Yigong Shi Lab - publications

2025

(***) Ying Zhang, Lu Tian, Gaoxingyu Huang, Xiaofei Ge, Fang Kong, Pengqi Wang, Yige Xu, Yigong Shi. Structural basis of BAX pore formation. Science. 388(6754):eadv4314. doi: 10.1126/science.adv4314. Epub 2025 Jun 26.

2024

Xuefei Guo, Haotian Li, Xiaoli Lu, Hao Liu, Kaicheng U, Chuangye Yan, Jianlin Lei, Jing Huang, Rui Zhou, Yigong Shi. Structural basis of human γ-secretase inhibition by anticancer clinical compounds. Nature Structural & Molecular Biology. 32(4):719-728. doi: 10.1038/s41594-024-01439-8. Epub 2024 Dec 9.
(***) Mengying Chen, Qiang Su & Yigong Shi. Molecular mechanism of IgE-mediated FcεRI activation. Nature. 637(8045):453-460. doi: 10.1038/s41586-024-08229-8. Epub 2024 Oct 23.
Fayang Zhou, Yuanyuan Zhang, Yuyao Zhu, Qiang Zhou, Yigong Shi, Qi Hu. Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase. Sci Adv. 10(41):eado4880. doi: 10.1126/sciadv.ado4880. Epub 2024 Oct 9.
Xiechao Zhan, Yichen Lu, Yigong Shi. Molecular basis for the activation of human spliceosome. Nature Communications. 15(1):6348. doi: 10.1038/s41467-024-50785-0. Epub 2024 Jul 27.
Ronald N Germain, Eliezer M Van Allen, Gosia Trynka, John S Tsang, Dominic Grün, Ashley L Kiemen, Yigong Shi, Aimee Pugh Bernard, Garry P Nolan. AI and immunology. Immunity. 57(6):1177-1181. doi: 10.1016/j.immuni.2024.05.016. Epub 2024 Jun 11.
(***) Xuefei Guo, Haotian Li, Chuangye Yan, Jianlin Lei, Rui Zhou, Yigong Shi. Molecular mechanism of substrate recognition and cleavage by human γ-secretase. Science. 384(6700):1091-1095. doi: 10.1126/science.adn5820. Epub 2024 Jun 6.
Wenyu Zhang, Xiaofeng Zhang, Xiechao Zhan, Rui Bai, Jianlin Lei, Chuangye Yan, Yigong Shi. Structural insights into human exon-defined spliceosome prior to activation. Cell Research. 34(6): 428-439. doi: 10.1038/s41422-024-00949-w. Epub 2024 Apr 24.
Hu Deng, Lingyu Liu, Xiaping Tang, Yingxian Lu, Xiaofei Wang, Yanyu Zhao, Yigong Shi. Impact of specific electromagnetic radiation on wakefulness in mice. Proc Natl Acad Sci U S A. 121(15): e2313903121.doi: 10.1073/pnas.2313903121. Epub 2024 Apr 1.
(***) Rui Bai, Meng Yuan, Pu Zhang, Ting Luo, Yigong Shi, Ruixue Wan. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science. 383(6688): 1245-1252. doi: 10.1126/science.adn7272. Epub 2024 Mar 14.
Zhifei Wang, Mengying Chen, Qiang Su, Tiago D C Morais, Yan Wang, Elianna Nazginov, Akhilraj R Pillai, Feng Qian, Yigong Shi, Yong Yu. Molecular and structural basis of the dual regulation of the polycystin-2 ion channel by small-molecule ligands. Proc Natl Acad Sci U S A. 121(12): e2316230121.doi: 10.1073/pnas.2316230121. Epub 2024 Mar 14.
Lu Tian, Yini Li, Yigong Shi. Dark and Dronc activation in Drosophila melanogaster. Proc Natl Acad Sci U S A. 121(9): e2312784121. doi: 10.1073/pnas.2312784121. Epub 2024 Feb 21.
Xiaofeng Zhang, Xiechao Zhan, Tong Bian, Fenghua Yang, Pan Li, Yichen Lu, Zhihan Xing, Rongyan Fan, Qiangfeng Cliff Zhang, Yigong Shi. Structural insights into branch site proofreading by human spliceosome. Nature Structural & Molecular Biology. 31(5): 835-845. doi: 10.1038/s41594-023-01188-0. Epub 2024 Jan 9.

2023

Xiaotong Wang, Rui Zhou, Xiaqin Sun#, Jun Li, Jinxin Wang, Weihua Yue, Lifang Wang, Hesheng Liu, Yigong Shi, and Dai Zhang. Preferential Regulation of Γ‐Secretase‐Mediated Cleavage of APP by Ganglioside GM1 Reveals a Potential Therapeutic Target for Alzheimer's Disease. Advanced Science. 10(32): e2303411.doi: 10.1002/advs.202303411. Epub 2023 Sep 27.
Yingxian Lu, Yigong Shi. A microfabricated lab-on-chip with three-dimensional electrodes for microscopic observation of bioelectromagnetic effects of cells. Bioelectrochemistry. 154:108554. doi: 10.1016/j.bioelechem.2023.108554. Epub 2023 Aug 28.
Yini Li, Lu Tian, Ying Zhang, Yigong Shi. Structural insights into CED-3 activation. Life Science Alliance. 6(9): e202302056. doi: 10.26508/lsa.202302056. Epub 2023 Jul 4.
Yingxian Lu, Xiaping Tang, Yanyu Zhao, Tianyu Jiang, Jiayao Zhou, Xiaofei Wang, Bing Huang, Lingyu Liu, Hu Deng, Yujing Huang, Yigong Shi. Analysis of electromagnetic response of cells and lipid membranes using a model-free method. Bioelectrochemistry. 152:108444. doi: 10.1016/j.bioelechem.2023.108444. Epub 2023 Apr 29.
Xiaofeng Zhang, Fenghua Yang, Xiechao Zhan, Tong Bian, Zhihan Xing, Yichen Lu, Yigong Shi. Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease. Molecular Cell. 83(8):1328-1339. doi: 10.1016/j.molcel.2023.03.015. Epub 2023 Apr 6.
Fenghua Yang, Tong Bian, Xiechao Zhan, Zhe Chen, Zhihan Xing, Nicolas A Larsen, Xiaofeng Zhang, Yigong Shi. Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Nature Communications. 14(1):897. doi: 10.1038/s41467-023-36489-x. Epub 2023 Feb 17.
Gaoxingyu Huang, Chao Zeng, Yigong Shi. Structure of the nuclear pore complex goes atomic. Structure of the nuclear pore complex goes atomic. Current Opinion in Structural Biology. 78:102523. doi: 10.1016/j.sbi.2022.102523. Epub 2023 Jan 13.
(***) Jiayao Zhou, Yumeng Wang, Gaoxingyu Huang, Min Yang, Yumin Zhu, Chen Jin, Dan Jing, Kai Ji, Yigong Shi (2023). LilrB3 is a putative cell surface receptor of APOE4. Cell Research. 33(2):116-130. doi: 10.1038/s41422-022-00759-y. Epub 2023 Jan 2.

