Selected publications

Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses

Published in Genome Biology, 2023

This paper discussed the pitfalls and opportunities when using latent variables in the single-cell eQTL mapping analysis.

Recommended citation: Angli Xue#, Seyhan Yazar, Drew Neavin, Joseph E. Powell#. "Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses". Genome Biology. 24.1 (2023): 1-11. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02873-5

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

Published in Nature Communications, 2021

This paper demonstrated that behavioural traits are subject to misreports and longitudinal changes (MLC) which can cause biases in GWAS and follow-up analyses.

Recommended citation: Angli Xue, Longda Jiang, Zhihong Zhu, Naomi R. Wray, Peter M. Visscher, Jian Zeng, Jian Yang. Genome-wide analyses of behavioral traits are subject to bias by misreports and longitudinal changes. Nature Communications. 12, 6450 (2021). https://www.nature.com/articles/s41467-020-20237-6

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

Published in Nature Communications, 2018

This paper conducted the largest T2D meta-analysis of GWAS and identified 139 common and 4 rare variants associated with T2D.

Recommended citation: Angli Xue*, Yang Wu*, Zhihong Zhu, Futao Zhang, Kathryn E Kemper, Zhili Zheng, …, Jian Zeng#, Jian Yang#. Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes. Nature Communications. 12, 6450 (2018). https://www.nature.com/articles/s41467-018-04951-w

Full publication

21. Angli Xue^#, Seyhan Yazar, Drew Neavin, Joseph E. Powell^#. Pitfalls and opportunities for applying PEER factors in single-cell eQTL analyses. Genome Biology. 24.1 (2023): 1-11.

20. Zhen Qiao, Julia Sidorenko, Joana A. Revez, Angli Xue, Xueling Lu, Katri Pärna, Harold Snieder, Lifelines Cohort Study, Peter M. Visscher, Naomi R. Wray, Loic Yengo. Estimation and implications of the genetic architecture of fasting and non-fasting blood glucose. Nature Communications. 14.1 (2023): 451.

19. Xuehao Xiu, Haoyang Zhang, Angli Xue, David N Cooper, Li Yan, Yuedong Yang, Yuanhao Yang, Huiying Zhao. Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians. BMC Medicine 20.1 (2022): 1-16.

18. Haoyang Zhang, Xuehao Xiu, Angli Xue, Yuedong Yang, Yuanhao Yang, Huiying Zhao. Mendelian randomization study reveals a population-specific putative causal effect of type 2 diabetes in risk of cataract. International Journal of Epidemiology. 2021.

17. Jian Zeng, Angli Xue, Longda Jiang, Luke R Lloyd-Jones, Yang Wu, Huanwei Wang, Zhili Zheng, Loic Yengo, Kathryn E Kemper, Naomi R Wray, Peter M Visscher, Jian Yang. Widespread signatures of natural selection across human complex traits and functional genomic categories. Nature Communications. 2021.

16. Christelle Adolphe, Angli Xue^* (co-first author), Laura Genovesi, Atefeh Taherian Fard, Jian Yang^# and Brandon Wainwright^#. Genome-wide meta-analyses and functional interaction network analysis reveal regulatory T-cell immune suppression as a key and novel process underlying basal cell carcinoma susceptibility. *Genome Medicine. 13 (1), 1-12. 2021.

15. Xiwei Sun, Angli Xue, Ting Qi, Yang Wu, Zhili Zheng, Jian Zeng, Jian Yang. Tumor mutational burden is polygenic and genetically associated with complex traits in humans. Cancer Research. 2021. (Cover Story)

14. Angli Xue, Longda Jiang, Zhihong Zhu, Naomi R. Wray, Peter M. Visscher, Jian Zeng, Jian Yang. Genome-wide analyses of behavioral traits are subject to bias by misreports and longitudinal changes. Nature Communications. 12, 6450 (2021). (Highlighted by Nature Asia-Pacific)

13. Joana Revez, Tian Lin, Zhen Qiao, Angli Xue, Yan Holtz, Zhihong Zhu, Jian Zeng, Huanwei Wang, Julia Sidorenko, Kathryn Kemper, Anna Vinkhuyzen, Julanne Frater, Darryl Eyles, Thomas Burne, Brittany Mitchell, Nicholas Martin, Gu Zhu, Peter Visscher, Jian Yang, Naomi Wray, John McGrath. Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration. Nature Communications. 11.1: 1-12. 2020.

