Henriette E. Autzen, Alexander G. Myasnikov, Melody G. Campbell, Daniel Asarnow, David Julius* and Yifan Cheng* (2018) Structure of the human TRPM4 ion channel in a lipid nanodisc. Science, 359, 228-232. doi: 10.1126/science.aar4510. PMID: 29217581.

Jennifer M. Binning, Amber M. Smith, Judd F. Hultquist, Charles S. Craik*, Nathalie Caretta Cartozo, Melody G. Campbell, Lily Burton, Florencia La Greca, Michael J. McGregor, Hai M. Ta, Koen Bartholomeeusen, B. Matija Peterlin, Nevan J. Krogan, Natalia Sevillano, Yifan Cheng* and John D. Gross* (2018) Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. PLoS Pathogens, 14, e1006830. doi: 10.1371/journal.ppat.1006830. PMID: 29304101. PMCID: PMC5773222.

Shangyu Dang§, Shengjie Feng§, Jason Tien§, Christian J. Peters, David Bulkley, Marco Lolicato, Jianhua Zhao, Kathrin Zuberbühler, Wenlei Ye, Lijun Qi, Tingxu Chen, Charles S. Craik, Yuh Nung Jan, Daniel L. Minor Jr, Yifan Cheng* and Lily Yeh Jan* (2017) Cryo-EM structures of the TMEM16A calcium-activated chloride channel. Nature, 552, 426-429. doi: 10.1038/nature25024. PMID: 29236684. PMCID: PMC5750132.

Yifan Cheng, Robert M. Glaeser*, Eva Nogales (2017) How Cryo-EM Became so Hot. Cell, 171, 1229-1231. doi: 10.1016/j.cell.2017.11.016. PMID: 29195065.

Anton A. A. Smith, Henriette E. Autzen, Tomas Laursen, Vincent Wu, Max Yen, Aaron Hall, Scott D. Hansen, Yifan Cheng, and Ting Xu* (2017) Controlling Styrene Maleic Acid Lipid Particles through RAFT. Biomacromolecules, 18(11), 3706-3713. doi: 10.1021/acs.biomac.7b01136. PMID: 28934548.

Peng Jin§, David Bulkley§, Yanmeng Guo, Wei Zhang, Zhenhao Guo, Walter Huynh, Shenping Wu, Shan Meltzer, Tong Cheng, Lily Yeh Jan, Yuh-Nung Jan* and Yifan Cheng* (2017) Electron cryo-microscopy structure of the mechanotransduction channel NOMPC. Nature, 547, 118-122. doi:10.1038/nature22981. PMID: 28658211. PMCID: PMC5669069.

Coral Y. Zhou, Caitlin I. Stoddard, Jonathan B. Johnston, Michael J. Trnka, Ignacia Echeverria, Eugene Palovcak, Andrej Sali, Alma L. Burlingame, Yifan Cheng, Geeta J. Narlikar* (2017) Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Reports, 19, 2033-2044. doi: 10.1016/j.celrep.2017.05.029. PMID: 28591576. PMCID: PMC5564220.

Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng* and David A. Agard* (2017) Anisotropic correction of beam-induced motion for improved single particle electron cryo-microscopy. Nature Methods, 14, 331-332. doi: 10.1038/nmeth.4193. PMID: 28250466. PMCID: PMC5494038.

Ray Yu-Ruei Wang, Yifan Song, Benjamin A. Barad, Yifan Cheng, James S. Fraser, and Frank DiMaio (2016) Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife, 2016 Sep 26;5. pii: e17219. doi: 10.7554/eLife.17219. PMID: 27669148. PMCID: PMC5115868.

Yuan Gao, Erhu Cao, David Julius* and Yifan Cheng* (2016) TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature, 534, 347-351. PMID: 27281200. PMCID: PMC4911334.

Jens Frauenfeld, Robin Löving, Jean-Paul Armache, Andreas Sonnen, Fatma Guettou, Per Moberg, Lin Zhu, Caroline Jegerschöld, Ali Flayhan, John A. Briggs, Henrik Garoff, Christian Löw, Yifan Cheng, Pär Nordlund (2016) A saposin-lipoprotein nanoparticle system for membrane proteins. Nature Methods, 13, 345-351. PMID: 26950744. PMCID: PMC4894539.

Yifan Cheng, Thomas Walz (2016) The Special Issue of Microscopy on single particle cryo-electron microscopy. Microscopy, 65, 1-2. PMID: 26586604.

