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2024 Journal Article Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestriesZheng, Zhili, Liu, Shouye, Sidorenko, Julia, Wang, Ying, Lin, Tian, Yengo, Loic, Turley, Patrick, Ani, Alireza, Wang, Rujia, Nolte, Ilja M., Snieder, Harold, Aguirre-Gamboa, Raul, Deelen, Patrick, Franke, Lude, Kuivenhoven, Jan A., Lopera Maya, Esteban A., Sanna, Serena, Swertz, Morris A., Vonk, Judith M., Wijmenga, Cisca, Yang, Jian, Wray, Naomi R., Goddard, Michael E., Visscher, Peter M., Zeng, Jian and LifeLines Cohort Study (2024). Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries. Nature Genetics, 56 (5), 1-11. doi: 10.1038/s41588-024-01704-y |
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2023 Journal Article Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypesWu, 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 |
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2023 Journal Article mBAT-combo: a more powerful test to detect gene-trait associations from GWAS dataLi, 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 |
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2021 Journal Article Widespread signatures of natural selection across human complex traits and functional genomic categoriesZeng, 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 |
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2021 Journal Article Correction: 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). 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 |
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2019 Journal Article Improved polygenic prediction by Bayesian multiple regression on summary statisticsLloyd-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 |
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2018 Journal Article Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetesXue, 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 |
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2018 Journal Article Signatures of negative selection in the genetic architecture of human complex traitsZeng, 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 |
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2018 Journal Article Integrative analysis of omics summary data reveals putative mechanisms underlying complex traitsWu, 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 |
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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. doi: 10.1093/bib/bbaf125 |
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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, 395. doi: 10.1038/s41467-024-55611-1 |
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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., 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 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 Conference Publication Genome-wide Fine-mapping Improves Identification Of Causal VariantsZeng, 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 |
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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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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 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. (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 |