2022

Xuefei Guo, Yumeng Wang, Jiayao Zhou, Chen Jin, Jiaoni Wang, Bojun Jia, Dan Jing, Chuangye Yan, Jianlin Lei, Rui Zhou, Yigong Shi. Molecular basis for isoform-selective inhibition of presenilin-1 by MRK-560. Nature Communications. 13(1):6299. doi: 10.1038/s41467-022-33817-5. Epub 2022 Oct 22.
(***) Qiang Su, Mengying Chen, Yan Shi, Xiaofeng Zhang, Gaoxingyu Huang, Bangdong Huang, Dongwei Liu, Zhangsuo Liu, Yigong Shi (2022). Cryo-EM structure of the human IgM B cell receptor. Science. 377(6608): 875-880.doi: 10.1126/science.abo3923. Epub 2022 Aug 18.
(***) Xiechao Zhan, Yichen Lu, Xiaofeng Zhang, Chuangye Yan, Yigong Shi (2022). Mechanism of exon ligation by human spliceosome. Molecular Cell. 82(15): 2769-2778.doi: 10.1016/j.molcel.2022.05.021. Epub 2022 Jun 14.
(***) Xuechen Zhu, Gaoxingyu Huang, Chao Zeng, Xiechao Zhan, Ke Liang, Qikui Xu, Yanyu Zhao, Pan Wang, Qifan Wang, Qiang Zhou, Qinghua Tao, Minhao Liu, Jianlin Lei, Chuangye Yan, Yigong Shi (2022). Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex. Science. 376(6598): eabl8280.doi: 10.1126/science.abl8280. Epub 2022 Jun 10.
(***) Gaoxingyu Huang, Xiechao Zhan, Chao Zeng, Ke Liang, Xuechen Zhu, Yanyu Zhao, Pan Wang, Qifan Wang, Qiang Zhou, Qinghua Tao, Minhao Liu, Jianlin Lei, Chuangye Yan, and Yigong Shi (2022). Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex. Cell Research. 32(5): 451-460. doi: 10.1038/s41422-022-00633-x. Epub 2022 Mar 18.
(***) Gaoxingyu Huang, Xiechao Zhan , Chao Zeng, Xuechen Zhu, Ke Liang, Yanyu Zhao, Pan Wang, Qifan Wang, Qiang Zhou, Qinghua Tao, Minhao Liu, Jianlin Lei, Chuangye Yan and Yigong Shi (2022). Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex. Cell Research. 32(4):349-358. doi: 10.1038/s41422-021-00610-w. Epub 2022 Feb 17.
(***) Chen Jin, Jiaoni Wang, Yumeng Wang, Bojun Jia, Xuefei Guo, Guanghui Yang, Peng Xu, Paul Greengard, Rui Zhou and Yigong Shi. (2022). Modulation of amyloid precursor protein cleavage by γ-secretase activating protein through phase separation. Proc Natl Acad Sci U S A. 119(12), e2122292119. doi: 10.1073/pnas.2122292119. Epub 2022 Mar 17.

2021

(***) Lingyu Liu, Hu Deng, Xiaping Tang, Yingxian Lu, Jiayao Zhou, Xiaofei Wang, Yanyu Zhao, Bing Huang, Yigong Shi. (2021). Specific electromagnetic radiation in the wireless signal range increases wakefulness in mice. Proc Natl Acad Sci U S A. 118(31), e2105838118. doi:10.1073/pnas.2105838118. July 30, 2021.
Qiang Su, Mengying Chen, Yan Wang, Bin Li, Dan Jing, Xiechao Zhan, Yong Yu, Yigong Shi (2021). Structural basis for Ca2+ activation of the heteromeric PKD1L3/PKD2L1 channel. Nature Communications. 12(1):4871. doi: 10.1038/s41467-021-25216-z. 11 August 2021.
(***) Rui Bai, Ruixue Wan, Lin Wang, Kui Xu, Qiangfang Zhang, Jianlin Lei, and Yigong Shi (2021). Structure of the activated human minor spliceosome. Science. Eabg0879. doi: 10.1126/science.abg0879. Epub 2021 Jan 28.

2020

(***) Guanghui Yang, Rui Zhou, Xuefeng Guo, Chuangye Yan, and Yigong Shi (2020). Structural basis of γ-secretase inhibition and modulation by small molecule drugs. Cell. 184(2):521-533. doi: 10.1016/j.cell.2020.11.049. Epub 2020 Dec 28.
(***) Rui Bai, Ruixue Wan, Chuangye Yan, Qi Jia, Jianlin Lei, and Yigong Shi (2020). Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Science. eabe8863. doi: 10.1126/science.abe8863. Epub 2020 Nov 26.
Hangping Yao, Yutong Song, Yong Chen, Nanping Wu, Jialu Xu, Chujie Sun, Jiaxing Zhang, Tianhao Weng, Zheyuan Zhang, Zhigang Wu, Linfang Cheng, Danrong Shi, Xiangyun Lu, Jianlin Lei, Max Crispin, Yigong Shi, Lanjuan Li, Sai Li (2020). Molecular Architecture of the SARS-CoV-2 Virus. Cell. 183(3):730-738.e13. Epub 2020 Sep 6.
Elena A Minina, ……Yigong Shi, …… Peter V Bozhkov (2020). Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases. Mol. Cell. 77(5):927-929. 2020 Mar 5.
(***) Gaoxingyu Huang, Yanqing Zhang, Xuechen Zhu, Chao Zeng, Qifan Wang, Qiang Zhou, Qinghua Tao, Minhao Liu, Jianlin Lei, Chuangye Yan, and Yigong Shi (2020). Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis. Cell Research. 30(6):532-540. Epub 2020 May 6.
(***) Yanqing Zhang, Sai Li, Chao Zeng, Gaoxingyu Huang, Xuechen Zhu, Qifan Wang, Kunpeng Wang, Qiang Zhou, Chuangye Yan, Wusheng Zhang, Guangwen Yang, Minhao Liu, Qinghua Tao, Jianlin Lei, and Yigong Shi (2020). Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex. Cell Research. 30(6):520-531. Epub 2020 May 4.

2019

Ruixue Wan, Rui Bai, Xiechao Zhan, and Yigong Shi (2019). How Is Precursor Messenger RNA Spliced by the Spliceosome?. Annu Rev Biochem. 89:333-358. Epub 2019 Dec 9.
Ruixue Wan, Rui Bai, and Yigong Shi (2019). Molecular choreography of pre-mRNA splicing by the spliceosome. Curr Opin Struct Biol. 59:124-133. Epub 2019 Dec.
Rui Zhou, Guanghui Yang, Yigong Shi. Macromolecular complex in recognition and proteolysis of amyloid precursor protein in Alzheimer’s disease. Current Opinion in Structural Biology. 61:1-8. 10.1016/j.sbi.2019.09.004. Epub 2019 Apr.
Chuangye Yan, Ruixue Wang, and Yigong Shi (2019). Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome. Cold Spring Harbor Perspectives in Biology. 11(1). Epub 2019 Jan.
(***) Xiaofeng Zhang, Xiechao Zhan, Chuangye Yan, Wenyu Zhang, Dongliang Liu, Jianlin Lei and Yigong Shi (2018). Structures of the human spliceosomes before and after release of the ligated exon. Cell Res. 29(4):274-285. Epub 2019 Feb 6.
(***) Ruixue Wan, Rui Bai, Chuangye Yan, Jianlin Lei, and Yigong Shi (2018). Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell. 177(2):339-351. Epub 2019 Mar 14.
(***) Rui Zhou, Guanghui Yang, Xuefei Guo, Qiang Zhou, Jianling Lei, and Yigong Shi(2019). Recognition of the amyloid precursor protein by human γ-secretase. Science. 363(6428). Epub 2019 Feb 15.

