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Aiyer, S., Baldwin, P.R., Tan, S.M., Shan, Z., Oh, J., Mehrani, A., Bowman, M.E., Louie, G., Passos, D.O., Đorđević-Marquardt, S., Mietzsch, M., Hull, J.A., Hoshika, S., Barad, B.A., Grotjahn, D.A., McKenna, R., Agbandje-McKenna, M., Benner, S.A., Noel, J.A.P., Wang, D., Tan, Y.Z., Lyumkis, D. Overcoming resolution attenuation during tilted cryo-EM data collection. (2024) Nature Communications. 15(1):389. DOI: 10.1038/s41467-023-44555-7

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Sun, Q., Biswas, A., Lyumkis, D., Levy, R., Deng, N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. (2024) Viruses. 16(1). DOI: 10.3390/v16010076

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Jing, T., Shan, Z., Dinh, T., Biswas, A., Jang, S., Greenwood, J., Li, M., Zhang, Z., Gray, G., Shin, H.J., Zhou, B., Passos, D., Aiyer, S., Li, Z., Craigie, R., Engelman, A.N., Kvaratskhelia, M., Lyumkis, D. Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. (2024) bioRxiv. DOI: 10.1101/2024.01.26.577436

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Haack, D.B., Rudolfs, B., Zhang, C., Lyumkis, D., Toor, N. Structural basis of branching during RNA splicing. (2023) Nature Structural & Molecular Biology. DOI: 10.1038/s41594-023-01150-0

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Oh, J., Shan, Z., Hoshika, S., Xu, J., Chong, J., Benner, S.A., Lyumkis, D., Wang, D. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. (2023) Nature Communications. 14(1):8219. DOI: 10.1038/s41467-023-43735-9

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Sun, Q., Biswas, A., Lyumkis, D., Levy, R., Deng, N. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. (2023) bioRxiv. DOI: 10.1101/2023.11.29.569269

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Xie, L., Bowman, M.E., Louie, G.V., Zhang, C., Ardejani, M.S., Huang, X., Chu, Q., Donaldson, C.J., Vaughan, J.M., Shan, H., Powers, E.T., Kelly, J.W., Lyumkis, D., Noel, J.P., Saghatelian, A. Biochemistry and Protein Interactions of the CYREN Microprotein. (2023) Biochemistry. DOI: 10.1021/acs.biochem.3c00397

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Sheng, K., Li, N., Rabuck-Gibbons, J.N., Dong, X., Lyumkis, D., Williamson, J.R. Assembly landscape for the bacterial large ribosomal subunit. (2023) Nature Communications. 14(1):5220. DOI: 10.1038/s41467-023-40859-w

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Li, M., Oliveira Passos, D., Shan, Z., Smith, S.J., Sun, Q., Biswas, A., Choudhuri, I., Strutzenberg, T.S., Haldane, A., Deng, N., Li, Z., Zhao, X.Z., Briganti, L., Kvaratskhelia, M., Burke, T.R., Levy, R.M., Hughes, S.H., Craigie, R., Lyumkis, D. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. (2023) Science Advances. 9(29):eadg5953. DOI: 10.1126/sciadv.adg5953

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Dong, X., Doerfel, L.K., Sheng, K., Rabuck-Gibbons, J.N., Popova, A.M., Lyumkis, D., Williamson, J.R. Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways. (2023) Nucleic Acids Research. DOI: 10.1093/nar/gkad082

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Li, M., Oliveira Passos, D., Shan, Z., Smith, S.J., Sun, Q., Biswas, A., Choudhuri , I., Struzenberg, T.S., Haldane, A., Deng, N., Li, Z., Zhao, X.Z., Burke, T.R. ., Levy, R.M., Hughes, S.H., Craigie, R., Lyumkis, D. Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants (2022) bioRxiv. DOI: doi: https://doi.org/10.1101/2022.12.04.519057

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Lyumkis, D., Horton, N.C. The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. (2022) Biochemical Society Transactions. DOI: 10.1042/BST20220547

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Sheng, K., Li, N., Rabuck-Gibbons, J.N., Ding, X., Lyumkis, D., Williamson, J.R. Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly (2022) bioRiv. DOI: https://doi.org/10.1101/2022.11.09.515851

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Dong, X., Doerfel, L.K., Sheng, K., Rabuck-Gibbons, J.N., Popova, A.M., Lyumkis, D., Williamson, J.R. Near-Physiological in vitro Assembly of 50S Ribosomes Involves Parallel Pathways (2022) bioRiv. DOI: https://doi.org/10.1101/2022.11.09.515862

