Publications

  1. Xiaofeng Yan#, Shudong Li, Weilin Huang, Hao Wang, Tianfang Zhao, Mingtao Huang, Niyun Zhou, Yuan Shen, Xueming Li*. MPicker: Visualizing and Picking Membrane Proteins for Cryo-Electron Tomography. Nature Communications, 2024, in press
  2. Sijia Liu#, Xuzhong Yang#, Xudong Chen#, Xiaochun Zhang#, Jinghui Jiang#, Jingyi Yuan, Wenhao Liu, Li Wang, Heng Zhou, Kun Wu, Boxue Tian, Xueming Li, Bailong Xiao*. An intermediate open structure reveals the gating transition of the mechanically activated PIEZO1 channel. Neuron, 2024, 113, 1-15.
  3. Hao Zhu#, Ming Li, Meijing Li, Xueming Li, Guangshuo Ou*. Cryo-electron tomography elucidates annular intraluminal configurations in Caenorhabditis elegans microtubules. Biology of the Cell, 2024, 116, e240006.
  4. Shouqing Li#, Ming Li, Yumei Wang, Xueming Li*. Subtraction of liposome signals in cryo-EM structural determination of protein–liposome complexes. Chinese Phys B, 2024, 33, 88702.
  5. Ranhao Zhang#, Yuan Shen, Xueming Li. Tilt-series-based joint CTF estimation for cryo-electron tomography. Structure, 2024, 32, 1239-47.
  6. Chao Lin#, Li Zhang#, Ziying Zhang#, Yifeng Jiang#, Xueming Li*. Locating cellular contents during cryoFIB milling using cellular secondary-electron imaging. Journal of Structural Biology, 2023, 215, 108005.
  7. Sihan Wang#, Heng Zhou#, Wei Chen#, Yifeng Jiang, Xuzhen Yan, Hong You, Xueming Li. CryoFIB milling large tissue samples for cryo-electron tomography. Scientific Reports, 2023,13, 5879.
  8. Keke Qu#, Kangjing Chen#, Hao Wang#, Xueming Li, Zhucheng Chen. Structure of the NuA4 acetyltransferase complex bound to the nucleosome. Nature, 2022, 610, 569-574.
  9. Hao Zhu#, Meijing Li#, Ruixue Zhao#, Ming Li, Yongping Chai, Zhiwen Zhu, Yihong Yang, Wei Li, Zhongyun Xie, Xiaomin Li, Kexin Lei, Xueming Li, Guangshuo Ou, In situ structure of intestinal apical surface reveals nanobristles on microvilli, Proceedings of the National Academy of Sciences, 2022, 119, e2122249119.
  10. Qin Li#, Chao Lin#, Zhipu Luo, Haitao Li, Xueming Li, Qianwen Sun. Cryo-EM structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids, Journal of Genetics and Genomics, 2022, 49, 677-80.
  11. Xuzhong Yang#, Chao Lin#, Xudong Chen#, Shouqin Li#, Xueming Li, Bailong Xiao, Structure deformation and curvature sensing of PIEZO1 in lipid membranes, Nature, 2022, 604, 377-383
  12. Xinyu Zhang#, Tianfang Zhao#, Jiansheng Chen, Yuan Shen, Xueming Li*, EPicker is an exemplar-based continual learning approach for knowledge accumulation in cryoEM particle picking, Nature Communications, 2022, 13, 2468
  13. Meijing Li#, Jianfei Ma#, Xueming Li, Sen-Fang Sui, In situ cryo-ET structure of phycobilisome - photosystem II supercomplex from red alga, ELife, 2021, 10, e69635.
  14. Xueming Li*, Cryo-electron tomography: observing the cell at the atomic level, Nature Methods, 2021, 18(5): 440-441.
  15. Mingxu Hu#, Qi Zhang#, Jing Yang, Xueming Li,Unit quaternion description of spatial rotations in 3D electron cryo-microscopy, Journal of Structural Biology, 2020, 212, 107601
  16. Jie Geng#, Wenhao Liu#, Heng Zhou#, Tingxin Zhang#, Li Wang#, Mingmin Zhang, Yiran Li, BoShen, Xueming Li, Bailong Xiao, A Plug-and-Latch Mechanism for Gating the Mechanosensitive Piezo Channel, Neuron, 2020, 106, 438-451.