2018

(***) Guanghui Yang, Rui Zhou, Qiang Zhou, Xuefei Guo, Chuangye Yan, Meng Ke, Jianling Lei, and Yigong Shi (2019). Structural basis of Notch recognition by human γ-secretase. Nature. 565(7738):192-197. Epub 2018 Dec 31.
(***) Shenjie Wu, Wenqi Song, Catherine C. L. Wong, and Yigong Shi (2018). Bax inhibitor 1 is a γ-secretase-independent presenilin-binding protein. Proc Natl Acad Sci U S A. 116(1):141-147. Epub 2018 Dec 17.
(***) Xiechao Zhan, Chuangye Yan, Xiaofeng Zhang, Jianlin Lei, and Yigong Shi (2018). Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Cell Res. 28(12):1129-1140. Epub 2018 Oct 12.
Chuangye Yan, Ruixue Wang, and Yigong Shi (2019). Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome. Cold Spring Harb Perspect Biol. 11(1). pii: a032409. (commissioned review).
(***) Qiang Su, Feizhuo Hu, Xiaofei Ge, Jianlin Lei, Shengqiang Yu, Tingliang Wang, Qiang Zhou, Changlin Mei, and Yigong Shi (2018). Structure of the human PKD1-PKD2 complex. Science. 361(6406):pii: eaat9819. Epub 2018 Aug 9.
(***) Rui Bai, Ruixue Wan, Chuangye Yan, Jianlin Lei, Yigong Shi (2018). Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Science. 360(6396):1423-1429. Epub 2018 May 24.
Xi Zhang, Qifan Wang, Jianping Wu, Jiawei Wang, Yigong Shi, and Minhao Liu (2018). Crystal structure of human lysyl oxidase-like 2 (hLOXL2) in a precursor state. Proc Natl Acad Sci U S A. 115(15):3828-3833. Epub 2018 Mar 26.
(***) Xiaofeng Zhang, Chuangye Yan, Xiechao Zhan, Lijia Li, Jianlin Lei, Yigong Shi (2018). Structure of the human activated spliceosome in three conformational states. Cell Res. 28(3):307-322. Epub 2018 Jan 23.
(***) Xiechao Zhan, Chuangye Yan, Xiaofeng Zhang, Jianlin Lei, Yigong Shi (2018). Structure of a human catalytic step I spliceosome. Science. 359(6375):537-545. Epub 2018 Jan 4.

2017

(***) Rui Bai, Chuangye Yan, Ruixue Wan, Jianlin Lei, and Yigong Shi (2017). Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae. Cell. 171(7):1589-1598. Epub 2017 Nov 16.
Rui Zhou, Guanghui Yang, and Yigong Shi (2017). Dominant negative effect of the loss-of-function γ-secretase mutants on the wild-type enzyme through heterooligomerization. Proc Natl Acad Sci U S A. 10.1073/pnas.1713605114. [Epub ahead of print].
Yigong Shi (2017). Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol. 10.1038/nrm.2017.86. Epub 2017 Sep 27. Review.
Ruixue Wan, Chuangye Yan, Rui Bai, Jianlin Lei, and Yigong Shi (2017). Structure of an intron lariat spliceosome from Saccharomyces cerevisiae. Cell. 171(1):120-132. Epub 2017 Sep 14.
Yigong Shi (2017). The Spliceosome: A Protein-Directed Metalloribozyme. J Mol Biol. 10.1016/j.jmb.2017.07.010. Epub 2017 Jul 19. Review.
Guanghui Yang, Rui Zhou, and Yigong Shi (2017). Cryo-EM structures of human γ-secretase. Curr Opin Struct Biol. 10.1016/j.sbi.2017.05.013. [Epub ahead of print] Review.
Xiaofeng Zhang, Chuangye Yan, Jing Hang, Lorenzo I. Finci, Jianlin Lei, and Yigong Shi (2017). An atomic structure of the human spliceosome. Cell. 10.1016/j.cell.2017.04.033. Epub 2017 May 11.
Yini Li, Mengying Zhou, Qi Hu, Xiao-chen Bai, Weiyun Huang, Sjors H. W. Scheres, Yigong Shi (2017). Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Proc Natl Acad Sci U S A. 10.1073/pnas.1620626114. Epub 2017 Jan 31.

2016

Chuangye Yan, Ruixue Wan, Rui Bai, Gaoxingyu Huang, Yigong Shi. (2017). Structure of a yeast step II catalytically activated spliceosome. Science. 355(6321):149-155. Epub 2016 Dec 15.
Linfeng Sun, Rui Zhou, Guanghui Yang, Yigong Shi. (2017). Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase. Proc Natl Acad Sci U S A. 114(4):E476-E485. Epub 2016 Dec 5.
Hongwei Wang, Jianlin Lei, Yigong Shi. (2017). Biological cryo-electron microscopy in China. Protein Sci. 26: 16-31. Epub 2016 Sep 2.
Ruixue Wan, Chuangye Yan, Rui Bai, Gaoxingyu Huang, Yigong Shi. (2016). Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. Science. 353(6302):895-904. Epub 2016 Jul 21.
Chuangye Yan, Ruixue Wan, Rui Bai, Gaoxingyu Huang, Yigong Shi. (2016). Structure of a yeast catalytically activated spliceosome at 3.5 Å resolution. Science. 353(6302):904-11. Epub 2016 Jul 21.
Xiuliang Huang, Bai Luan, Jianping Wu, Yigong Shi. (2016). An atomic structure of the human 26S proteasome. Nat Struct Mol Biol. 23(9):778-85.. Epub 2016 Jul 18.
Bai Luan, Xiuliang Huang, Jianping Wu, Ziqing Mei, Yiwei Wang, Xiaobin Xue, Chuangye Yan, Jiawei Wang, Daniel J. Finley, Yigong Shi#, Feng Wang#. (2016). Structure of an endogenous yeast 26S proteasome reveals two major conformational states.. Proc Natl Acad Sci U S A. 113(10):2642-7. Epub 2016 Feb 29.
Tianyu Jiang, Minhao Liu, Jianping Wu, Yigong Shi. (2016). Structural and biochemical analysis of Bcl-2 interaction with the hepatitis B virus protein HBx. Proc Natl Acad Sci U S A. 113(8):2074-9. Epub 2016 Feb 8.
Linfeng Sun, Xiaochun Li, Yigong Shi. (2016). Structural biology of intramembrane proteases: mechanistic insights from rhomboid and S2P to γ-secretase. Curr Opin Struct Biol. 37:97-107. Epub 2016 Jan 24.
Ruixue Wan, Chuangye Yan, Rui Bai, Lin Wang, Min Huang, Catherine C. L. Wong,Yigong Shi. (2016). The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis. Science. 351(6272):466-75. Epub 2016 Jan 7.

2015

Mengying Zhou, Yini Li, Qi Hu, Xiao-chen Bai, Weiyun Huang, Chuangye Yan, Sjors H.W. Scheres and Yigong Shi. (2015). Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes & Dev. 2015. 29: 2349-2361. Epub 2015 Nov 5.
Xiao-chen Bai, Eeson Rajendra, Guanghui Yang, Yigong Shi, Sjors HW Scheres. (2015). Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife. 10.7554/eLife.11182.
Jing Hang, Ruixue Wan, Chuangye Yan, Yigong Shi. (2015). Structural basis of pre-mRNA splicing. Science. 349(6253):1191-1198. Epub 2015 Aug 20.
Chuangye Yan, Jing Hang, Ruixue Wan, Min Huang, Catherine C. L. Wong, Yigong Shi. (2015). Structure of a yeast spliceosome at 3.6-angstrom resolution. Science. 349(6253):1182-1191. Epub 2015 Aug 20.
Xiao-chen Bai, Chuangye Yan, Guanghui Yang, Peilong Lu, Dan Ma, Linfeng Sun, Rui Zhou, Sjors H. W. Scheres, Yigong Shi. (2015). An atomic structure of human γ-secretase. Nature. 525(7568):212-217. Epub 2015 Aug 17.
Linfeng Sun, Lingyun Zhao, Guanghui Yang, Chuangye Yan, Rui Zhou, Xiaoyuan Zhou, Tian Xie, Yanyu Zhao, Shenjie Wu, Xueming Li, Yigong Shi. (2015). Structural basis of human γ-secretase assembly. Proc Natl Acad Sci U S A. 112(19):6003-6008. Epub 2015 Apr 27.
Shangyu Dang, Shenjie Wu, Jiawei Wang, Hongbo Li, Min Huang, Wei He, Yue-Ming Li, Catherine C. L. Wong, Yigong Shi. (2015). Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH. Proc Natl Acad Sci U S A. 112(11):3344-3349. Epub 2015 Mar 2.
Yuxuan Pang, Xiao-chen Bai, Qi Hao, Chuangye Yan, Zheqin Chen, Jia-Wei Wang, Sjors H.W. Scheres, Yigong Shi. (2015). Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila. Genes Dev. 29(3):277-287.