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Jóźwik, I.K., Li, W., Zhang, D.W., Wong, D., Grawenhoff, J., Ballandras-Colas, A., Aiyer, S., Cherepanov, P., Engelman, A.N., Lyumkis, D. B-to-A transition in target DNA during retroviral integration. (2022) Nucleic Acids Research. DOI: 10.1093/nar/gkac644

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Harrison, J.J.E.K., Oliveira Passos, D., Bruhn, J.F., Bauman, J.D., Tuberty, L., DeStefano, J.J., Xavier Ruiz, F., Lyumkis, D., Arnold, E. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation (2022) Science Advances. DOI: https://doi.org/10.1126/sciadv.abn9874

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Aiyer, S., Strutzenberg, T.S., Bowman, M.E., Noel, J.P., Lyumkis, D. Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon. (2022) JoVE.(185) DOI: 10.3791/64136

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Ballandras-Colas, A., Chivukula, V., Gruszka, D.T., Shan, Z., Singh, P.K., Pye, V.E., McLean, R.K., Bedwell, G.J., Li, W., Nans, A., Cook, N.J., Fadel, H.J., Poeschla, E.M., Griffiths, D.J., Vargas, J., Taylor, I.A., Lyumkis, D., Yardimci, H., Engelman, A.N., Cherepanov, P. Multivalent interactions essential for lentiviral integrase function. (2022) Nature Communications. 13(1):2416. DOI: 10.1038/s41467-022-29928-8

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Horton, N., Ghadirian, N., Shan, Z., Lyumkis, D. Mechanism of Activation of SgrAI via Enzyme Filamentation and Mechanism of DNA Sequence Specificity Expansion. (2022) FASEB Journal. 36 Suppl 1:THIS IS ONLY AN ABSTRACT. DOI: 10.1096/fasebj.2022.36.S1.0R839

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Rabuck-Gibbons, J.N., Lyumkis, D., Williamson, J.R. Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates. (2022) Structure. DOI: 10.1016/j.str.2021.12.005

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Shan, Z., Ghadirian, N., Lyumkis, D., Horton, N.C. Pre-Transition State and Apo Structures of the Filament-Forming Enzyme SgrAI Elucidate Mechanisms of Activation and Substrate Specificity. (2022) Journal of Biological Chemistry.:101760 DOI: 10.1016/j.jbc.2022.101760

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Passos, D.O., Li, M., Craigie, R., Lyumkis, D. Book chapter – Retroviral integrase: Structure, mechanism, and inhibition (2021) The Enzymes. 50:249-300. DOI: https://doi.org/10.1016/bs.enz.2021.06.007

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Lyumkis, D. Book Chapter: Preferred Orientation. How to recognize and deal with adverse effects. (2021) Single-particle Cryo-EM of Biological Macromolecules. DOI: 10.1088/978-0-7503-3039-8


Smith, S.J., Zhao, X.Z., Passos, D.O., Pye, V.E., Cherepanov, P., Lyumkis, D., Burke, T.R., Hughes, S.H. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. (2021) ACS Infect Dis. DOI: 10.1021/acsinfecdis.0c00819

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Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., Hughes, S.H. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. (2021) Viruses. 13(2). DOI: 10.3390/v13020205

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Aiyer, S., Zhang, C., Baldwin, P.R., Lyumkis, D. Evaluating Local and Directional Resolution of Cryo-EM Density Maps. (2020) Methods in Molecular Biology. 2215:161-187. DOI: 10.1007/978-1-0716-0966-8_8

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Jóźwik, I.K., Passos, D.O., Lyumkis, D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. (2020) Trends in Pharmacological Sciences. DOI: 10.1016/j.tips.2020.06.003

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Baldwin, P.R., Lyumkis, D. Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. (2020) Progress in Biophysics and Molecular Biology. DOI: 10.1016/j.pbiomolbio.2020.06.003

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Brugger, C., Zhang, C., Suhanovsky, M.M., Kim, D.D., Sinclair, A.N., Lyumkis, D., Deaconescu, A.M. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. (2020) Nature Communications. 11(1):3740. DOI: 10.1038/s41467-020-17457-1

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Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., Hughes, S.H. HIV-1 Integrase Inhibitors that are active against Drug-Resistant Integrase Mutants. (2020) Antimicrobial Agents and Chemotherapy. DOI: 10.1128/AAC.00611-20

