Publications

2023

Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization and prediction of chronological age. Dean Li , Shuwen Ge, Yandong Liu, Miaomiao Pan, Xueting Wang, Guojing Han, Sili Zou, Rui Liu, Kongyan Niu, Chao Zhao, Nan Liu, Lefeng Qu  iScience 26(12):108558.

Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle. Shuwen Ge, Xueting Wang, Yingqin Wang, Minghui Dong, Dean Li, Kongyan Niu, Tongyao Wang, Rui Liu, Chao Zhao, Nan Liu, Ming Zhong   iScience 27:108618

Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila.  ingshu Li, Ye Cao, Yun Yang, Huanhuan Ma, Jing Zhao, Yaoyang Zhang, Nan Liu Journal of Proteome Research 22(9):2909-2924

2022

ONE-seq: epitranscriptome and gene-specific profiling of NAD-capped RNA. Kongyan Niu, Jinyang Zhang, Shuwen Ge, Dean Li , Kunfeng Sun, Yingnan You, Jiaqian Qiu, Kun Wang, Xueting Wang, Rui Liu, Yandong Liu, Bing Li, Zheng-Jiang Zhu, Lefeng Qu,*, Hong Jiang ,* and Nan Liu ,*

Nucleic Acids Research, 2023, Vol. 51, No. 2 e12

Quantitative Acetylomics Reveals Dynamics of Protein Lysine Acetylation in Mouse Livers During Aging and Upon the Treatment of Nicotinamide Mononucleotide. Jingshu Li, Ye Cao, Kongyan Niu, Jiaqian Qiu, Han Wang, Yingnan You, Dean Li, Yu Luo, Zhengjiang Zhu, Yaoyang Zhang, and Nan Liu  2022, Mol Cell Proteomics 21(9), 100276

2021

Induced lineage promiscuity undermines the efficiency of all-trans-retinoid-acid-induced differentiation of acute myeloid leukemia. Yijia Tang , Xin Tian , Zihan Xu , Junke Cai, Han Liu, Nan Liu, Zhu Chen, Saijuan Chen, Feng Liu. iScience. 2021 24(5):102410

2020

Subacute Toxicity Study of Nicotinamid Mononucleotide via Oral Administration. Yingnan You, Yang Gao , Han Wang , Jingshu Li, Xiang Zhang, Zhengjiang Zhu, Nan Liu.

Front Pharmacol. 11:604404

Hepatocyte-Specific TAK1 Deficiency Drives RIPK1 Kinase-dependent Inflammation to Promote Liver Fibrosis and Hepatocellular Carcinoma. Shuixia Tan, Jing Zhao, Ziyu Sun, Shuangyi Cao, Kongyan Niu, Yedan Zhong, Han Wang, Linyu Shi, Heling Pan, Junhao Hu, Lihui Qian, Nan Liu*, and Junying Yuan*. Proceedings of National Academy of Sciences. 2020 doi/10.1073/pnas.2005353117

2019

Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila. Yang L, Cao Y, Zhao J, Fang Y, Liu N*, Zhang Y*. Mol Cell Proteomics. 2019 Oct;18(10):2078-2088. doi: 10.1074/mcp.RA119.001621.

Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker. L Yang, Z Ma, H Wang, K Niu, Y Gao, L Sun, Y Geng, B Yang, F Gao, Z Chen, Z Wu, Q Li, Y Shen, X Zhang, H Jiang, Y Chen, R Liu, N Liu*, and Y Zhang*. Nature Communications 10, Article number: 2191 （Recommended by Faculty of 1000, https://f1000.com/prime/735813510)

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. X Shen, R Wang, X Xiong, Y Yin, Y Cai, Z Ma, N Liu, and Z Zhu. Nature Communications 10:1516 | https://doi.org/10.1038/s41467-019-09550

Age-dependent changes in transcription factor FOXO targeting in female Drosophila. A Birnbaum, X Wu, M Tatar, N Liu*, H Bai*. Frontiers in Genetics. 10, 312 2019

Multi-omic analyses reveal minimal impact of the CRISPR-Cas9 nuclease on cultured human cells. J Qiang, Z Ma, X Xie, L Shi, Y Geng, J Hu, R Liu, N Liu, and Y Zhang. Journal of Proteome Res. DOI: 10.1021/acs.jproteome.8b00751

2018

Selenocysteine-specific mass spectrometry reveals tissue-distinct selenoproteomes and candidate selenoproteins. L Guo, W Yang, Q Huang, J Qiang, JR Hart, W Wang, J Hu, J Zhu, N Liu, and Zhang Y. Cell Chemical Biology 25 (11), 1380-1388. e4 2018

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila. Z Ma, H Wang, Y Cai, H Wang, K Niu, X Wu, H Ma, Y Yang, W Tong, F Liu, Z Liu, Y Zhang, R Liu, Z Zhu* and N Liu*. elife 7, e35368 7 2018 (Featured by Science Editors' Choice)

Quantitative ChIP-seq by adding Spike-in from another species. K Niu, R Liu, N Liu*. Bio-protocol DOI: 10.21769/BioProtoc.2981.

Stable-isotope labeled metabolic analysis in Drosophila Melanogaster: from experimental setup to data analysis. Y Cai, N Liu*, ZJ Zhu*. Bio-protocol DOI: 10.21769/BioProtoc.3015.

Necroptosis promotes cell-autonomous activation of proinflammatory cytokine gene expression. K Zhu, W Liang, Z Ma, D Xu, S Cao, X Lu, N Liu, B Shan, L Qian, J Yuan. Cell Death & Disease 9 (5) 11 2018

MiR-34 inhibits polycomb repressive complex 2 to modulate chaperone expression and promote healthy brain aging. J Kennerdell, N Liu, N Bonini. Nature Communications 9 2018

2017

Systematic analysis reveals tumor-enhancing and -suppressing microRNAs in Drosophila epithelial tumors. Z Shu, Y Huang, W Palmer, Y Tamori, G Xie, H Wang, N Liu and WM Deng. Oncotarget 1;8(65):108825-108839. doi: 10.18632/oncotarget.22226.

2016

Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3′ ends in Drosophila. H Wang, Z Ma, K Niu, Y Xiao, X Wu, C Pan, Y Zhao, K Wang, Y Zhang*,and N Liu*. Development 143 (3), 530-539 30 2016

2015

Twin promotes the maintenance and differentiation of germline stem cell lineage through modulation of multiple pathways. Z Fu, C Geng, H Wang, Z Yang, C Weng, H Li, L Deng, L Liu, N Liu, J Ni, and T Xie. Cell reports 13 (7), 1366-1379,11

Prior to 2013

The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. N Liu, M Landreh, K Cao, M Abe, GJ Hendriks, JR Kennerdell, Y Zhu, and B Nancy. Nature 482 (7386), 519 312 2012