2020
1. Wang, C., Duan, Y., Duan, G., Wang, Q.,Zhang, K., Deng, X., Qian, B., Gu, J., Ma, Z., Zhang, S., Guo, L., Liu, C.*, and FANG, Y*. (2020) StressInduces Dynamic, Cytotoxicity-Antagonizing TDP-43 Nuclear Bodies via ParaspeckleLncRNA NEAT1-Mediated Liquid-Liquid Phase Separation. Molecular Cell, 79(3):443-458.e7. (Highlighted withcommentary by Malik and Barmada in Molecular Cell.)
2. Shuixia Tana,b,1, Jing Zhaoa,b,1,Ziyu Suna,b, Shuangyi Caoa, Kongyan Niua,Yedan Zhonga, Han Wanga,b, Linyu Shia,HelingPana, Junhao Hua, Lihui Qiana, Nan Liua,2, and Junying Yuanc,2. (2020)“Hepatocyte-Specific TAK1 Deficiency Drives RIPK1 Kinase-dependent Inflammationto Promote Liver Fibrosis and Hepatocellular Carcinoma”. ProcNatl Acad Sci U S A., 117 (25) 14231-14242.
3. Wang, Z.;Liu, H.; Yan, Y.; Yang, X.; Zhang, Y.*;Wu, L.*, Integrated Proteomic and N-Glycoproteomic Analyses of Human BreastCancer. J Proteome Res 2020, 19 (8), 3499-3509.
4. Guo, L.;Gao, J.; Gao, Y.; Zhu, Z.; Zhang, Y.*,Aspirin Reshapes Acetylomes in Inflammatory and Cancer Cells via CoA-Dependentand CoA-Independent Pathways. J Proteome Res 2020, 19(2), 962-972.
5. Naito, M. G.; Xu, D.; Amin, P.; Lee, J.; Wang, H.; Li, W.; Kelliher, M.;Pasparakis, M.; Yuan, J., Sequential activation of necroptosis and apoptosiscooperates to mediate vascular and neural pathology in stroke. Proceedingsof the National Academy of Sciences of the United States of America 2020,117 (9), 4959-4970.
6. He,Z.*;McBride, J. D.; Xu, H.; Changolkar, L.; Kim, S. J.; Zhang, B.; Narasimhan, S.;Gibbons, G. S.; Guo, J. L.; Kozak, M.; Schellenberg, G. D.; Trojanowski, J. Q.;Lee, V. M.*, Transmission of tauopathy strains is independent of their isoformcomposition. Nat Commun 2020, 11 (1), 7.
7. Dai, J.; Zhang,C.; Guo, L.; He, H.; Jiang, K.; Huang, Y.; Zhang,X.; Zhang, H.; Wei, W.; Zhang, Y.; Lu, L.#; Hu,J.#, A necroptotic-independent function of MLKL in regulating endothelialcell adhesion molecule expression. Cell Death Dis 2020, 11 (4),282.(#, co-correspondingauthors)
8. Panfeng Tao1, 12, Jinqiao Sun1,12, Zheming Wu2, 12, Shihao Wang1, 12, Jun Wang1,12, Heling Pan2, 12, Renkui Bai3, Jiahui Zhang1,Ying Wang1, Pui Y. Lee4, Wenjing Ying1, QinhuaZhou1, Jia Hou1, Wenjie Wang1, BijunSun1,Mi Yang1, Danru Liu1，Huan Han1,Zhaohui Yang1, Ran Fang1, Natalie Deuitch5,Yuan Zhang6, Dilan Dissanayake7, Katrina Haude3,Kirsty McWalter3, Roadhouse Chelsea8, Jennifer J.MacKenzie8,9, Ronald Laxer7, Ivona Aksentijevich10,Xiaomin Yu1,*, Xiaochuan Wang1,*, Junying Yuan1,*, Qing Zhou1. (2020) “Adominant autoinflammatory disease caused by non-cleavable variants of RIPK1”. Nature,577:109–114.