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Passos, D.O., Li, M., Jóźwik, I.K., Zhao, X.Z., Santos-Martins, D., Yang, R., Smith, S.J., Jeon, Y., Forli, S., Hughes, S.H., Burke, T.R., Craigie, R., Lyumkis, D. Structural basis for strand transfer inhibitor binding to HIV intasomes. (2020) Science. DOI: 10.1126/science.aay8015

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Rabuck-Gibbons, J.N., Popova, A.M., Greene, E.M., Cervantes, C.F., Lyumkis, D., Williamson, J.R. SrmB Rescues Trapped Ribosome Assembly Intermediates. (2019) Journal of Molecular Biology. DOI: 10.1016/j.jmb.2019.12.013

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Baldwin, P.R., Lyumkis, D. Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM. (2019) Prog. Biophys. Mol. Biol. DOI: 10.1016/j.pbiomolbio.2019.09.002

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Polley, S., Lyumkis, D., Horton, N.C. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. (2019) Structure. 27(10):1497-1507. DOI: 10.1016/j.str.2019.08.001

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Haack, D.B., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., Toor, N. Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. (2019) Cell. 178(3):612-623.e12. DOI: 10.1016/j.cell.2019.06.035

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Koneru, P.C., Francis, A.C., Deng, N., Rebensburg, S.V., Hoyte, A.C., Lindenberger, J., Adu-Ampratwum, D., Larue, R.C., Wempe, M.F., Engelman, A.N., Lyumkis, D., Fuchs, J.R., Levy, R.M., Melikyan, G.B., Kvaratskhelia, M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. (2019) Elife. 8. DOI: 10.7554/eLife.46344

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Lyumkis, D. Challenges and Opportunities in Cryo-EM Single-Particle Analysis. (2019) Journal of Biological Chemistry. DOI: 10.1074/jbc.REV118.005602

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Zhang, C., Cantara, W., Jeon, Y., Musier-Forsyth, K., Grigorieff, N., Lyumkis, D. Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification. (2018) Ultramicroscopy. DOI: 10.1016/j.ultramic.2018.11.016

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Tan, Y.Z., Aiyer, S., Mietzsch, M., Hull, J.A., McKenna, R., Grieger, J., Samulski, R.J., Baker, T.S., Agbandje-McKenna, M., Lyumkis, D. Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. (2018) Nature Communications. 9(1):3628. DOI: 10.1038/s41467-018-06076-6

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Zhang, C., Konermann, S., Brideau, N.J., Lotfy, P., Wu, X., Novick, S.J., Strutzenberg, T., Griffin, P.R., Hsu, P.D., Lyumkis, D. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. (2018) Cell. 175(1):212-223.e17. DOI: 10.1016/j.cell.2018.09.001

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Tan, Y.Z., Baldwin, P.R., Davis, J.H., Williamson, J.R., Potter, C.S., Carragher, B., Lyumkis, D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. (2017) Nature Methods. 14(8):793-796. DOI: 10.1038/nmeth.4347

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Ozorowski, G., Pallesen, J., de Val, N., Lyumkis, D., Cottrell, C.A., Torres, J.L., Copps, J., Stanfield, R.L., Cupo, A., Pugach, P., Moore, J.P., Wilson, I.A., Ward, A.B. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. (2017) Nature. 547(7663):360-363. DOI: 10.1038/nature23010

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Passos, D.O., Li, M., Yang, R., Rebensburg, S.V., Ghirlando, R., Jeon, Y., Shkriabai, N., Kvaratskhelia, M., Craigie, R., Lyumkis, D. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. (2017) Science. 355(6320):89-92. DOI: 10.1126/science.aah5163

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Davis, J.H., Tan, Y.Z., Carragher, B., Potter, C.S., Lyumkis, D., Williamson, J.R. Modular Assembly of the Bacterial Large Ribosomal Subunit. (2016) Cell. 167(6):1610-1622.e15. DOI: 10.1016/j.cell.2016.11.020

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Polley, S., Passos, D.O., Huang, D.B., Mulero, M.C., Mazumder, A., Biswas, T., Verma, I.M., Lyumkis, D., Ghosh, G. Structural Basis for the Activation of IKK1/α. (2016) Cell Reports. 17(8):1907-1914. DOI: 10.1016/j.celrep.2016.10.067

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Ballandras-Colas, A., Brown, M., Cook, N.J., Dewdney, T.G., Demeler, B., Cherepanov, P., Lyumkis, D., Engelman, A.N. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. (2016) Nature. 530(7590):358-61. DOI: 10.1038/nature16955