Shenping Wu, Jean-Paul Armache and Yifan Cheng (2016) Single particle cryo-EM data acquisition by using direct electron detection camera. Microscopy. 65, 35-41. PMID: 26546989.

Michel Goedert and Yifan Cheng (2015) Parkinson’s disease: Crystals of a toxic core. Nature, 525, 458-459. PMID: 26352470.

Xueming Li, Shawn Zheng, David A. Agard* and Yifan Cheng* (2015) Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryo-EM images by UCSFImage. Journal of Structural Biology. 192, 174-178. PMID: 26370395, PMCID: PMC4633327.

Juan Du, Wei Lu, Shenping Wu, Yifan Cheng, Eric Gouaux (2015) Glycine receptor mechanism illuminated by electron cryo-microscopy. Nature, 526, 224-229. PMID: 26344198. PMCID: PMC4659708.

Po-Lin Chiu, Xueming Li, Zongli Li, Brain Beckett, Axel F. Brilot, Nikolaus Grigorieff, David Agard, Yifan Cheng* and Thomas Walz* (2015) Evaluation of super-resolution performance of the K2 electron counting camera using 2D crystals of aquaporin-0. Journal of Structural Biology, 192, 163-173. PMID: 26318383, PMCID: PMC4633381.

Benjamin A Barad, Nathaniel Echols, Ray Y-R Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser (2015) Side-chain-directed model and map validation for 3D Electron Cryomicroscopy. Nature Methods, 12, 943-946. PMID: 26280328, PMCID: PMC4589481.

Yifan Cheng (2015) Leading Edge Review: Single particle cryo-EM at crystallographic resolution. Cell, 161, 450-457. PMID: 25910205.

Yifan Cheng, Nikolaus Grigorieff, Pawel A. Penczek and Thomas Walz (2015) Leading Edge Primer: A primer to single-particle cryo-electron microscopy, commissioned primer, Cell, 161, 438-449. PMID: 25910204.

Oren S. Rosenberg, Dustin Dovala, Xueming Li, Lynn Connolly, Anastasia Bendebury, Janet Finer-Moore, James Holton, Yifan Cheng, Robert M. Stroud, and Jeffery S. Cox (2015) Substrates control multimerization and activation of the multi-domain ATPase motor of type VII secretion. Cell, 161, 501-512. PMID: 25865481.

Candice E. Paulsen§, Jean-Paul Armache§, Yuan Gao, Yifan Cheng* and David Julius* (2015) Structure of the human TRPA1 ion channel suggests regulatory mechanisms. Nature, 520, 511-517¶. PMID: 25855297.
EMDB: 6267, 6268, 6269, PDB: 3J9P.
¶ Featured in Nature News and Views:David E. Clapham (2015) Pain-sensing TRPA1 channel resolved. Nature, 520, 439-440. PMID: 25855290.

Frank DiMaio, Yifan Song, Xueming Li, Matthias Brunner, Chunfu Xu, Vincent Conticello, Edward Egelman, Thomas Marlovits, Yifan Cheng and David Baker (2015) Atomic-accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement. Nature Methods, 12, 361-365. PMID: 25707030.

Ray Yu-Ruei Wang, Mikhail Kudryashev, Xueming Li, Edward Egelman, Marek Basler, Yifan Cheng, David Baker and Frank DiMaio (2015) De novo protein structure determination from near-atomic resolution cryo-EM maps. Nature Methods, 12, 335-338. PMID: 25707029.

Vahid Abrishami, Javier Vargas, Xueming Li, Yifan Cheng, Roberto Marabini, Carlos Óscar Sánchez Sorzano, José María Carazo (2015) Alignment of direct detection device micrographs using a robust optical flow approach. Journal of Structural Biology. 189, 163-176. PMID: 25681631.

Minglei Zhao§, Shenping Wu§, Qiangjun Zhou, Sandro Vivona, Daniel Cipriano, Yifan Cheng* and Axel T. Brunger* (2014) Mechanistic insight into the recycling machine of the SNARE complex. Nature, 518, 61-67. PMID: 25581794. EMDB: 6204, 6205, 6206, 6206, 6207, 6208, 6209, 6210, PDB: 3J94, 3J95, 3J96, 3J97, 3J98, 3J99.

JungMin Kim§, Shenping Wu§, Thomas Tomasiak§, Claudia Mergel, Michael B. Winter, Sebastian B. Stiller, Yaneth Robles-Colmanares, Robert M. Stround*, Robert Tampé*, Chaeles S. Craik* and Yifan Cheng* (2015) Subnanometer resolution electron cryo-microscopy structure of a heterodimeric ABC exporter. Nature, 517, 396-400. PMID: 25363761. EMDB: 6085, 6086, 6087.