2014

Zhen Yan, Xiao-chen Bai, Chuangye Yan, Jianping Wu, Zhangqiang Li, Tian Xie, Wei Peng, Chang-cheng Yin, Xueming Li, Sjors H. W. Scheres, Yigong Shi, Nieng Yan. (2015). Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution. Nature. 517(7532):50-55. Epub 2014 Dec 15.
Yigong Shi. (2014). A Glimpse of Structural Biology through X-Ray Crystallography. Cell. 159(5):995-1014.
Qi Hu, Di Wu, Wen Chen, Zhen Yan, Chuangye Yan, Tianxi He, Qionglin Liang, Yigong Shi. (2014). Molecular determinants of caspase-9 activation by the Apaf-1 apoptosome. Proc Natl Acad Sci U S A. 111(46):16254-16261. Epub 2014 Oct 13.
Tian Xie, Chuangye Yan, Rui Zhou, Yanyu Zhao, Linfeng Sun, Guanghui Yang, Peilong Lu, Dan Ma, Yigong Shi. (2014). Crystal structure of the γ-secretase component nicastrin. Proc Natl Acad Sci U S A. 111(37):13349-13354. Epub 2014 Sep 2.
Sheng Wang, Renhong Yan, Xi Zhang, Qi Chu, Yigong Shi. (2014). Molecular mechanism of pH-dependent substrate transport by an arginine-agmatine antiporter. Proc Natl Acad Sci U S A. 111(35):12734-12739. Epub 2014 Aug 18.
Peilong Lu, Xiao-chen Bai, Dan Ma, Tian Xie, Chuangye Yan, Linfeng Sun, Guanghui Yang, Yanyu Zhao, Rui Zhou, Sjors H. W. Scheres, Yigong Shi. (2014). Three-dimensional structure of human γ-secretase. Nature. 512(7513):166-170. Epub 2014 Jun 29.
Yigong Shi. (2014). Life, career, and structural biology. Phys Scripta. 89(6):68004-68024.
Jijie Chai, Yigong Shi. (2014). Apoptosome and inflammasome: conserved machineries for caspase activation. Nati Sci Rev. 1(1):101-108.
Lijun Zhou, Yulin Zhou, Jing Hang, Ruixue Wan, Guifeng Lu, Chuangye Yan, Yigong Shi. (2014). Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex. Cell Res. 24(4):497-500. Epub 2014 Feb 11.
Peilong Lu, Dan Ma, Chuangye Yan, Xinqi Gong, Mingjian Du, Yigong Shi. (2014). Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase. Proc Natl Acad Sci U S A. 111(5):1813-1818. Epub 2014 Jan 21.

2013

Lijun Zhou, Jing Hang, Yulin Zhou, Ruixue Wan, Guifeng Lu, Ping Yin, Chuangye Yan, Yigong Shi. (2014). Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA. Nature. 506(7486):116-120. Epub 2013 Nov 17.
Ping Yin, Quanxiu Li, Chuangye Yan, Ying Liu, Junjie Liu, Feng Yu, Zheng Wang, Jiafu Long, Jianhua He, Hong-Wei Wang, Jiawei Wang, Jian-Kang Zhu, Yigong Shi, Nieng Yan. (2013). Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 504(7478):168-171. Epub 2013 Oct 27.
Tian Xie, Wei Peng, Chuangye Yan, Jianping Wu, Xinqi Gong, Yigong Shi. (2013). Structural insights into RIP3-mediated necroptotic signaling. Cell Rep. 5(1):70-78. Epub 2013 Oct 3.
Weijiao Huang, Tianyu Jiang, Wooyoung Choi, Shiqian Qi, Yuxuan Pang, Qi Hu, Yanhui Xu, Xinqi Gong, Philip D. Jeffrey, Jiawei Wang, Yigong Shi. (2013). Mechanistic insights into CED-4-mediated activation of CED-3. Genes Dev. 27(18):2039-2048.
Yigong Shi. (2013). Common folds and transport mechanisms of secondary active transporters. Annu Rev Biophys. 42:51-72.
Dan Ma, Peilong Lu, Yigong Shi. (2013). Substrate Selectivity of the Acid-activated Glutamate-GABA Antiporter GadC from E. coli. J Biol Chem. 288(21):15148-15153. Epub 2013 Apr 15.
Tingliang Wang, Guobin Fu, Xiaojing Pan, Jianping Wu, Xinqi Gong, Jiawei Wang, Yigong Shi. (2013). Structure of a bacterial energy-coupling factor transporter. Nature. 497(7448):272-276. Epub 2013 Apr 14.
Qi Hu, Di Wu, Wen Chen, Zhen Yan, Yigong Shi. (2013). Proteolytic Processing of Caspase-9 Zymogen Is Required for Apoptosome-mediated Activation of Caspase-9. J Biol Chem. 288(21):15142-15147. Epub 2013 Apr 9.
Hanchi Yan, Weiyun Huang, Chuangye Yan, Xinqi Gong, Sirui Jiang, Yu Zhao, Jiawei Wang, Yigong Shi. (2013). Structure and mechanism of a nitrate transporter. Cell Rep. 3(3):716-723. Epub 2013 Mar 21.
Tian Xie, Wei Peng, Yexing Liu, Chuangye Yan, Jenny Maki, Alexei Degterev, Junying Yuan, Yigong Shi. (2013). Structural Basis of RIP1 Inhibition by Necrostatins. Structure. 21(3):493-499.
Weijiao Huang, Wooyoung Choi, Yuling Chen, Qi Zhang, Haiteng Deng, Wei He, Yigong Shi. (2013). A proposed role for glutamine in cancer cell growth through acid resistance. Cell Res. 23(5):724-727. Epub 2013 Jan 29.
Peilong Lu, Dan Ma, Yuling Chen, Yingying Guo, Guo-Qiang Chen, Haiteng Deng, Yigong Shi. (2013). L-glutamine provides acid resistance for Escherichia coli through enzymatic release of ammonia. Cell Res. 23(5):635-644. Epub 2013 Jan 22.