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Passos, D.O., Lyumkis, D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. (2015) Journal of Structural Biology. 192(2):235-44. DOI: 10.1016/j.jsb.2015.10.002

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Lee, J.H., de Val, N., Lyumkis, D., Ward, A.B. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. (2015) Structure. 23(10):1943-51. DOI: 10.1016/j.str.2015.07.020

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Lyumkis, D., Oliveira dos Passos, D., Tahara, E.B., Webb, K., Bennett, E.J., Vinterbo, S., Potter, C.S., Carragher, B., Joazeiro, C.A. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(45):15981-6. DOI: 10.1073/pnas.1413882111

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Sashital, D.G., Greeman, C.A., Lyumkis, D., Potter, C.S., Carragher, B., Williamson, J.R. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. (2014) Elife. 3. DOI: 10.7554/eLife.04491

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Lyumkis, D., Julien, J.P., de Val, N., Cupo, A., Potter, C.S., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Carragher, B., Wilson, I.A., Ward, A.B. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1484-90. DOI: 10.1126/science.1245627

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Julien, J.P., Cupo, A., Sok, D., Stanfield, R.L., Lyumkis, D., Deller, M.C., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Ward, A.B., Wilson, I.A. Crystal structure of a soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1477-83. DOI: 10.1126/science.1245625

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Lyumkis, D., Vinterbo, S., Potter, C.S., Carragher, B. Optimod–an automated approach for constructing and optimizing initial models for single-particle electron microscopy. (2013) Journal of Structural Biology. 184(3):417-26. DOI: 10.1016/j.jsb.2013.10.009

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Lyumkis, D., Talley, H., Stewart, A., Shah, S., Park, C.K., Tama, F., Potter, C.S., Carragher, B., Horton, N.C. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. (2013) Structure. 21(10):1848-58. DOI: 10.1016/j.str.2013.08.012

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Lyumkis, D., Brilot, A.F., Theobald, D.L., Grigorieff, N. Likelihood-based classification of cryo-EM images using FREALIGN. (2013) Journal of Structural Biology. 183(3):377-388. DOI: 10.1016/j.jsb.2013.07.005

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Yoshioka, C., Lyumkis, D., Carragher, B., Potter, C.S. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. (2013) Journal of Structural Biology. 182(2):155-63. DOI: 10.1016/j.jsb.2013.02.007

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Lyumkis, D., Doamekpor, S.K., Bengtson, M.H., Lee, J.W., Toro, T.B., Petroski, M.D., Lima, C.D., Potter, C.S., Carragher, B., Joazeiro, C.A. Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(5):1702-7. DOI: 10.1073/pnas.1210041110

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Campbell, M.G., Cheng, A., Brilot, A.F., Moeller, A., Lyumkis, D., Veesler, D., Pan, J., Harrison, S.C., Potter, C.S., Carragher, B., Grigorieff, N. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. (2012) Structure. 20(11):1823-8. DOI: 10.1016/j.str.2012.08.026

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Milazzo, A.C., Cheng, A., Moeller, A., Lyumkis, D., Jacovetty, E., Polukas, J., Ellisman, M.H., Xuong, N.H., Carragher, B., Potter, C.S. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. (2011) Journal of Structural Biology. 176(3):404-8. DOI: 10.1016/j.jsb.2011.09.002

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Voss, N.R., Lyumkis, D., Cheng, A., Lau, P.W., Mulder, A., Lander, G.C., Brignole, E.J., Fellmann, D., Irving, C., Jacovetty, E.L., Leung, A., Pulokas, J., Quispe, J.D., Winkler, H., Yoshioka, C., Carragher, B., Potter, C.S. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. (2010) Journal of Structural Biology. 169(3):389-98. DOI: 10.1016/j.jsb.2009.12.005

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Lyumkis, D., Moeller, A., Cheng, A., Herold, A., Hou, E., Irving, C., Jacovetty, E.L., Lau, P.W., Mulder, A.M., Pulokas, J., Quispe, J.D., Voss, N.R., Potter, C.S., Carragher, B. Automation in single-particle electron microscopy connecting the pieces. (2010) Meth. Enzymol. 483:291-338. DOI: 10.1016/S0076-6879(10)83015-0

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Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S., Carragher, B. Appion: an integrated, database-driven pipeline to facilitate EM image processing. (2009) Journal of Structural Biology. 166(1):95-102. DOI: 10.1016/j.jsb.2009.01.002

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