Peter S. Shen, Joseph Park, Yidan Qin, Xueming Li, Matthew Larson, Yifan Cheng, Alan Lambowitz, Jonathan S. Weissman, Onn Brandman and Adam Frost (2015) Tae2p and the 60S ribosomal subunit elongate stalled nascent chains with an alanine and threonine tail. Science, 347, 75-78. PMID: 25554787.

David Booth, Yifan Cheng* and Alan Frankel* (2014) HIV utilizes a Crm1 dimer to promote RNA nuclear export. eLife 2014;3:e04121. PMID: 25486595.

Gira Bhabha, Hui-Chun Cheng, Nan Zhang, Arne Moeller, Maofu Liao, Jeffrey A. Speir, Yifan Cheng, Ronald D. Vale (2014) Allosteric communication in the dynein motor domain. Cell, 159, 857-868. PMID: 25417161.

Yina Wang, Joerg Schnitzbauer, Zhe Hu, Xueming Li, Yifan Cheng, Zhen-Li Huang and Bo Huang (2014) Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm. Optics Express, 22, 15982-15991. PMID: 24977854.

Maofu Liao, Erhu Cao, David Julius* and Yifan Cheng* (2014) Single particle electron cryo-microscopy of a mammalian ion channel. Current Opinion in Structural Biology, 27: 1-7. PMID: 24681231.

Shunsuke Minagawa, Jianlong Lou, Robert I. Seed, Anthony Cormier, Shenping Wu, Yifan Cheng Lynne Murray, Ping Tsui, Jane Connor, Ronald Herbst, Cedric Govaerts, Tyren Barker, Stephanie Cambier, Haruhiko Yanagisawa, Amanda Goodsell, Mitsuo Hashimoto, Oliver J. Brand, Ran Cheng, Royce Ma, Kate J. McKnelly, Weihua Wen, Arthur Hill, David Jablons, Paul Wolters, Hideya Kitamura, Jun Araya, Andrea J. Barczak, David J. Erle, Louis Reichardt, James D. Marks, Jody L. Baron, Stephen L. Nishimura (2014) Selective targeting of TGF-β activation to treat fibroinflammatory airway disease.Science Translational Medicine, 6, 241ra79. PMID: 24944194.

Jinghua Lu, Yadong Yu, Yifan Cheng and Peter D. Sun (2014) Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis. Proc. Natl. Acad. Sci. U.S.A. 111, 5189-5194. PMID: 24706838.

Pawel Penczek, Jia Fang, Xueming Li, Yifan Cheng, Justus Loerke, Christian M Spahn, (2014) CTER - rapid estimation of CTF parameters with error assessment. Ultramicroscopy, 140, 9-19. PMID: 24562077.

Maofu Liao§, Erhu Cao§, David Julius* and Yifan Cheng* (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature, 504, 107-112¶. PMID: 24305160.

Erhu Cao§, Maofu Liao§, Yifan Cheng* and David Julius* (2013) TRPV1 structures in distinct conformations reveal activation mechanisms. Nature, 504, 113-118¶. PMID: 24305161. EMDB: 5776, 5777, 5778, PDB: 3J5P, 3J5Q, 3J5R.
¶ Both papers are featured in Nature News and Views: Richard Henderson (2013) Structural biology: Ion channel seen by electron microscopy. Nature, 504, 93-94. PMID: 24305155.

Cédric S. Asensio, Daniel W. Sirkis, James W. Maas Jr., Kiyoshi Egami, Tsz-Leung To, Frances M. Brodsky, Xiaokun Shu, Yifan Cheng and Robert H. Edwards (2013) Self-assembly of VPS41 promotes sorting regired for biogenesis of the regulated secretory pathway. Developmental Cell, 27, 425-437. PMID: 24210660.

Xueming Li, Shawn Q. Zheng, Kiyoshi Egami, David A. Agard and Yifan Cheng (2013) Influence of electron dose rate on electron counting images recorded with the K2 camera. Journal of Structural Biology, 184, 251-260. PMID: 23968652.