  17. Zhaofeng Yan#, Meng Yin#, Jianan Chen#, Xueming Li*, Assembly and Substrate Recognition of Curli Biogenesis System, Nature Communication, 2020, 11, 241
  18. Kun Zhao#, Yaowang Li#, Zhenying Liu, Houfang Long, Chunyu Zhao, Feng Luo, Yunpeng Sun, Youqi Tao, Xiao-Dong Su, Dan Li, Xueming Li, Cong Liu*, Parkinson's disease associated mutation E46K of alpha-synuclein triggers the formation of a distinct fibril structure, Nature Communications, 2020, 11, 2643
  19. Li Wang#, Heng Zhou#, Mingmin Zhang#, Wenhao Liu#, Tuan Deng, Qiancheng Zhao, Yiran Li, Jianlin Lei, Xueming Li, Bailong Xiao, Structure and mechanogating of the mammalian tactile channel PIEZO2, Nature, 2019, 573, 225-229
  20. Heng zhou#, Feng Luo#, Zhipu Luo#, Dan Li, Cong Liu, Xueming Li, Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules, Analytical Chemistry, 2019, 91, 10996-11003
  21. Meijing Li#, Xian Xia#, Yuanyuan Tian#, Qi Jia#, Xiaoyu Liu#, Ying Lu, Ming Li, Xueming Li, and Zhucheng Chen*, Mechanism of DNA translocation underlying chromatin remodeling by Snf2, Nature, 2019, 567, 409-413
  22. Heng Zhou#, Zhipu Luo#, Xueming Li*, Using Focus Ion Beam to Prepare Crystal Lamella for Electron Diffraction, Journal of Structural Biology, 2019, 205, 59-64
  23. Meng Yin#, Zhaofeng Yan#, Xueming Li*, Architecture of type VI secretion system membrane core complex, Cell Research, 2019, 29, 251-253
  24. Mingxu Hu#, Hongkun Yu#, Kai Gu#, Zhao Wang, Huabin Ruan, Kunpeng Wang, Siyuan Ren, Bing Li, Lin Gan, Shizhen Xu, Guangwen Yang, Yuan Shen, Xueming Li*, A particle-filter framework for robust cryoEM 3D reconstruction, Nature Methods, 2018, 15, 1083-1089
  25. Yaowang Li#, Chunyu Zhao#, Feng Luo#, Zhenying Liu, Xinrui Gui, Zhipu Luo, Xiang Zhang, Dan Li, Cong Liu and Xueming Li*, Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy, Cell Research, 2018, 28, 897-903.
  26. Meng Yin#, Zhaofeng Yan#, Xueming Li*, Structural insight into the assembly of the Type II Secretion System Pilotin-Secretin Complex from enterotoxigenic Escherichia coli, Nature Microbiology, 2018, 3,581-587.
  27. Feng Luo#, Xinrui Gui#, Heng Zhou#, Jinge Gu, Yichen Li, Xiangyu Liu, Minglei Zhao, Dan Li, Xueming Li, Cong Liu*, Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation, Nature Structural & Molecular Biology, 2018, 25, 341–346
  28. Qiancheng Zhao#, Heng Zhou#, Shaopeng Chi#, Yanfeng Wang#, Jianhua Wang, Jie Geng, Kun Wu, Wenhao Liu, Tingxin Zhang, Meng-Qiu Dong, Jiawei Wang, Xueming Li, Bailong Xiao. Structure and mechanogating mechanism of the Piezo1 channel. Nature, 2018, 554, 487-492.
  29. Xiaoyuan Zhou#, Minghui Li#, Deyuan Su, Qi Jia, Huan Li, Xueming Li & Jian Yang, Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states, Nature Structural & Molecular Biology, 2017, 24, 1146-1154
  30. Zhaofeng Yan#, Meng Yin#, Dandan Xu, Yongqun Zhu, Xueming Li, Structural Insights into Secretin Translocation Channel in Type II Secretion System, Nature Structure & Molecular Biology, 2017, 24, 177-183.
  31. Minghui Li#, Xiaoyuan Zhou#, Shu Wang, Ye Gong, Deyuan Su, Huan Li, Xueming Li, and Jian Yang, Structure of a eukaryotic cyclic nucleotide-gated channel, Nature, 2017, 542, 60-65.
  32. Xiaoyu Liu#, Meijing Li#, Xian Xia#, Xueming Li, and Zhucheng Chen, Mechanism of chromatin remodeling revealed by the Snf2-nucleosome structure, Nature, 2017, 544, 440-445.
  33. Minghui Li, Wei K Zhang, Nicole M Benvin, Xiaoyuan Zhou,Deyuan Su, Huan Li, Shu Wang, Ioannis E Michailidis, Liang Tong, Xueming Li and Jian Yang, Structural basis of dual Ca2+/pH regulation of the endolysosomal TRPML1 channel, Nature Structure & Molecular Biology, 2017, 24, 205-213.