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

11. Mike A Nalls, Cornelis Blauwendraat, Costanza L Vallerga, Karl Heilbron, Sara Bandres-Ciga, Diana Chang, Manuela Tan, Demis A Kia, Alastair J Noyce, Angli Xue, Jose Bras, Emily Young, Rainer von Coelln, Javier Simon-Sanchez, Claudia Schulte, Manu Sharma, Lynne Krohn, Lasse Pihlstrom, Ari Siitonen, Hirotaka Iwaki, Hampton Leonard, Faraz Faghri, J Raphael Gibbs, Dena G Hernandez, Sonja W Scholz, Juan A Botia, Maria Martinez, Jean-Christophe Corvol, Suzanne Lesage, Joseph Jankovic, Lisa M Shulman, Margaret Sutherland, Pentti Tienari, Kari Majamaa, Mathias Toft, Ole A Andreassen, Tushar Bangale, Alexis Brice, Jian Yang, Ziv Gan-Or, Thomas Gasser, Peter Heutink, Joshua M Shulman, Nicolas Wood, David A Hinds, John A Hardy, Huw R Morris, Jacob Gratten, Peter M Visscher, Robert R Graham, Andrew B Singleton, 23andMe Research Team, International Parkinson’s Disease Genomics Consortium. Identification of novel risk loci, causal insights, and heritable risk for Parkinson’s disease: a meta-analysis of genome-wide association studies. The Lancet Neurology. 18 (12), 1091-1102. 2019. (Top 0.1% cited paper in 2019-2020)

10. Regina H. Reynolds, Juan Botía, Mike A. Nalls, International Parkinson’s Disease Genomics Consortium (IPDGC), System Genomics of Parkinson’s Disease (SGPD), John Hardy, Sarah A. Gagliano Taliun & Mina Ryten. Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson’s disease heritability. NPJ Parkinson’s disease, 5(1), 1-14. 2019.

9. Alastair Noyce, Sara Bandres Ciga, Jonggeol Kim, Karl Heilbron, Gibran Hemani, Angli Xue, Deborah A Lawlor, George Davey Smith, Raquel Duran, Ziv Gan-Or, Cornelis Blauwendraat, Raphael Gibbs, David Hinds, Jian Yang, Peter M Visscher, Jack Cuzick, Huw Morris, John Hardy, Nicholas Wood, Mike A Nalls, Andrew Singleton. The Parkinson’s Disease Mendelian Randomization Research Portal. Movement disorders. 34.12: 1864-1872. 2019.

8. Enda M Byrne, Manuel Ferreira, Angli Xue, Sara Lindström, Xia Jiang, Douglas Easton, Naomi R Wray, Georgia Chenevix-Trench. Is schizophrenia a risk factor for breast cancer? – Evidence from genetic data. Schizophrenia Bulletin. 2018.

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

6. Jian Zeng, Ronald de Vlaming, Yang Wu, Matthew Robinson, Luke Lloyd-Jones, Loic Yengo, Chloe Yap, Angli Xue, Julia Sidorenko, Allan McRae, Joseph Powell, Grant Montgomery, Andres Metspalu, Tonu Esko, Greg Gibson, Naomi Wray, Peter Visscher, Jian Yang. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50.5 (2018): 746.

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

4. Angli Xue, Hongcheng Wang, Jun Zhu. Dissecting genetic architecture of complex trait using multi-omics information: A case of association mapping for startle response in Drosophila melanogaster. Scientific Reports. 2017, 7(1):12367.

3. Yongjun Mei^*, Jiwen Yu^*, Angli Xue^* (co-first author), Shuli Fan, Meizhen Song, Chaoyou Pang, Wenfeng Pei, Shuxun Yu, Jun Zhu. Dissecting Genetic Network of Fruit Branch Traits in Upland Cotton by Association Mapping Using SSR Markers. PLOS one. 2017, 12(1), p.e0162815.

2. Yongjun Mei^*, Jiwen Yu^*, Angli Xue^* (co-first author), Shuli Fan, Meizhen Song, Chaoyou Pang, Wenfeng Pei, Shuxun Yu, Jun Zhu. Association mapping of genetic network for plant morphological traits in cotton. Journal of Zhejiang University (Agric. & Life Sci.). 2015, 42(2), 127-136.

1. Jiasheng Wang, Ke Ding, Yujie Chen, Lifeng Zhang, Zukai Liu, Angli Xue, Wenjia Gu, Xiaoyue Yang, Xihan Li, Jin Huang, Congcong Xing, Yunlong Cao, Ming Chen. Detection of Thrombin with an Aptamer-based Macromolecule Biosensor Using Bacterial Ghost System. ACS Synth. Biol., 2014, 3 (12), 963–965.

* co-first author

# corresponding author