Min-Xian Qian, Ye Pang, Cui Hua Liu, Kousuke Haratake, Bo-Yu Du, Dan-Yang Ji, Guang-Fei Wang, Qian-Qian Zhu, Wei Song, Yadong Yu, Xiao-Xu Zhang, Hai-Tao Huang, Shiying Miao, Lian-Bin Chen, Zi-Hui Zhang, Ya-Nan Liang, Shan Liu, Hwangho Cha, Dong Yang, Yonggong Zhai, Takuo Komatsu, Fuminori Tsuruta, Haitao Li, Cheng Cao, Wei Li, Guo-Hong Li, Yifan Cheng, Tomoki Chiba, Linfang Wang, Alfred L. Goldberg, Yan Shen, and Xiao-Bo Qiu (2013) Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis. Cell, 153, 1012-1024. PMID: 23706739.

Xueming Li, Paul Mooney, Shawn Zheng, Chris Booth, Michael B. Braunfeld, Sander Gubbens, David A. Agard* and Yifan Cheng* (2013) Electron counting and beam-induced motion correction enables near atomic resolution single particle cryoEM. Nature Methods, 10, 584-590¶. PMID: 23644547, EMDB: 5623.
¶ Featured in Nature Methods News and Views: Robert M. Glaeser (2013) Stroboscopic imaging of macromolecular complexes. Nature Methods 10, 475-476. PMID: 23722205.
¶ Featured in Nature Methods: Method of the Year 2013.

Soyeon Park§, Xueming Li§, Ho Min 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* (2013) Reconfiguration of the proteasome during chaperone-mediated assembly. Nature, 497, 512-516. PMID: 23644457, EMDB: 5593, 5611, 5612, 5613, 5614, 5615, 5616, 5617.

Daniele Canzio, Maofu Liao, Nariman Naber, Ed Pate, Adam Larson, Shenping Wu, Roger Cooke, Peter Schuck, Yifan Cheng, Geeta J. Narlikar (2013) A conformational switch in HP1 allows conditional activation and drives assembly of the minimal heterochromatin unit. Nature, 496(7445): 377-381. PMID: 23485968.

Dina Schneidman-Duhovny, Andrea Rossi, Agustin Avila-Sakar, Seung Joong Kim, Javier Velázquez-Muriel, Pavel Strop, Hong Liang, Kristin A. Krükenberg, Maofu Liao, Homin Kim, Solmaz Sobhanifar, Volker Dötsch, Arvind Rajpal, Jaume Pons, David A. Agard, Yifan Cheng, Andrej Sali (2012) A method for integrative structure determination of protein-protein complexes: Application to a therapeutical antibody-antigen complex. Bioinformatics, 28(24), 3282-3289. PMID: 23093611.

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 (2012) Fabs enable single particle cryoEM studies of small proteins. Structure, 20, 582-592¶. PMID: 22483106, EMDB: 5294, 5295.
¶ Featured in PSI-SBKB gateway.

David S. Booth, Agustin Avila-Sakar and Yifan Cheng (2011) Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition. Journal of Visualized Experiments, 58, pii: 3227, doi: 10.3791/3227. PMID: 22215030.

Olga Maria Martinez-Avila, Shenping Wu, Yifan Cheng, Robert Lee, Feroz Khan, Stefan Habelitz (2011) Self assembly of amelogenin proteins at the water-oil interface. European Journal of Oral Sciences, 119, (Suppl. 1), 75-82. PMID: 22243231.

Shawn Q. Zheng, Eric Branlund, Bettina Keszthelyi, Michael B. Braunfeld, Yifan Cheng, John W. Sedat and David Agard (2011) A distributed multi-GPU system for high-speed electron microscopy tomographic reconstruction. ultramicroscopy, 111, 1137-1143. PMID: 21741915.

Ken Nakamura, Venu M. Nemani, Farnaz Azarbal, Gaia Skibinski, Jon M. Levy, Kiyoshi Egami, Larissa Munishkina, Jue Zhang, Brooke Gardner, Junko Wakabayashi, Hiromi Sesaki, Yifan Cheng, Steven Finkbeiner, Robert L. Nussbaum, Eliezer Masliah and Robert H. Edwards (2011) Direct membrane association drives mitochondrial fission by the Parkinson disease-associated protein a-synuclein. The Journal of Biological Chemistry, 286, 20710-20726. PMID: 21489994.

Xiaodong He, Shenping Wu, Olga Martinez-Avila, Yifan Cheng and Stefan Habelitz (2011) Self-aligning amelogenin nanoribbons in oil-water system. Journal of Structural Biology, 174, 203-212. PMID: 21134461.

Ho Min Kim, Yadong Yu, Yifan Cheng (2011) Structural Characterization of the 26S proteasome. Biochmica et Biophysica Acta – Gene Regulatory Mechanisms, 1809: 67-79. PMID: 20800708.

