wu, Yang, Zeng, Jian, Zhang, Futao, Zhu, Zhihong, Qi, Ting, Zheng, Zhili, Lloyd-Jones, Luke R., Marioni, Riccardo E., Martin, Nicholas G., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018). Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nature Communications, 9 (918) 918, 918. doi: 10.1038/s41467-018-03371-0

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

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

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

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

Zeng, Jian, Garrick, Dorian J., Dekkers, Jack C. and Fernando, Rohan L (2016). A nested mixture model for genomic prediction using whole-genome SNP genotypes. Iowa State University Animal Industry Report, 13 (1). doi: 10.31274/ans_air-180814-452

Dissecting the genetic architecture of frost tolerance in Central European winter wheat

Zhao, Yusheng, Gowda, Manje, Wuerschum, Tobias, Longin, C. Friedrich H., Korzun, Viktor, Kollers, Sonja, Schachschneider, Ralf, Zeng, Jian, Fernando, Rohan, Dubcovsky, Jorge and Reif, Jochen C. (2013). Dissecting the genetic architecture of frost tolerance in Central European winter wheat. Journal of Experimental Botany, 64 (14), 4453-4460. doi: 10.1093/jxb/ert259

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Zeng, Jian, Toosi, Ali, Fernando, Rohan L., Dekkers, Jack C. M. and Garrick, Dorian J. (2013). Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action. Genetics Selection Evolution, 45 (1) 11. doi: 10.1186/1297-9686-45-11

Genomic prediction of hybrid wheat performance

Zhao, Yusheng, Zeng, Jian, Fernando, Rohan and Reif, Jochen C. (2013). Genomic prediction of hybrid wheat performance. Crop Science, 53 (3), 802-810. doi: 10.2135/cropsci2012.08.0463

Genomic breeding value prediction and QTL mapping of QTLMAS2011 data using Bayesian and GBLUP methods

Zeng, Jian, Pszczola, Marcin, Wolc, Anna, Strabel, Tomasz, Fernando, Rohan L., Garrick, Dorian J. and Dekkers, Jack C. M. (2012). Genomic breeding value prediction and QTL mapping of QTLMAS2011 data using Bayesian and GBLUP methods. BMC Proceedings, 6 (S2) S7. doi: 10.1186/1753-6561-6-S2-S7

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

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

Zeng, Jian, Zheng, Zhili, Liu, Shouye, Sidorenko, Julia, Yengo, Loic, Turley, Patrick, Ani, Alireza, Wang, Rujia, Nolte, Ilja, Snieder, Harold, Yang, Jian, Wray, Naomi, Goddard, Michael and Visscher, Peter (2023). Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries. World Congress of Psychiatric Genetics (WCPG), Montreal, ON, Canada, 10 - 14 October 2023. Amsterdam, Netherlands: Elsevier BV. doi: 10.1016/j.euroneuro.2023.08.063

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.

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Zeng, Jian, Toosi, Ali, Fernando, Rohan L., Dekkers, Jack C. M. and Garrick, Dorian J. (2013). Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action. Ames: Iowa State University, Digital Repository. doi: 10.31274/ans_air-180814-1249

Whole genome association analysis of idiopathic eosinophilic enteritis in brown egg layers

Deng, Xuemei, Arango, Jesus, Kizilkaya, Kadir, Zeng, Jian, Cai, Weiguo, Fulton, Janet, O'Sullivan, Neil and Dekkers, Jack C.M. (2011). Whole genome association analysis of idiopathic eosinophilic enteritis in brown egg layers. Ames, United States: Iowa State University. doi: 10.31274/ans_air-180814-77