2019
1. Wu Z, Geng Y, Lu X, ShiY, Wu G, Zhang M, Shan B, Pan H, Yuan J*.(2019) “Chaperone-mediated autophagy is involved in the execution offerroptosis”. Proc Natl Acad Sci U S A., 116(8):2996-3005.
2.ZhixiangChen, Yongwen Jiang, Li Zhang, Yinlong Guo, Dawei Ma*, Oxalic Diamides and tert-Butoxide: Two Types of LigandsEnabling Practical Access to Alkyl Aryl Ethers via Cu-Catalyzed CouplingReaction, J. Am. Chem. Soc., 2019, 141 (8), 3541–3549.
3. Junjie Wang, Dawei Ma* 6-Methylenebicyclo[3.2.1]oct-1-en-3-one: Twisted Olefinas Diels-Alder Dienophile for Expedited Syntheses of Four Kaurane Diterpenoids,Angew. Chem. Int. Ed., 2019, 58(44), 15731-15735
4 Weiming He, Zhigao Zhang, Dawei Ma*, A scalable total synthesisof the antitumor agents Et-743 and lurbinectedin, Angew. Chem. Int. Ed., 2019,58(12), 3972-3975
5. Duan, Y., Du, A., Gu, J., Duan, G., Wang,C., Gui, X., Ma, Z., Qian, B., Deng, X., Zhang, K., Sun, L., Tian, K., Zhang, Y.,Jiang, H., Liu, C.*, and FANG, Y*. (2019) “PARylation regulates stressgranule dynamics, phase separation, and neurotoxicity of disease-relatedRNA-binding proteins.” Cell Research,29(3):233-247.
6. Wang, H., Wang, X., Zhang, K., Wang, Q.,Cao, X., Wang, Z., Zhang, S., Li, A.*, Liu, K.*, and FANG, Y*. (2019) “Rapiddepletion of ESCRT protein Vps4 underlies injury-induced autophagic impedimentand Wallerian degeneration.” ScienceAdvances, 5(2):eaav4971.
7. HengyiCao,Guangya Zhu,Lin Sun,Ge Chen,Xinxin Ma,Xiao Luo,Jidong Zhu ；(2019) ”Discovery of newsmall molecule inhibitors targeting isocitrate dehydrogenase 1 (IDH1) withblood-brain barrier penetration”; European Journal of Medicinal Chemistry, 183,111694；
8. GeChen, Chunyi Niu, Jianhua Yi, Lin Sun, Hengyi Cao , Yanjia Fang, Taijie Jin,Ying Li, Chunli Lou, Jingwu Kang,Wanguo Wei*, Jidong Zhu；(2019)”Novel TriapineDerivative Induces Copper-Dependent Cell Death in Hematopoietic Cancers”；J. Med. Chem， 62, 3107−3121
9. X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, andZ.-J. Zhu*(2019) “Metabolic Reaction Network-based RecursiveMetabolite Annotation for Untargeted Metabolomics” Nature Communications,2019, 10: 1516.
10. J. Tu†, Z. Zhou†,T. Li†, and Z.-J. Zhu*（2019）“The Emerging Role of Ion Mobility-MassSpectrometry in Lipidomics to Facilitate Lipid Separation and Identification” Trendsin Analytical Chemistry, 2019, 116, 332-339.
11. Z. Wang†, B. Cui†, F. Zhang, Y. Yang, X.Shen, Z. Li, W. Zhao, Y. Zhang, K. Deng, Z. Rong, K. Yang, X. Yu, K. Li*, P.Han*, and Z.-J. Zhu(2019)“Development of A Correlative Strategyto Discover Colorectal Tumor Tissue Derived Metabolite Biomarkers in PlasmaUsing Untargeted Metabolomics” Analytical Chemistry, 2019, 91,2401-2408.
12. X. Shen, and Z.-J. Zhu* (2019)“MetFlow: AnInteractive and Integrated Workflow for Metabolomics Data Cleaning andDifferential Metabolite Discovery” Bioinformatics, 2019, 35, 2870-2872.