2012

Xiaochun Li, Shangyu Dang, Chuangye Yan, Xinqi Gong, Jiawei Wang, Yigong Shi. (2013). Structure of a presenilin family intramembrane aspartate protease. Nature. 493(7430):56-61. Epub 2012 Dec 19.
Ping Yin, Dong Deng, Chuangye Yan, Xiaojing Pan, Jianzhong Jeff Xi, Nieng Yan, Yigong Shi. (2012). Specific DNA-RNA Hybrid Recognition by TAL Effectors. Cell Rep. 2(4):707-713. Epub 2012 Sep 27.
Dong Deng, Ping Yin, Chuangye Yan, Xiaojing Pan, Xinqi Gong, Shiqian Qi, Tian Xie, Magdy Mahfouz, Jian-Kang Zhu, Nieng Yan, Yigong Shi. (2012). Recognition of methylated DNA by TAL effectors. Cell Res. 22(10):1502-1504. Epub 2012 Sep 4.
Ada Hang-Heng Wong, Chuangye Yan, Yigong Shi. (2012). Crystal structure of the yeast metacaspase yca1. J Biol Chem. 287(35):29251-29259. Epub 2012 Jul 2.
Dan Ma, Peilong Lu, Chuangye Yan, Chao Fan, Ping Yin, Jiawei Wang, Yigong Shi. (2012). Structure and mechanism of a glutamate-GABA antiporter. Nature. 483(7391):632-636.
Di Wu, Qi Hu, Zhen Yan, Wen Chen, Chuangye Yan, Xi Huang, Jing Zhang, Panyu Yang, Haiteng Deng, Jiawei Wang, XingWang Deng, Yigong Shi. (2012). Structural basis of ultraviolet-B perception by UVR8. Nature. 484(7393):214-219.
Weijiao Huang, Wooyoung Choi, Wanqiu Hu, Na Mi, Qiang Guo, Meisheng Ma, Mei Liu, Yuan Tian, Peilong Lu, Feng-Liang Wang, Haiteng Deng, Lei Liu, Ning Gao, Li Yu, Yigong Shi. (2012). Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein. Cell Res. 22(3):473-489. Epub 2012 Feb 7.
Dong Deng, Chuangye Yan, Xiaojing Pan, Magdy Mahfouz, Jiawei Wang, Jian-Kang Zhu, Yigong Shi*, Nieng Yan* (2012). Structural basis for the specific recognition of DNA by TAL effectors. Science. 335(6069):720-723. Epub 2012 Jan 5.

2011

Jong W. Yu, Philip D. Jeffrey, Jun Yong Ha, Xiaolu Yang, Yigong Shi. (2011). Crystal structure of the mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) paracaspase region. Proc Natl Acad Sci U S A. 108(52):21004-21009. Epub 2011 Dec 7.
Xiaochun Li, Jiawei Wang, Yigong Shi. (2011). Structural mechanisms of DIAP1 auto-inhibition and DIAP1-mediated inhibition of drICE. Nat Commun. 2:408.
Feng Wang, Ziqing Mei, Yutao Qi, Chuangye Yan, Qi Hu, Jiawei Wang, Yigong Shi. (2011). Structure and mechanism of the hexameric MecA-ClpC molecular machine. Nature. 471(7338):331-335. Epub 2011 Mar 2.

2010

Peng Zhang, Jiawei Wang, Yigong Shi. (2010). Structure and mechanism of the S component of a bacterial ECF transporter. Nature. 468(7324):717-720. Epub 2010 Oct 24.
Shiqian Qi, Yuxuan Pang, Qi Hu, Qun Liu, Hua Li, Yulian Zhou, Tianxi He, Qionglin Liang, Yexing Liu, Xiaoqiu Yuan, Guoan Luo, Huilin Li, Jiawei Wang, Nieng Yan, Yigong Shi. (2010). Crystal Structure of the Caenorhabditis elegans Apoptosome Reveals an Octameric Assembly of CED-4. Cell. 141(3):446-457. 30 April 2010.
Yide Mei, Jeongsik Yong, Hongtu Liu, Yigong Shi, Judy Meinkoth, Gideon Dreyfuss, Xiaolu Yang. (2010). tRNA Binds to Cytochrome c and Inhibits Caspase Activation. Mol Cell. 37(5):668-678.
Xiang Gao, Lijun Zhou, Xuyao Jiao, Feiran Lu, Chuangye Yan, Xin Zeng, Jiawei Wang, Yigong Shi. (2010). Mechanism of substrate recognition and transport by an amino acid antiporter. Nature. 463(7282):828-832. Epub 2010 Jan 20.

2009

Feng Wang, Ziqing Mei, Yutao Qi, Chuangye Yan, Siheng Xiang, Zhiyuan Zhou, Qi Hu, Jiawei Wang, Yigong Shi. (2009). Crystal structure of the MecA degradation tag. J Biol Chem. 284(49):34376-34381. Epub 2009 Oct 2.
Ziqing Mei, Feng Wang, Yutao Qi, Zhiyuan Zhou, Qi Hu, Han Li, Jiawei Wu, Yigong Shi. (2009). Molecular determinants of MecA as a degradation tag for the ClpCP protease. J Biol Chem. 284(49):34366-34375. Epub 2009 Sep 18.
David A Gell, Liang Feng, Suiping Zhou, Philip D. Jeffrey, William Avigdor, Andrew Gow, Mitchell J. Weiss, Yigong Shi, Joel P Mackay. (2009). A cis-Proline in α-Hemoglobin Stabilizing Protein Directs the Structural Reorganization of α-Hemoglobin. J Biol Chem. 284(43):29462-29469. Epub 2009 Aug 25.
(***) Xiaochun Li, Boyuan Wang, Lihui Feng, Hui Kang, Yang Qi, Jiawei Wang, Yigong Shi. (2009). Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage. Proc. Natl. Acad. Sci. U S A. 106(35):14837-14842. Epub 2009 Aug 17.
(***) Xiang Gao, Feiran Lu, Lijun Zhou, Shangyu Dang, Linfeng Sun, Xiaochun Li, Jiawei Wang, Yigong Shi. (2009). Structure and Mechanism of an Amino Acid Antiporter. Science. 324(5934):1565-1568. Epub 2009 May 28.
Yigong Shi. (2009). Serine/Threonine Phosphatases: Mechanism through Structure. Cell. 139(3):468-484.
(***) Yi Wang, Yongjian Huang, Jiawei Wang, Chao Cheng, Weijiao Huang, Peilong Lu, Ya-Nan Xu, Pengye Wang, Nieng Yan, Yigong Shi. (2009). Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature. 462(7272):467-472.
(***) Fan Zhang , Zhuoru Wu, Ping Zhang, Geng Tian, Daniel Finley, Yigong Shi. (2009). Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell. 34(4):485-496.
(***) Fan Zhang , Min Hu, Geng Tian, Ping Zhang, Daniel Finley, Philip D. Jeffrey, Yigong Shi. (2009). Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell. 34(4):473-484.
(***) Jong W. Yu, Philip D. Jeffrey, Yigong Shi. (2009). Mechanism of procaspase-8 activation by c-FLIPL. Proc Natl Acad Sci U S A. 106(20):8169-8174. Epub 2009 May 4.
Yigong Shi. (2009). Assembly and structure of protein phosphatase 2A. Sci China C Life Sci. 52(2):135-146. Epub 2009 Mar 11.
David C. Clarke, Meredith L. Brown, Richard A. Erickson, Yigong Shi, Xuedong Liu. (2009). Transforming growth factor β depletion is the primary determinant of Smad signaling kinetics. Mol Cell Biol. 29(9):2443-2455. Epub 2009 Feb 17.

2008

Xu Zhang, Jiawei Wang, Chao Fan, Hubo Li, Honghong Sun, Shunyou Gong, Youhai H. Chen, Yigong Shi. (2008). Crystal structure of TIPE2 reveals insights into immune homeostasis. Nature Struct Mol Biol. 16(1):89-90. Epub 2008 Dec 14.
Jong W. Yu, Yigong Shi. (2008). FLIP and the death effector domain family. Oncogene. 27(48):6216-6227.
(***) Yanhui Xu, Yu Chen, Ping Zhang, Philip D. Jeffrey, Yigong Shi. (2008). Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation. Mol Cell. 31(6):873-885.
Yigong Shi. (2008). Apoptosome assembly. Methods Enzymol. 442:141-156.
Sinisa Urban, Yigong Shi. (2008). Core principles of intramembrane proteolysis: comparison of rhomboid and site-2 family proteases. Curr Opin Struct Biol. 18(4):432-441. Epub 2008 Apr 26.
(***) Yongna Xing, Zhu Li, Yu Chen, Philip D. Jeffery, Yigong Shi. (2008). Structural mechanism of demethylation and inactivation of protein phosphatase 2A. Cell. 133(1):154-163.
Yigong Shi. (2008). Deubiquitination of Lys63-linkage by a CYLD UBP. Structure. 16(3):338-340.
(***) Yan Xu, Liang Feng, Philip D. Jeffrey, Yigong Shi*, Francois M. M. Morel*. (2008). Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Nature. 452(7183):56-61.