  34. Li Zhang#, Xiaojing Wang#, Fenghui Fan, Hong-Wei Wang, Jiawei Wang, Xueming Li and Sen-Fang Sui*, Cryo-EM structure of Nma111p, a unique HtrA protease composed of two protease domains and four PDZ domains, Cell Research, 2017, 27, 582-585
  35. Feng Wang#, Huichao Gong#, Gaochao Liu,# Meijing Li , Chuangye Yan, Tian Xia, Xueming Li, Jianyang Zeng*, DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM, Journal of Structural Biology, 2016(195), 325-336
  36. Xueming Li*, Recent technical advancements enabled atomic resolution CryoEM, Chin. Phys. B, 25, 018710, 2016
  37. Guang Yang, Xiang Zhang, Zdravko Kochovski, Yufei Zhang, Bin Dai, Fuji Sakai, Lin Jiang, Yan Lu, Matthias Ballauff, Xueming Li, Cong Liu, Guosong Chen, and Ming Jiang, Precise and Reversible Protein-Microtubule-Like Structure with Helicity Driven by Dual Supramolecular Interactions, J. Am. Chem. Soc., 138 (6), 1932–1937, 2016
  38. Xueming Li, Shawn Zheng, David A. Agard, Yifan Cheng, Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage, Journal of Structural Biology, 192, 174-178, 2015
  39. Po-Lin Chiua#, Xueming Li#, Zongli Li, Brian Beckett,Axel F. Brilot, Nikolaus Grigorieff,David A. Agard, Yifan Cheng, Thomas Walz, Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0, Journal of Structural Biology, 192, 163-173, 2015
  40. Linfeng Sun, Lingyun Zhao, Guanghui Yang, Chuangye Yan, Rui Zhou, Xiaoyuan Zhou, Tian Xie, Yanyu Zhao, Shenjie Wu, Xueming Li, and Yigong Shi*, Structural basis of human γ-secretase assembly, PNAS, 112, 6003-6008, 2015
  41. Qiang Zhou, Xuan Huang, Shan Sun, Xueming Li, Hong-Wei Wang and Sen-Fang Sui, Cryo-EM structure of SNAP-SNARE assembly in 20S particle, Cell Research, 25, 551-560, 2015
  42. Oren S. Rosenberg#, Dustin Dovala#, Xueming Li, Lynn Connolly, Anastasia Bendebury, Janet Finer-Moore, James Holton, Yifan Cheng, Robert M. Stroud, Jeffery S. Cox*, Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion, Cell, 161, 501-512, 2015
  43. Frank DiMaio#, Yifan Song#, Xueming Li, Matthias J Brunner, Chunfu Xu, Vincent Conticello, Edward Egelman, Thomas C Marlovits, Yifan Cheng and David Baker*, Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement, Nature Methods, 12, 361-365, 2015
  44. Ray Yu-Ruei Wang, Mikhail Kudryashev, Xueming Li, Edward H Egelman, Marek Basler, Yifan Cheng, David Baker and Frank DiMaio*, De novo protein structure determination from near-atomic-resolution cryo-EM maps, Nature Methods, 12, 335-338, 2015
  45. Vahid Abrishami, Javier Vargas, Xueming Li, Yifan Cheng, Roberto Marabini, Carlos Oscar Sanchez Sorzanoa, Jose Maria Carazo*, Alignment of direct detection device micrographs using a robust Optical Flow approach, Journal of Structural Biology, 189, 163-176, 2015
  46. Peter S. Shen, Joseph Park, Yidan Qin, Xueming Li, Krishna Parsawar, Matthew H. Larson, James Cox, Yifan Cheng, Alan M. Lambowitz, Jonathan S. Weissman, Onn Brandman, Adam Frost*, Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains, Science, 347, 75-78, 2015
  47. 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 and Nieng Yan*, Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution, Nature, 517, 50-55, 2015
  48. Yina Wang, Joerg Schnitzbauer, Zhe Hu, Xueming Li, Yifan Cheng, Zhen-Li Huang, and Bo Huang*, Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm, Opt Express, 22, 15982-15991, 2014
  49. Pawel A. Penczek*, Jia Fang, Xueming Li, Yifan Cheng, Justus Loerke, Christian M.T. Spahn,CTER-rapid estimation of CTF parameters with error assessment, Ultramicroscopy, 140, 9-19, 2014
  50. Soyeon Park#, Xueming Li#, Homin Kim#, Chingakham Ranjit Singh, Geng Tian, Martin A. Hoyt, Scott Lovell, Kevin P. Battaile, Michal Zolkiewski, Philip Coffino, Jeroen Roelofs, Yifan Cheng, and Daniel Finley, Reconfiguration of the proteasome during chaperone-mediated assembly, Nature, 497, 512-516, 2013. (co-first author)
  51. Xueming Li, Paul Mooney, Shawn Zheng, Chris Booth, Michael B. Braunfeld, Sander Gubbens, David A. Agard and Yifan Cheng, Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM, Nature Methods, 10, 584-590, 2013. ¶ Featured in Nature Methods News and Views: Robert M. Glaeser (2013) Stroboscopic imaging of macromolecular complexes. Nature Methods 10, 475-476. ¶ Featured in Nature Methods: Method of the Year 2013. ¶ Featured in Science: Martin T.J. Smith and John L. Rubinstein (2014), Beyond blob-ology: Advanced cryo-electron microscopy yields high-resolution structures of proteins, Science 345, 617
  52. Xueming Li, Shawn Zheng, Kiyoshi Egami,David A. Agard, Yifan Cheng, Influence of electron dose rate on electron counting images recorded with the K2 camera, J Struct. Biol., 184, 251-260, 2013.