13. Z. Zhou, X. Shen, X. Chen, J. Tu, X. Xiong,and Z.-J. Zhu*(2019)“LipidIMMS Analyzer: IntegratingMulti-dimensional Information to Support Lipid Identification in IonMobility–Mass Spectrometry based Lipidomics” Bioinformatics, 2019, 35，698-700.
14. Yang, L.; Ma,Z.; Wang, H.; Niu, K.; Cao, Y.; Sun, L.; Geng, Y.; Yang, B.; Gao, F.; Chen, Z.;Wu, Z.; Li, Q.; Shen, Y.; Zhang, X.; Jiang, H.; Chen, Y.; Liu, R.; Liu, N.*; Zhang, Y.*, Ubiquitylome studyidentifies increased histone 2A ubiquitylation as an evolutionarily conservedaging biomarker. Nat Commun 2019, 10 (1), 2191.
15. Yang, L.;Cao, Y.; Zhao, J.; Fang, Y.; Liu, N.*; Zhang,Y.*, Multidimensional Proteomics Identifies Declines in Protein Homeostasisand Mitochondria as Early Signals for Normal Aging and Age-associated Diseasein Drosophila. Mol Cell Proteomics 2019, 18 (10),2078-2088.
16. Qiang, J.; Ma,Z.; Xie, X.; Shi, L.; Geng, Y.; Hu, J.; Liu, R.; Liu, N.; Zhang, Y.*, Multi-omic Analyses Reveal Minimal Impact of theCRISPR-Cas9 Nuclease on Cultured Human Cells. J Proteome Res 2019,18 (3), 1054-1063.
17. Yang, L.; Cao, Y.; Zhao, J.; Fang, Y.; Liu, N*.; Zhang,Y*., Multidimensional Proteomics Identifies Declines in Protein Homeostasisand Mitochondria as Early Signals for Normal Aging and Age-associated Diseasein Drosophila. Mol Cell Proteomics 2019,18(10):2078-2088.
18. Yang, L.; Ma, Z.; Wang, H.; Niu, K.; Gao, Y.; Sun, L.; Geng, Y.; Yang,B.; Gao, F.; Chen, Z.; Wu, Z.; Li, Q.; Shen, Y.; Zhang, X.; Jiang, H.; Chen, Y.;Liu,R.; Liu, N*.; Zhang, Y*., Ubiquitylome study identifies increasedhistone 2A ubiquitylation as an evolutionarily conserved aging biomarker. NatureCommunications 2019,10: 2191 (Recommended by Faculty of 1000)
2018
1. Zhu, K.; Liang, W.; Ma, Z.; Xu, D.; Cao, S.; Lu, X.; Liu, N.; Shan,B.; Qian, L.; Yuan, J., Necroptosis promotes cell-autonomous activation ofproinflammatory cytokine gene expression. Cell death & disease 2018,9 (5), 500.
2. Meng H, Liu Z, Li X, Wang H, Jin T, Wu G,Shan B, Christofferson DE, Qi C, Yu Q, Li Y, Yuan J*.(2018) “Death-domaindimerization-mediated activation of RIPK1 controls necroptosis andRIPK1-dependent apoptosis”. Proc Natl Acad Sci U S A.,115(9):E2001-E2009.
3. He, Z.; Guo, J. L.; McBride, J. D.;Narasimhan, S.; Kim, H.; Changolkar, L.; Zhang, B.; Gathagan, R. J.; Yue, C.;Dengler, C.; Stieber, A.; Nitla, M.; Coulter, D. A.; Abel, T.; Brunden, K. R.;Trojanowski, J. Q.; Lee, V. M.*, Amyloid-beta plaques enhance Alzheimer's braintau-seeded pathologies by facilitating neuritic plaque tau aggregation. NatMed 2018, 24 (1), 29-38.