Richard K. Hite, Andreas D. Schenk, Zongli Li, Yifan Cheng and Thomas Walz (2010) Collecting electron crystallographic data of two-dimensional protein crystals. Chapter 11, pp. 251-282 in: Methods in Enzymology, 481: Cryo-Electron Microscopy, edited by Grant Jensen. Academic Press, Burlington, CA. PMID: 20887861.

Matthew D. Daugherty, David S. Booth, Bhargavi Jayaraman, Yifan Cheng and Alan D. Frankel (2010) HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc. Natl. Acad. Sci. U.S.A., 107: 12481-12486. PMID: 20616058.

Xueming Li, Nikolaus Grigorieff and Yifan Cheng (2010) GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of Structural Biology, advanced publication online June 14 2010. PMID: 20558298.

Yadong Yu, David M. Smith, Ho Min Kim, Victor Rodriguez, Alfred L. Goldberg and Yifan Cheng (2010) Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions. EMBO Journal, 29: 692-702. PMID: 20019667; PDB: 3IPM; EMDB: 5130.

Zongli Li, Richard K. Hite, Yifan Cheng and Thomas Walz (2010) Evaluation of imaging plates as the recording medium for images of negatively stained single particles and electron diffraction patterns of two-dimensional crystals. Journal of Electron Microscopy, 59: 53-63. PMID: 19643814.

Metka Lenassi, Gerard Cagney, Maofu Liao, Tomaz Vaupotic, Koen Bartholomeeusen, Yifan Cheng, Nevan J. Krogan, Ana Plemenitas, and B. Matija Peterlin (2010) HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells. Traffic, 11: 110-122. PMID: 19912576.

Lisa R. Racki, Nariman Naber, Peretz Partensky, Janet G. Yang, Ashley Acevedo, Tom J. Purcell, Roger Cooke, Yifan Cheng* and Geeta J. Narlikar* (2009) The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature, 462: 1016-1021. PMID: 20033039.

Yifan Cheng and Thomas Walz (2009) The advent of near-atomic resolution in single-particle electron microscopy. Annual Review of Biochemistry, 78: 723-742. PMID: 19489732.

Hak-Zoo Kim, Keehoon Jung, Ho Min Kim, Yifan Cheng, Gou Young Koh (2009) A designed angiopoietin-2 variant, pentameric COMP-Ang2, strongly activate Tie2 receptor and stimulates angiogenesis. Biochimica et Biophysica Acta - Molecular Cell Research, 1793: 772-780. PMID: 19339208.

Yifan Cheng (2009) Towards an atomic model of the 26S proteasome. Current Opinion in Structural Biology, 19: 203-208. PMID: 19286367.

Julius Rabl, David M. Smith, Yadong Yu, Shih-Chung Chang, Alfred L. Goldberg and Yifan Cheng (2008) Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Molecular Cell, 30: 360-368. PMID: 18471981; PDB: 3C91, 3C92; EMDB: 1733, 1740.

Edward R. Ballister, Angela H. Lai, Ronald N. Zuckermann, Yifan Cheng and Joseph D. Mougous (2008) In vitro self-assembly of tailored protein nanotubes from a simple protein building block. Proc. Natl. Acad. Sci. U.S.A., 105: 3733-3738. PMID: 18310321.

Gary Frey, Hanqin Peng, Sophia Rits-Volloch, Marco Morelli, Yifan Cheng and Bing Chen (2008) A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies. Proc. Natl. Acad. Sci. U.S.A., 105: 3739-3744. PMID: 18322015.

Tamir Gonen, Richard K. Hite, Yifan Cheng, Benjamin M. Petre, Joerg Kistler and Thomas Walz (2008) Structural characterization of oligomers formed by lens-specific tetraspanin MP20. Journal of Molecular Biology, 376: 380-392. PMID: 1816619.

Melanie D. Ohi, Anna Feoktistova, Liping Ren, Calvin Yip, Yifan Cheng, Jun-Song Chen, Hyun-Joo Yoon, Joseph S. Wall, Zhong Haung, Pawel A. Penczek, Kathleen L. Gould and Thomas Walz (2007) Structural organization of anaphase-promoting cmplex bound to the mitotic activator slp1. Molecular Cell, 28: 871-885. PMID: 18082611.

David M. Smith, Shih-Chung Chang, Soyeon Park, Danniel Finley, Yifan Cheng and Alfred L. Goldberg (2007) Docking of the proteasomal ATPases’ carboxy-termini in the 20S proteasome's alpha ring opens the gate for substrate entry. Molecular Cell, 27: 731-744. PMID: 17803938.

