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2025 Journal Article Harnessing functional annotation to improve the accuracy and transferability of polygenic scoresZeng, 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 |
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2025 Journal Article MUTATE: a human genetic atlas of multiorgan artificial intelligence endophenotypes using genome-wide association summary statisticsBoquet-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 |
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2025 Journal Article Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapiesAdams, 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 |
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2025 Journal Article Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivityYao, 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 |
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2025 Journal Article Tracing human trait evolution through integrative genomics and temporal annotationsZeng, 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 |
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2024 Journal Article DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traitsHwang, 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 |
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2024 Journal Article Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and geneticsYap, 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 |
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2024 Journal Article Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traitsKeaton, 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 |
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2024 Journal Article Unravelling the complex causal effects of substance use behaviours on common diseasesXue, 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 |
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2024 Journal Article HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and functionFriedman, 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 |
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2023 Journal Article Developing flexible models for genetic evaluations in smallholder crossbred dairy farmsCostilla, 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 |
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2023 Journal Article Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traitsLi, 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 |
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2023 Journal Article Leveraging base-pair mammalian constraint to understand genetic variation and human diseaseSullivan, 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 |
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2022 Journal Article Genetic control of RNA splicing and its distinct role in complex trait variationQi, 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 |
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2022 Journal Article Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics dataZhao, 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 |
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2022 Journal Article Comparative analysis reveals novel changes in plasma metabolites and metabolomic networks of infants with retinopathy of prematurityYang, 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 |
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2021 Journal Article A comparison of ten polygenic score methods for psychiatric disorders applied across multiple cohortsNi, 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 |
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2021 Journal Article Tumor mutational burden is polygenic and genetically associated with complex traits and diseasesSun, 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 |
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2021 Journal Article Analysis of common genetic variation and rare CNVs in the Australian Autism BiobankYap, 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 |
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2021 Journal Article Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changesXue, 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 |