4. Guo, L.;Yang, W.; Huang, Q.; Qiang, J.; Hart, J. R.; Wang, W.; Hu, J.; Zhu, J.; Liu,N.; Zhang, Y.*,Selenocysteine-Specific Mass Spectrometry Reveals Tissue-DistinctSelenoproteomes and Candidate Selenoproteins. Cell Chem Biol 2018,25 (11), 1380-1388 e4.
5. Zhu K, Liang W, Ma Z, Xu D, Cao, S, Lu X,Liu N, Shan B, Qian L, Yuan J*.(2018) “Necroptosis promotes cell-autonomous activation of proinflammatorycytokine gene expression”. Cell Death & Disease, 9(5):500.
6. Xu D, Jin T, Zhu H, Chen H, Ofengeim D, Zou C, Mifflin L, PanL, Amin P, Li W, Shan B, Naito MG, Meng H, Li Y, Pan H, Aron L, Adiconis X,Levin JZ, Yankner BA, Yuan J*.(2018) “TBK1 Suppresses RIPK1-Driven Apoptosis and Inflammation duringDevelopment and in Aging”. Cell, 174(6):1477-1491.
7. HaoyanLi, Yanjia Fang , Chunyi Niua, Hengyi Cao, Ting Mi , Hong Zhu；Junying Yuan*,JidongZhu；(2018)”Inhibition of cIAP1 as a strategy for targeting c-MYC–drivenoncogenic activity”；PNAS， 115 (40) E9317-E9324
8. Pingluan Wang, Yang Gao, Dawei Ma*, Divergent entry togelsedine-type alkaloids: total syntheses of (-)-Gelsedilam, (-)-Gelsenicine,(-)-Gelsedine, and (-)-Gelsemoxonine. J.Am. Chem.Soc., 2018,140, 11608-11612.
9. Z. Zhou†, J. Tu†, and Z.-J. Zhu* （2018）“Advancing the Large-Scale CCS Database forMetabolomics and Lipidomics at the Machine-Learning Era” CurrentOpinion in Chemical Biology, 2018, 42, 34-41.
10. H. Zha†, Y. Cai†, Y. Yin†, Z. Wang, K. Li,and Z.-J. Zhu* （2018）“SWATHtoMRM: Development of High-Coverage Targeted Metabolomics MethodUsing SWATH Technology for Biomarker Discovery” Analytical Chemistry,2018, 90, 4062-4070.
11. Singhal, M.*; Liu, X.*; Inverso, D.; Jiang, K.; Dai, J.; He, H.; Bartels, S.; Li, W.; Abdul Pari, A. A.; Gengenbacher, N.; Besemfelder, E.; Hui,L.; Augustin, H. G.;# Hu, J.#, Endothelial cell fitnessdictates the source of regenerating liver vasculature. J Exp Med 2018, 215 (10),2497-2508. (#, co-corresponding authors)
12. &nnbsp; Hu, C.*; Li, W.*; Tian, F.; Jiang,K.; Liu, X.; Cen, J.; He, Q.; Qiu, Z.; Kienast,Y.; Wang, Z.; Zhang, H.; Ji, Y.#; Hu, J.#;Hui, L.#, Arid1a regulates response to anti-angiogenic therapy in advancedhepatocellular carcinoma. J Hepatol 2018, 68 (3),465-475. (#, co-corresponding authors)
13. Ma, Z.; Wang, H.; Cai, Y.; Wang, H.; Niu, K.; Wu, X.; Ma,H.; Yang, Y.; Tong, W.; Liu, F.; Liu, Z.; Zhang, Y.; Liu,R.; Zhu, Z*.;Liu,N*., Epigenetic drift of H3K27me3 in aging links glycolysis to healthylongevity in Drosophila. elife 2018, 7:e35368 (Science editor’s choice)
2017
1. Yang, X.;Wang, Z.; Guo, L.; Zhu, Z.; Zhang, Y.*,Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology.J Proteome Res 2017, 16 (10), 3830-3840.