Yifan Cheng*, Werner Boll, Tomas Kirchhausen, Stephen C. Harrison and Thomas Walz (2007) Cryo-electron tomography of clathrin coated vesicles – structural implications for coat assembly. Journal of Molecular Biology, 365: 892-899. * corresponding author; PMID: 17095010.

Yifan Cheng and Thomas Walz (2007) Chapter 18: Reconstructing the endocytotic machinery, (464 - 485) in: Methods in Cell Biology, 79: Cellular Electron Microscopy, edited by J. Richard McIntosh. Elsevier Academic Press, San Diego, CA. PMID: 17327169.

Alexander Fotin, Tomas Kirchhausen, Nikolaus Grigorieff, Stephen C. Harrison, Thomas Walz and Yifan Cheng (2006) Structure determination of clathrin coats to subnanometer resolution by single particle cryo-electron microscopy. Journal of Structure Biology, 156: 453-460. PMID: 16908193.

Noritaka Nishida, Can Xie, Motomu Shimaoka, Yifan Cheng, Thomas Walz, Timothy A. Springer (2006) Activation of Leukocyte β2 integrins by conversion from bent to extended conformation. Immunity, 25: 583-594. PMID: 17045822.

Jun Liu, Shenping Wu, Mary C. Reedy, Hanspeter Winkler, Carmen Lucaveche, Yifan Cheng, Michael K. Reedy and Kenneth A. Taylor (2006) Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled S2 domain. Journal of Molecular Biology, 362: 844-60. PMID: 16949613.

Yifan Cheng, Elmar Wolf, Mykol Larvie, Olga Zak, Philip Aisen, Nikolaus Grigorieff, Stephen C. Harrison & Thomas Walz (2006) Single Particle Reconstructions of the Transferrin Receptor – Transferrin Complex Obtained with Different Specimen Preparation Techniques. Journal of Molecular Biology, 355: 1048-1065. PMID: 16343539.

Terunaga Nakagawa, Yifan Cheng, Morgan Sheng and Thomas Walz (2006) Three-dimensional structure of an AMPA receptor without associated stargazin/TARP proteins. Biological Chemistry, 387: 179-187. PMID: 16497150.

Yifan Cheng*, Olga Zak, Philip Aisen, Stephen C. Harrison and Thomas Walz* (2005) Single Particle Reconstruction of the Human Apo-Transferrin – Transferrin Receptor Complex. Journal of Structure Biology, 152: 204-210. * corresponding authors; PMID: 16343946.

Tamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C. Harrison and Thomas Walz (2005) Lipid-protein interactions in double-layered two-dimensional crystals of aquaporin-0. Nature, 438: 633-638¶. PMID: 16319884; PDB: 2B6O.

Tamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C. Harrison and Thomas Walz (2005) Lipid-protein interactions in double-layered two-dimensional crystals of aquaporin-0. Nature, 438: 633-638¶. PMID: 16319884; PDB: 2B6O.

Tamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C. Harrison and Thomas Walz (2005) Lipid-protein interactions in double-layered two-dimensional crystals of aquaporin-0. Nature, 438: 633-638¶. PMID: 16319884; PDB: 2B6O.

Tamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C. Harrison and Thomas Walz (2005) Lipid-protein interactions in double-layered two-dimensional crystals of aquaporin-0. Nature, 438: 633-638¶. PMID: 16319884; PDB: 2B6O.
¶ Featured in Nature News and Views: Anthony G. Lee (2005) Cell biology: A greasy grip. Nature 438, 569-570, Nature Editor’s Summary and front cover of the issue.

Tamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C. Harrison and Thomas Walz (2005) Lipid-protein interactions in double-layered two-dimensional crystals of aquaporin-0. Nature, 438: 633-638¶. PMID: 16319884; PDB: 2B6O.

David M. Smith, Galit Kafri, Yifan Cheng, David Ng, Thomas Walz and Alfred L. Goldberg (2005) ATP Binding to PAN or the 26S ATPases Causes Association with the 20S Proteasome, Gate Opening, and Translocation of Unfolded Proteins. Molecular Cell, 20: 687-698. PMID: 16337593.

Terunaga Nakagawa, Yifan Cheng, Elizabeth Ramm, Morgan Sheng and Thomas Walz (2005) Structure and different conformational states of native AMPA receptor complexes. Nature, 433: 545-549. PMID: 15690046.