2007

(***) Liang Feng, Hanchi Yan, Zhuoru Wu, Nieng Yan, Zhe Wang, Philip D. Jeffrey, Yigong Shi. (2007). Structure of a Site-2 Protease Family Intramembrane Metalloprotease. Science. 318, 1608-1612.
Nieng Yan, Yigong Shi. (2007). Allosteric activation of a bacterial stress sensor. Cell. 131, 441-443.
Guozhou Chen, Philip D. Jeffrey, Clay Fuqua, Yigong Shi, Lingling Chen. (2007). Structural basis for antiactivation in bacterial quorum sensing. Proc Natl Acad Sci U S A. 104, 16474-16479. Epub 2007 Oct 5.
(***) Yu Chen, Yanhui Xu, Qing Bao, Yongna Xing, Zhu Li, Zheng Lin, Jeffry B Stock, Philip D Jeffrey, Yigong Shi. (2007). Structural and biochemical insights into the regulation of protein phosphatase 2A by small t antigen of SV40. Nat Struct & Mol Biol. 14, 527-534. Epub 2007 May 27.
Adam Oberstein, Philip D Jeffrey, Yigong Shi. (2007). Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein. J Biol Chem. 282, 13123-13132. Epub 2007 Mar 2.
Aislyn D. Wist, Stefan J. Riedl, Yigong Shi, George L. McLendon. (2007). Structure-activity based study of the Smac-binding pocket within the BIR3 domain of XIAP. Bioorg Med Chem. 5, 2935-2943.
(***) Qing Bao, Wenyu Lu, Joshua D. Rabinowitz, Yigong Shi. (2007). Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Molecular Cell. 25, 181-192.
Qing Bao, Yigong Shi. (2007). Apoptosome: a platform for the activation of initiator caspases. Cell Death Differ. 14, 56-65.

2006

(***)Yanhui Xu, Yongna Xing, Yu Chen, Yang Chao, Zheng Lin, Eugene Fan, Jong W. Yu, Stefan Strack, Philip D. Jeffrey, Yigong Shi. (2006). Structure of the protein phosphatase 2A holoenzyme. Cell. 127, 1239-1251.
(***)Zhuoru Wu, Nieng Yan, Liang Feng, Adam Oberstein, Hanchi Yan, Rosanna P Baker, Lichuan Gu, Philip D Jeffrey, Sinisa Urban, Yigong Shi. (2006). Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct & Mol Biol. 13, 1084-1091. Epub 2006 Nov 10.
(***)Yongna Xing, Yanhui Xu, Yu Chen, Philip D Jeffrey, Yang Chao, Zheng Lin, Zhu Li, Stefan Strack, Jeffry B. Stock, Yigong Shi. (2006). Structure of protein phosphatase 2A core enzyme bound to tumor-inducing toxins. Cell. 127, 341-353.
Yigong Shi. (2006). Mechanical aspects of apoptosome assembly. Curr Opin Cell Biol. 18, 677-684. Epub 2006 Oct 12.
(***)Yang Chao, Yongna Xing, Yu Chen, Yanhui Xu, Zheng Lin, Zhu Li, Philip D. Jeffrey, Jeffry B. Stock, Yigong Shi. (2006). Structure and Mechanism of the Phosphotyrosyl Phosphatase Activator. Mol Cell. 23, 535-546.
Xia Lin, Xueyan Duan, Yao-Yun Liang, Ying Su, Katharine H. Wrighton, Jianyin Long, Min Hu, Candi M. Davis, Jinrong Wang, F. Charles Brunicardi, Yigong Shi, Ye-Guang Chen, Anming Meng, Xin-Hua Feng. (2006). PPM1A functions as a Smad phosphatase to terminate TGFbeta signaling. Cell. 125, 915-928.
Chonglin Yang, Nieng Yan, Jay Parish, Xiaochen Wang, Yigong Shi, Ding Xue. (2006). RNA aptamers targeting the cell death inhibitor CED-9 induce cell kiling in C. elegans. J Biol Chem. 281, 9137-9144. Epub 2006 Feb 8.
Nieng Yan, Jun R. Huh, Vrigil Schirf, Borries Demeler, Bruce A. Hay, Yigong Shi. (2006). Structure and activation mechanism of the Drosophila initiator caspase Dronc. J Biol Chem. 281, 8667-8674. Epub 2006 Jan 30.
(***) Min Hu, Lichuan Gu, Muyang Li, Philip D. Jeffrey, Wei Gu, Yigong Shi. (2006). Structural Basis of Competitive Recognition of p53 and MDM2 by HAUSP/USP7: Implications for the Regulation of the p53-MDM2 Pathway. PLoS Biology. 4, e27. Epub 2006 Jan 17.
Nieng Yan, Yanhui Xu, Yigong Shi. (2006). 2:1 Stoichiometry of the CED-4-CED-9 Complex and the Tetrameric CED-4: Insights into the Regulation of CED-3 Activation. Cell Cycle. 5, 31-34. Epub 2006 Jan 18.

2005

Feng-Yen Li, Philip D. Jeffrey, Jong W. Yu, Yigong Shi. (2006). Crystal Structure of a Viral FLIP: INSIGHTS INTO FLIP-MEDIATED INHIBITION OF DEATH RECEPTOR SIGNALING. J Biol Chem. 281, 2960-2968. Epub 2005 Nov 29.
(***) Min Hu, Pingwei Li, Ling Song, Philip D Jeffrey, Tatiana A Chenova, Keith D Wilkinson, Robert E Cohen, Yigong Shi. (2005). Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. EMBO J. 24, 3747-3756. Epub 2005 Oct 6.
(***) Nieng Yan, Jijie Chai, Eui Seung Lee, Lichuan Gu, Qun Liu, Jiaqing He, Jia-Wei Wu, David Kokel, Huilin Li, Quan Hao, Ding Xue, Yigong Shi. (2005). Structure of the CED-4/CED-9 complex reveals insights into programmed cell death in Caenorhabditis elegans. Nature. 437, 831-837.
Nieng Yan, Yigong Shi. (2005). Mechanisms of Apoptosis through Structural Biology. Annual Review Cell Dev Biol. 21, 35-56.
Qing Bao, Stefan J. Riedl, Yigong Shi. (2005). Structure of Apaf-1 in the Auto-Inhibited Form: A Critical Role for ADP. Cell Cycle. 4(8). Epub 2005 Aug 13.
Xinchao Yu, Devrim Acehan, Jean-François Ménétret, Christopher R. Booth, Steven J. Ludtke, Stefan J. Riedl, Yigong Shi, Xiaodong Wang, and Christopher W. Akey. (2005). A structure of the human apoptosome at 12.8 A resolution provides insights into this cell death platform. Structure. 1,1725-35.
(***) Yang Chao, Eric N. Shiozaki, Srinivasa M. Srinivasula, Daniel J. Rigotti, Robert Fairman, Yigong Shi. (2005). Engineering a Dimeric Caspase-9: A Re-evaluation of the Induced Proximity Model for Caspase Activation. PLoS Biology. 3, e183. Epub 2005 May 10.
(***) Liang Feng, Suiping Zhou, Lichuan Gu, David A. Gell, Joel P. Mackay, Mitchell J. Weiss, Andrew J. Gow, Yigong Shi. (2005). Structure of oxidized alpha-haemoglobin bound to AHSP reveals a protective mechanism for haem. Nature. 435, 697-701.
(***) Stefan J. Riedl, Wenyu Li, Yang Chao, Robert Schwarzenbacher, Yigong Shi. (2005). Structure of the apoptotic protease activating factor 1 (Apaf-1) bound to ADP. Nature. 434, 926-933.