2.. XiangboZhao, Wu Li, Junjie Wang, Dawei Ma*, Convergent route to ent-Kauranediterpenoids: Total synthesis of Lungshengenin D and 1,6-Diacetoxy-ent-kaura-9(11),16-dien-12,15-dione. J. Am. Chem.Soc., 2017, 139(8),2932-2935.
3.. Jie Gao, Subhajit Bhunia, KailiangWang, Lu Gan, Shanghua Xia, Dawei Ma*,Discovery of N-(naphthalen-1-yl)-N′-alkyl oxalamide ligands enablesCu-catalyzed aryl amination with high turnovers. Org. Lett., 2017, 19(11), 2809-2812.
4. Z. Zhou, J. Tu, X. Xiong, X. Shen, and Z.-J. Zhu*（2017）“LipidCCS: Prediction of Collision Cross-SectionValues for Lipids with High Precision to Support Ion Mobility-Mass Spectrometrybased Lipidomics” Analytical Chemistry, 2017, 89, 9559–9566.
5. Z. Zhou, X. Xiong, and Z.-J. Zhu*（2017）“MetCCS Predictor: A Web Server for PredictingCollision Cross-Section Values of Metabolites in Metabolomic” Bioinformatics,2017, 33, 2235-2237
6. Cao, X., Wang, H., Wang, Z., Wang, Q.,Zhang. S., Deng, Y., and FANG, Y*. (2017) “In vivo imaging reveals mitophagy independence in the maintenanceof axonal mitochondria during normal aging.” Aging Cell, 16(5):1180-1190.
7. Xu D, Liu J, Fu T, Shan B, Qian L, Pan L,Yuan J. (2017) “USP25 regulates Wnt signaling by controlling the stability oftankyrases”. Genes Dev., 31(10):1024-1035.
8. Wang H, Meng H, Li X, Zhu K, Dong K,Mookhtiar AK, Wei H, Li Y, Sun SC, YuanJ*. (2017) “PELI1 functions as a dual modulator of necroptosis andapoptosis by regulating ubiquitination of RIPK1 and mRNA levels of c-FLIP”. ProcNatl Acad Sci U S A., 2017 Nov 7;114(45):11944-11949.
9. JingjingXie, Xiaojia Si, Shoulai Gu, Mingliang Wang, Jian Shen, Haoyan Li, Dan Li,Yanjia Fang，Cong Liu, Jidong Zhu ；(2017)”Allosteric inhibitors of SHP2 with therapeuticpotential for cancer treatment”；J. Med. Chem， 60(24): 10205-10219
10. MingliangWang, Yanjia Fang, Shoulai Gu, Fangfang Chen，Zhengjiang Zhu, Jidong Zhu；(2017)”Discovery of novel1,2,3,4-tetrahydrobenzo[4, 5]thieno[2, 3-c]pyridine derivatives as potent andselective CYP17 inhibitors”；Eur J Med Chem , 132: 157~172
11. Wei R1, Xu LW, Liu J, Li Y, Zhang P, Shan B, Lu X, Qian L, Wu Z,Dong K, Zhu H, Pan L, Yuan J*, Pan H*.(2017) “SPATA2 regulates the activation of RIPK1 by modulating linearubiquitination”. Genes Dev., 31(11):1162-1176.
12. Z. Zhou, X. Shen, J. Tu, and Z.-J. Zhu*（2016）“Large-Scale Prediction of Collision Cross-SectionValues for Metabolites in Ion Mobility - Mass Spectrometry”, AnalyticalChemistry, 2016, 88, 11084-11091.
13. H. Li, Y. Cai, Y. Guo, F. Chen, and Z.-J.Zhu*（2016）“MetDIA: TargetedMetabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-IndependentAcquisition, Analytical Chemistry” 2016, 88, 8757-8764.
14. Mengyang Fan,Wei Zhou, Yongwen Jiang, Dawei Ma*, CuI/oxalamidecatalyzed couplings of (hetero)aryl chlorides and phenols for diaryl etherformation. Angew. Chem. Int. Ed., 2016, 55(21), 6211-6215.