Yifan Cheng, Olga Zak, Philip Aisen, Stephen C. Harrison and Thomas Walz (2004) Structure of the Human Transferrin Receptor-Transferrin Complex. Cell, 116: 565-576¶. PMID: 14980223; PDB: 1SUV.
¶ Featured in Cell preview: D. R. Richardson, (2004) Mysteries of the Transferrin-Transferrin Receptor 1 Interaction Uncovered. Cell 116, 483-489.

Alexander Fotin, Yifan Cheng, Piotr Sliz, Nikolaus Grigorieff, Stephen C. Harrison, Tomas Kirchhausen and Thomas Walz (2004) Molecular model for a complete clathrin lattice from electron cryomicroscopy. Nature, 432: 573-579¶. PMID: 15502812; PDB: 1XI4; EMDB: 5119

Alexander Fotin, Yifan Cheng, Nikolaus Grigorieff, Thomas Walz, Stephen C. Harrison, and Tomas Kirchhausen (2004) Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Nature, 432: 649-653¶. PMID: 15502813; PDB: 1XI5; EMDB: 5120.
¶ Both papers are featured in Nature News and Views: Frances M. Brodsky (2004) Clathrin’s Achilles’ ankle. Nature 432, 568-569.

Tamir Gonen, Piotr Sliz, Joerg Kistler, Yifan Cheng and Thomas Walz (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature, 429: 193-197. PMID: 15141214; PDB: 1SOR.

Tamir Gonen, Yifan Cheng, Joerg Kistler and Thomas Walz (2004) Aquaporin-0 Membrane Junctions Form upon Proteolytic Cleavage. Journal of Molecular Biology, 342: 1337-1345. PMID: 15351655.

Melanie Ohi, Ying Li, Yifan Cheng and Thomas Walz (2004) Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy. Biological Procedures Online, 6: 23-34. PMID: 15103397.

Bing Chen, Yifan Cheng, Lesley Calder, Stephen C. Harrison, Ellis L. Reinherz, John J. Skehel and Don C. Wiley (2004) A Chimeric Protein of Simian Immunodeficiency Virus Envelope Glycoprotein gp140 and Escherichia coli Aspartate Transcarbamoylase. Journal of Virology, 78: 4508-4516. PMID: 15078931.

Eric A. Toth, Ying Li, Michael R. Sawaya, Yifan Cheng, and Tom Ellenberger (2003) The crystal structure of Bifunctional Primase-Helicase of Bacteriophage T7. Molecular Cell, 12: 1-20. PMID: 14636571.

Gerardo Z. Lederkremer*, Yifan Cheng*, Benjamin M. Petre, Erik Vogan, Sebastian Springer, Randy Shekman, Thomas Walz and Tomas Kirchhausen (2001) Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Proc. Natl. Acad. Sci. U.S.A., 98: 10704-10709. * equal contributions; PMID: 11535824.

I. Schmidt-Krey, K. Mitsuoka, T. Hirai, K. Murata, Y. Cheng, Y. Fujiyoshi, R. Morgenstern and H. Hebert (2000) The three-dimensional map of microsomal glutathione transferase 1 at 6 Å resolution. EMBO Journal, 19: 6311-6316. PMID: 11101503.

Ingeborg Schmidt-Krey, Kazuyoshi Murata, Teruhisa Hirai, Kaoru Mitsuoka, Yifan Cheng, Ralf Morgenstern, Yoshinori Fujiyoshi and Hans Hebert (1999) The projection structure of the membrane protein microsomal glutathione transferase at 3A resolution hexagonal crystals. Journal of Molecular Biology, 288: 243-253. PMID: 10329140.

Yoko Hiroaki, Kaoru Mitsuoka, Yifan Cheng, Hidekazu Hiroaki and Yoshinori Fujiyoshi (1999) Influence of various nucleotides on the in situ crystallization of Ca+2-ATPase. Biochimica et Biophysica Acta, 1415: 361-368. PMID: 9889398.

Yifan Cheng and Kenneth A. Taylor (1998) Characterizing the low magnification performance of an intermediate voltage electron microscope with field emission electron gun, CM300FEG. Ultramicroscopy, 74: 209-220. PMID: 9809458.

Kenneth A. Taylor, Jinghua Tang, Yifan Cheng and Hanspeter Winkler (1997) The use of electron tomography for structural analysis of disordered protein arrays. Journal of Structural Biology, 120: 372-386. PMID: 9441940.