  53. Patricia Grob, Derek Bean, Dieter Typke, Xueming Li, Eva Nogales, and Robert M. Glaeser*, Ranking TEM cameras by their response to electron shot noise, Ultramicroscopy, 133, 1-7, 2013
  54. Shenping Wu, Agustin Avila-Sakar, JungMin Kim, David S. Booth, Charles H. Greenberg, Andrea Rossi, Maofu Liao, Xueming Li, Akram Alian, Sarah L. Griner, Narinobu Juge, Yadong Yu, Claudia M. Mergel, Javier Chaparro-Riggers, Pavel Strop, Robert Tampé, Robert H. Edwards, Robert M. Stroud, Charles S. Craik, Yifan Cheng*, Fabs enable single particle cryoEM studies of small proteins, Structure, 20, 582-592, 2012.
  55. Agustin Avila-Sakar, Xueming Li, Shawn Q. Zheng, and Yifan. Cheng*, Recording high-resolution images of two-dimensional crystals of membrane proteins, Chapter 8, Electron crystallography of soluble and membrane proteins, Methods in Molecular Biology, 955, 129- 152, 2012.
  56. Xueming Li, Nikolaus Grigorieff, Yifan. Cheng*, GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors, J Struct Biol., 172, 407-12, 2010

In Physics and material science

  1. Xueming Li, Fanghua Li*, Huiqian Luo, Lei Fang, Hai-hu Wen, Transmission electron microscopy study of one-dimensional incommensurate structural modulation in superconducting oxides Bi2+xSr2-xCuO6+δ (0.1≤x≤0.4), Superconductor Science and Technology, 22, 065003, 2009
  2. Xueming Li, Fanghua Li, Haifu Fan*, A revised version of the program VEC, Chinese Physics B, 18(6), 2459-2463, 2009
  3. Binghui Ge, Yumei Wang, Xueming Li, Fanghua Li , H.L. Song, H.J. Zhang*, A study of an incommensurately modulated structure in Ca0.28Ba0.72Nb2O6 by electron microscopy, Philosophical Magazine Letters, 88, 213 – 217, 2008
  4. Binghui Ge, Fanghua Li*, Xueming Li, Yumei Wang, Zhenhua Chi, Changqing Jin, Study of superstructure II in multiferroic BiMnO3, Chinese Physics B, 17, 3163-3169, 2008
  5. Xueming Li, Fanghua Li, Yumei Wang, Huiqian Luo, Haihu Wen, The investigation of incommensurate modulation waves in Bi2.1Sr1.9CuO6+δ by image deconvolution, Proceedings of International 12th Beijing Conference and Exhibition on Instrumental Analysis, 2007, Beijing, China
  6. Xueming Li, Rong Wang, Fanghua Li, Superstructure of La0.4Ca2.6Mn2O7 Studied with Maximum Entropy Image Deconvolution, J. Chin. Electr. Microsc. Soc., 25, 22-23, 2006
  7. Xueming Li, Si-ze Yang*, Xingfang Wu, Preparation of Silicon Carbide Nitride Films on Si Substrate by Pulsed High-Energy Density Plasma, Journal of University of Science and Technology Beijing, 13(3), 272-276, 2006
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