15. Shanghua Xia, Lu Gan, Kailiang Wang, ZhengLi, Dawei Ma*, Copper-catalyzedhydroxylation of (hetero)aryl halides under mild conditions. J. Am. Chem. Soc., 2016, 138(41), 13493-13496.
16. Wang, H.; Ma, Z.; Niu, K.; Xiao, Y.; Wu, X.; Pan, C.; Zhao, Y.; Wang,K.; Zhang, Y*.; Liu, N*., Antagonistic roles of Nibbler and Hen1in modulating piRNA 3′ ends in Drosophila. Development 2016,143(3):530-9
17. Cao, X., and FANG, Y*. (2015)“Transducing oxidative stress to death signals in neurons”. Journal of Cell Biology, 211(4):741-743.
18. Huang, Q.;Yang, L.; Luo, J.; Guo, L.; Wang, Z.; Yang, X.; Jin, W.; Fang, Y.; Ye, J.;Shan, B.; Zhang, Y.*, SWATH enablesprecise label-free quantification on proteome scale. Proteomics 2015,15 (7), 1215-23.
19. He K, Huertas M, Hong SZ, Tie X, Hell JW, Shouval H, KirkwoodA* (2015) Distinct Eligibility Traces for LTP and LTD in Cortical Synapses. Neuron88: 528-38
20. XuesongLiu, Linqian Yu, Mupeng Luo，Wanguo Wei*, Jidong Zhu；(2015)”Radical-Induced Metal-Free Alkynylation of Aldehydes by Direct CHActivation”；Chem. Eur. J, 21, 1–6.
21. MingliangWang, Xixi Liu, Lu Zhou，Jidong Zhu , Xun Sun*，(2015)”Fluorination of 2-substitutedbenzo[b]furans with Selectfluor”；J ROY SOC MED， 13, 3190-3193
22. HuangS#, Trevino M#, He K#, Ardiles A,Pasquale R, Guo Y, Palacios A, Huganir R, Kirkwood A* (2012) Pull-pushneuromodulation of LTP and LTD enables bidirectional experience-inducedsynaptic scaling in visual cortex. Neuron 73: 497-510
23. He K, Petrus E, Gammon N, Lee HK* (2012) Distinct sensoryrequirements for unimodal and cross-modal homeostatic synaptic plasticity. JNeurosci32: 8469-74
24. He, Z.; Jia, C.; Feng, S.; Zhou, K.;Tai, Y.; Bai, X.; Wang, Y.*, TRPC5 channel is the mediator of neurotrophin-3 inregulating dendritic growth via CaMKIIalpha in rat hippocampal neurons. JNeurosci 2012, 32 (27), 9383-95.
25. He K, Lee A, Song L, Kanold PO, Lee HK* (2011) AMPA receptorsubunit GluR1 (GluA1) serine-845 site is involved in synaptic depression butnot in spine shrinkage associated with chemical long-term depression. JNeurophysiol 105: 1897-907
26. Ding,X.#; He, Z.#;Zhou, K.#; Cheng, J.; Yao, H.; Lu, D.; Cai, R.; Jin, Y.; Dong, B.;Xu, Y.; Wang, Y.*, Essential role of TRPC6 channels in G2/M phase transitionand development of human glioma. J Natl Cancer Inst 2010, 102(14), 1052-68.
27. He K, Song L, Cummings LW, Goldman J, Huganir RL, Lee HK*(2009) Stabilization of Ca2+-permeable AMPA receptors at perisynaptic sites byGluR1-S845 phosphorylation. Proc Natl Acad Sci USA 106: 20033-8
28. Shi,Y. #; Ding, X. #; He,Z. H. #; Zhou, K. C.; Wang, Q.; Wang, Y. Z.*, Critical role ofTRPC6 channels in G2 phase transition and the development of human oesophagealcancer. Gut 2009, 58 (11), 1443-50.