2004

Michael D. Tibbetts, Eric N. Shiozaki, Lichuan Gu, E. Robert McDonald III, Wafik S. El-Deiry, Yigong Shi. (2004). Crystal Structure of a Novel FYVE-type Zinc Finger Domain from the Caspase Regulator CARP2. Structure. 12, 2257-2263.
(***) Liang Feng, David A. Gell, Suiping Zhou, Lichuan Gu, Yi Kong, Jianqing Li, Min Hu, Nieng Yan, Christopher Lee, Anne M. Rich, Robert S. Armstrong, Peter A. Lay, Andrew J. Gow, Mitchell J. Weiss, Joel P. Mackay, Yigong Shi. (2004). Molecular Mechanism of AHSP-mediated Stabilization of alpha-hemoglobin. Cell. 119, 629-640.
Ping La, Albert C. Silva, Zhaoyuan Hou, Haoren Wang, Robert W. Schnepp, Nieng Yan, Yigong Shi, Xianxin Hua. (2004). Direct Binding of DNA by Tumor Suppressor Menin. J Biol Chem. 279, 49045-49054. Epub 2004 Aug 24.
Stefan J. Riedl, Yigong Shi. (2004). Molecular mechanisms of caspase regulation during apoptosis. Nature Review - Mol Cell Biol. 5, 897-907.
(***) Nieng Yan, Lichuan Gu, David Kokel, Jijie Chai, Wenyu Li, Aidong Han, Lin Chen, Ding Xue, Yigong Shi. (2004). Structural, Biochemical and Functional Analyses of CED-9 Recognition by the Pro-apoptotic Proteins EGL-1 and CED-4.. Mol Cell. 15, 999-1006.
Eric N. Shiozaki, Yigong Shi. (2004). Caspases, IAPs, and Smac/DIABLO: Mechanisms from Structural Biology. Trends Biochem Sci. 29 (9), 486-494.
Yigong Shi. (2004). Caspase Activation, Inhibition, and Re-activation: A Mechanistic View. Protein Science. 13,1979-1987.
Yigong Shi. (2004). Caspase Activation: Revisiting the Induced Proximity model. Cell. 117, 855-858.
(***) Eric N.Shiozaki, Lichuan Gu, Nieng Yan, Yigong Shi. (2004). Structure of the BRCT Repeats of BRCA1 bound to a BACH1 Phosphopeptide: Implications for Signaling. Mol Cell. 14, 405-412.
(***) Nieng Yan, Jia-Wei Wu, Jun R. Huh, Jijie Chai, Wenyu Li, Bruce A. Hay, Yigong Shi. (2004). Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim. Nat Struct & Mol Biol. 11 (5), 420-428. Epub 2004 Apr 25.
Joshua P. Frederick, Nicole T. Liberati, David S. Waddell, Yigong Shi, Xiao-Fan Wang. (2004). Transforming Growth Factor beta-Mediated Transcriptional Repression of c-myc Is Dependent on Direct Binding of Smad3 to a Novel Repressive Smad Binding Element. . Mol Cell Biol. 24 (6), 2546-2559.

2003

Jun R. Huh, Stephanie Y. Vernooy, Hong Yu, Nieng Yan, Yigong Shi, Ming Guo, Bruce A. Hay. (2004). Multiple apoptotic caspase cascades are required in non-apoptotic roles for Drosophila spermatid individualization. PLoS Biology. 2, 43-53. Epub 2003 Dec 15.
Nieng Yan, Yigong Shi. (2003). Histone H1.2 as a trigger for apoptosis. Nature-Structural Biology. 10, 983-985.
(***) Jijie Chai, Nieng Yan, Jun R. Huh, Jia-Wei Wu, Wenyu Li, Bruce A. Hay, Yigong Shi. (2003). Molecular mechanism of Reaper-Grim-Hid-mediated suppression of DIAP1-dependent Dronc ubiquitination. Nature Structure Biololgy. 10, 892-898. Epub 2003 Sep 28.
Constance J. Glover, Karen Hite, Renee DeLosh, Dominic A. Scudiero, Matthew J. Fivash, Lindsey R. Smith, Robert J. Fisher, Jia-Wei Wu, Yigong Shi, Rachael A. Kipp, George L. McLendon, Edward A. Sausville, Robert H. Shoemaker. (2003). A high-throughput screen for identification of molecular mimics of Smac/DIABLO utilizing a fluorescence polarization assay. Analytical Biochemistry. 320, 157-169.
Yigong Shi, Joan Massagué. (2003). Mechanisms of TGF-beta signaling from Cell Membrane to the Nucleus(commissioned review article). Cell. 113, 685-700.
Jijie Chai, Jia-Wu Wu, Nieng Yan, Joan Massagué, Nikola P. Pavletich, Yigong Shi. (2003). Features of a Smad3 MH1-DNA complex: Roles of water and zinc in DNA binding. J Biol Chem. 278, 20327-20331. Epub 2003 Apr 9.
Yigong Shi (2003). Structural Biology of Programmed Cell Death(Book chapter). in Essentials of Apoptosis: A Guide for Basic and Clinical Research, Humana Press. pages 47-66.
(***) Eric N. Shiozaki, Jijie Chai, Daniel J. Rigotti, Stefan J. Riedl, Pingwei Li, Srinivasa M. Srinivasula, Emad S. Alnemri, Robert Fairman, Yigong Shi. (2003). Mechanism of XIAP-mediated Inhibition of Caspase-9. Mol.Cell. 11, 519-527.

2002

(***) Min Hu, Pingwei Li, Muyang Li, Wenyu Li, Tingting Yao, Jia-Wei Wu, Wei Gu, Robert E. Cohen, Yigong Shi. (2002). Crystal Structure of a UBP-Family Deubiquitinating Enzyme in Isolation and in Complex with Ubiquitin Aldehyde. Cell. 111, 1041-1054.
Xiaochen Wang, Chonglin Yang, Jijie Chai, Yigong Shi, Ding Xue. (2002). Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. Science. 298, 1587-1592.
(***) Jia-Wei Wu, Ariel R. Krawitz, Jijie Chai, Wenyu Li, Fangjiu Zhang, Kunxin Luo, Yigong Shi. (2002). Structural Mechanism of Smad4 Recognition by the Nuclear Oncoprotein Ski: Insights on Ski-Mediated Repression of TGF-beta Signaling. Cell. 111, 357-367.
Rachael A. Kipp, Martin A. Case, Aislyn D. Wist, Catherine M. Cresson, Maria Carrell, Erin Griner, Arun Wiita, Philip A. Albiniak, Yigong Shi, Martin F. Semmelhack, George L. McLendon. (2002). Molecular Targeting of Inhibitor of Apoptosis Proteins Based on Small Molecule Mimics of Natural Binding Partners. Biochem. 41, 7344-7349.
(***) Wenyu Li, Jijie Chai, Srinivasa M. Srinivasula, Emad S. Alnemri, Yigong Shi. (2002). Structure of the Mitochondrial Serine Portease Omi/HtrA2: Insights for Its Proapoptotic Function. Nature Struct. Biol. 9, 436-441.
Eric Shiozaki, Jijie Chai, Yigong Shi. (2002). Oligomerization and Activation of Caspase-9 Induced by the CARD Domain of Apaf-1. Proc Natl Acad Sci U S A. 99, 4197-4202. Epub 2002 Mar 19.
Yigong Shi. (2002). Mechanisms of Caspase Activation and Inhibition During Apoptosis. Mol Cell. 9, 459-470.
Yigong Shi. (2002). Apoptosome: the cellular engine for the activation of caspase-9. Structure. 10, 285-288.
Srinivasa M. Srinivasula, Pinaki Datta, Masatomo Kobayashi, Miki Fujioka, Jia-Wei Wu, Ramesh Hegde, ZhiJia Zhang, Rula Mukattash, Teresa Fernandes-Alnemri, Yigong Shi, James B. Jaynes, Emad S. Alnemri. (2002). Sickle , a novel Drosophila death gene in the reaper/hid/grim region encodes an IAP-inhibitory protein. Curr Biol. 12, 125-130.
Yigong Shi. (2002). A conserved tetrapeptide motif: Potentiating apoptosis through IAP-binding. Cell Death Differ. 9, 93-95.