J. Gjønnes, V. Hansen, B.S. Berg, P. Runde, Y.F. Cheng, K. Gjønnes and C. Gilmore (1998) Structure model for the phase AlmFe derived from electron diffraction intensities collected by combination of a precession technique and convergent-beam diffraction. Acta Crystallographica A54, 306-319.

Kjersti Gjønnes, Yifan Cheng, Bjørn S. Berg and Vidar Hansen (1998) Correction for multiple scattering in integrated electron diffraction intensities - Application to determination of structure factors in the [001] projection of AlmFe. Acta Crystallographica A54, 102-119.

Y.F. Cheng*, W. Nüchter, J. Mayer, A. Weickenmeier and J. Gjønnes (1996) Low order structure factor amplitude and sign measurement of an unknown structure AlmFe by quantitative CBED. Acta Crystallographica A52, 923-936.
* Corresponding author

Y.F. Cheng, F. Dettenwanger, J. Mayer, E. Schumann and M. Rühler (1996) Identification of a new phase formed during the oxidation of γ-Titanium Aluminum. Scripta Materialia 34, 707-711.

Y.F. Cheng and J. Gjønnes (1994) Strip projection approach to the new model of AlMnSi icosahedral quasicrystal. Acta Crystallographica A50, 455-461.

Y.F. Cheng, V. Hansen, J. Gjønnes and L.R.Wallenberg (1992) TEM study of the early stages of precipitation process in strip-cast Al3003 alloys. Journal of Materials Research 7, 3225-3241.

Y.F. Cheng and F.H. Li (1992) An attempt to describe one-dimensional incommensurate composite structure as phason-defected one dimensional quasiperiodic structure. Acta Crystallographica A48, 796-804.

Y.F. Cheng, G.Z. Pan and F.H. Li (1992) Real space approach to the linear phason strain. physica status solidi (b) 170, 47-55.

Y.F. Cheng, M.J. Hui and F.H. Li (1991) A new commensurate and its related incommensurate phase in Al-Cu-Fe alloys. Philosophical Magazine Letter 63, 49-55.

Y.F. Cheng, M.J. Hui and F.H. Li (1991) An intermediate State between the decagonal and monoclinic phase in an Al-Cu-Fe alloy. Philosophical Magazine Letter 64, 129-132.

Y.F. Cheng, M.J. Hui, X.S. Chen and F.H. Li (1990) Relationship between icosahedral phase and monoclinic phase in Al-Cu-Fe alloy. Philosophical Magazine Letter 61, 173-179.

Z.F. Ren, Y.F. Cheng, Y.D. Jiang and W.Y Guan (1990) Single crystal growth and characterization in Ca-Doped Y-Ba-Cu-O system. Journal of Material Science Letter 9, 738-740.

G.Z. Pan, Y.F. Cheng and F.H. Li (1990) A six-dimensional crystal related T2-Al6CuLi3 icosahedral quasicrystal and R-Al5CuLi3 body centered cubic crystal. Physical Review B 41, 3401-3405.

F.H. Li and Y.F. Cheng (1990) A simple approach to quasicrystal structure and defect formulation. Acta Crystallographica A46, 142 - 149.

Cheng Yifan, Hui Mengjun, Wu Xiaojing, Yang Dayu, Chen Xishen and Li Fanghua (1989) R-phase and icosahedral phase in Al-Cu-Fe alloys. Chinese Physics Letter 5, 529-532.

Li Fanghua, Pan Guangzhao and Cheng Yifan (1989) Transformation from icosahedral phase to body center cubic phase in cut description. Chinese Physics Letter 5, 464-468.

Yifan Cheng and Renhui Wang (1988) Convergent beam electron diffraction determination of the extinction distance of the quasicrystalline icosahedral phase. Solid State Communications 68, 795-797.

Yifan Cheng and Renhui Wang (1988) Dynamical theory of electron diffraction of quasicrystal. phyiscal status solidi (b) 152, 33-37.

Danshan Zhao, Renhui Wang, Yifan Cheng and Zhouguang Wang (1988) Calculation of diffraction patterns of icosahedral phase. Journal of Physics F: Metal Physics 18, 1893-1904.

Reihui Wang and Yifan Cheng (1987) Dynamical theory of electron diffraction and its application to the rocking curve simulation for quasicrystal. Materials Science Forum 22-24, 409-420.

R. Wang, J. Gui, S. Yao, Y. Cheng, G. Lu and M. Huang (1986) High-temperature X-ray diffraction study of the crystallization process in rapidly quenched Al6(Mn,Fe) alloy. Philosophical Magazine B54, L33-37.