2001

(***) Jia-Wei Wu, Min Hu, Jijie Chai, Morgan Huse, Carey Li, Saw Kyin, Robert Fairman, Tom Muir, Joan Massagué, Yigong Shi. (2001). Crystal Structure of a Phosphorylated Smad2: Recognition of Phosphoserine Motif and Insights on Smad Function in TGF-beta Signaling. Mol Cell. 8, 1277-1289.
Stephen W. Fesik, Yigong Shi. (2001). Controlling the Caspases. Science. 294, 1477-1478.
(***) Jijie Chai Qi Wu, Eric Shiozaki, Srinivasa M. Srinivasula, Emad S. Alnemri, Yigong Shi. (2001). Crystal Structure of a Procaspase-7 Zymogen: Mechanisms of Activation and Substrate Binding. Cell. 107, 399-407.
(***) Jia-Wei Wu, Amy Cocina, Jijie Chai, Bruce Hay, Yigong Shi. (2001). Structural Analysis of a Functional DIAP1 Fragment Bound to Grim and Hid Peptides. Mol Cell. 8, 95-104.
Jia-Wei Wu, Jack Penry, Robert Fairman, Yigong Shi. (2001). Formation of a Stable Heterodimer between Smad2 and Smad4. J Biol Chem. 276, 20688-20694.
Yigong Shi. (2001). A Structural View of the Mitochondria-mediated Apoptosis. Nature Struct. Biol. 8, 394-401.
(***) Jijie Chai, Eric Shiozaki, Srinivasa M. Srinivasula, Qi Wu, Pinaki Datta, Emad S. Alnemri, Yigong Shi. (2001). Structural Basis of Caspase-7 Inhibition by XIAP. Cell. 104, 769-780.
Srinivasa M. Srinivasula, Ayman Saleh, Ramesh Hedge, Pinaki Datta, Eric Shiozaki, Paul D. Robbins, Teresa Fernandes-Alnemri, Yigong Shi, Emad S. Alnemri. (2001). A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO mediates opposing effects on caspase activity and apoptosis. Nature. 409, 112-116.
Yigong Shi. (2001). Structural Insights on Smad Function in TGF-beta signaling. BioEssays. 23, 223-232.

2000

(***) Geng Wu, Jijie Chai, Tomeka Suber, Jia-Wei Wu, Chunying Du, Xiaodong Wang, Yigong Shi. (2000). Structural Basis of IAP Recognition by Smac/DIABLO. Nature. 408, 1008-1012.
(***) Jijie Chai, Chunying Du, Jia-Wei Wu, Saw Kyin, Xiaodong Wang, Yigong Shi. (2000). Structural and Biochemical Basis of Apoptotic Activation by Smac/DIABLO. Nature. 406, 855-862.
Yigong Shi. (2000). Survivin structure: crystal unclear. Nature Struct Biol. 7, 620-623.
Sha Ha, Debbie Walker, Yigong Shi, Suzanne Walker. (2000). The 1.9 Å crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis. Portein Sci. 9, 1045-1052.
(***) Geng Wu, Ye-Guang Chen, Barish Ozdamar, Cassie Gyuricza, P. Andrew Chong, Jeffrey L. Wrana, Joan Massagué, Yigong Shi (2000). Structural Basis of Smad2 Recruitment by the Smad Anchor for Receptor Activation (SARA). Science. 287, 92-97.

1998-1999

Xianxin Hua, Zachary Miller, Geng Wu, Yigong Shi, Harvey F. Lodish. (1999). Specificity in TGF-beta-induced Transcription: Interactions of Promoter DNA, Smad3 and TFE3. Proc Natl Acad Sci U S A. 96, 13130-13135.
Jie-Oh Lee, Haijuan Yang, Maria-Magdalena, Antonio Di Cristofano, Tomohiko Maehama, Yigong Shi, Jack E. Dixon, Pier P. Pandolfi, Nikola P. Pavletich. (1999). Crystal Structure of the PTEN Tumor Suppressor: Implications for Its Phosphoinositide Phosphatase Activity and Membrane Association. Cell. 99, 323-334.
(***) Hongxu Qin, Srinivasa M. Srinivasula, Geng Wu, Emad S. Alnemri, Yigong Shi. (1999). Structural Basis of Procaspase-9 Recruitment by the Apoptotic Protease Activating Factor 1. Nature. 399, 549-557.
Shi-Du Yan, Yigong Shi, et al. (1999). Role of ERAB/L-3-hydroxyacyl-coenzyme A dehydrogenase type II activity in beta-Amyloid-induced cytotoxicity. J Biol Chem. 274, 2145-2156.
(***) Yigong Shi, Yan-Fei Wang, Lata Jayaraman, Haijuan Yang, Joan Massagué, Nikola Pavletich. (1998). Crystal Structure of A Smad MH1 Domain Bound to DNA: Insights on DNA-binding in TGF-beta Signaling. Cell. 94, 585-594.
Akiko Hata, Yigong Shi, Joan Massagué. (1998). TGF-beta Signaling and Cancer: Structural and Functional Consequences of Mutations in Smads. Molecular Medicine Today. 4, 257-262.
Ye-Guang Chen, Akiko Hata, Roger S. Lo, David Wotton, Yigong Shi, Nikola P.Pavletich, Joan Massagué. (1998). Determinants of Specificity in TGF-beta Signal Transduction. Genes & Dev. 12, 2144-2152.

Prior to 1998

Roger S. Lo, Ye-Guang Chen, Yigong Shi, Nikola P. Pavletich, Joan Massagué. (1997). The L3 loop: a structural motif determining specific interactions between SMAD proteins and TGF-beta receptors. EMBO J. 17, 996-1005.
Yang-Gyun Kim, Yigong Shi, Jeremy M. Berg, Srinivasan Chandrasegaran. (1997). Site-specific cleavage of DNA-RNA hybrids by zinc finger/Fok I cleavage domain fusions. Gene. 203, 43-49.
(***) Yigong Shi, Akiko Hata, Joan Massagué, Nikola P. Pavletich. (1997). A structural basis for mutational inactivation of the tumour suppressor Smad4. Nature. 388, 87-93.
Yigong Shi, Jeremy M. Berg. (1996). DNA unwinding induced by zinc finger protein binding. Biochemistry. 35, 3845-3848.
Jeremy M. Berg, Yigong Shi. (1996). The Galvanization of Biology: A Growing Appreciation for the Roles of Zinc. Science. 271, 1081-1085.
(***) Yigong Shi, Jeremy M. Berg. (1995). Specific DNA-RNA Hybrid Binding by Zinc Finger Proteins. Science. 268, 282-284.
Yigong Shi, Jeremy M. Berg. (1995). A Direct Comparison of the Properties of Natural and Designed Zinc Finger Proteins. Chemistry and Biology. 2, 83-89.
Yigong Shi, Richard D. Beger, Jeremy M. Berg. (1993). Metal Binding Properties of Single Amino Acid Deletion Mutants of Zinc Finger Peptides: Studies Using Cobalt(II) as a Spectroscopic Probe. Biophysical J. 64, 749-753.