Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • D.Phil., University of Minnesota, Twin Cities 2005
• 

  Previous Appointments & Affiliations

  • Associate Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2018 - 2022
  • Associate Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2018 - 2021
  • Scholar In Residence of Computer Science, Computer Science, Trinity College of Arts & Sciences 2018
• Recognition
• 

  In the News

  • JUN 17, 2021

    Chan Zuckerberg Initiative Invests in Duke Team’s Work to Improve Cryo-EM Images

  • APR 6, 2021

    Duke Team Makes Cryo-EM Microscope Even Better Than Before

  • MAR 5, 2021

    Duke & UNC: Rivals on the Court, Teammates in Science
• Expertise
• 

  Subject Headings

  • Muser Mentor
• Research
• 

  Selected Grants

  • Mechanisms of LRRK2 Mediated Neurotoxicity awarded by National Institutes of Health 2018 - 2026
  • Mechanistic Insights into the Plant Disease Resistance Mediated by NPR1 awarded by National Institutes of Health 2022 - 2026
  • Molecular elucidation of the Francisella tularensis virulence mechanism awarded by National Institutes of Health 2021 - 2026
  • A Hybrid Computational Platform for High-resolution Structure Determination Using Cryo-EM awarded by National Institutes of Health 2021 - 2025
  • CC* Data Storage - Flexible Affordable Scalable Technology for Research Storage - FAST-Research Storage awarded by  National Science Foundation 2022 - 2024
  • Multi-task learning to map proteins inside cells at near-atomic resolution awarded by Chan Zuckerberg Initiative 2021 - 2024
  • Structural characterization of HIV-1 fusion using time resolved cryo-electron tomography (TR-cryo-ET) awarded by National Institute of Environmental Health Sciences 2021 - 2022
  • Structural studies of virulence activation in Francisella tularensis awarded by National Institutes of Health 2020 - 2022
  • Cryo-EM Investigation of Protein Structures awarded by Syngenta Corp Protection, LLC 2021 - 2022
  • Structural Elucidation of the Novel RNA Polymerase Underlying Francisella Tularensis Virulence awarded by National Institutes of Health 2020 - 2022
  • Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
  • Structural Analysis of Env During HIV-1 Maturation Using In-situ Cryo-electron Tomography awarded by National Institute of Environmental Health Sciences 2019 - 2020
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Bouvette, Jonathan, Qinwen Huang, Amanda A. Riccio, William C. Copeland, Alberto Bartesaghi, and Mario J. Borgnia. “Automated systematic evaluation of cryo-EM specimens with SmartScope.” Elife 11 (August 23, 2022). https://doi.org/10.7554/eLife.80047.
       Full Text  Link to Item
    • Liu, Hsuan Fu, Ye Zhou, and Alberto Bartesaghi. “High-resolution structure determination using high-throughput electron cryo-tomography.” Acta Crystallographica. Section D, Structural Biology 78, no. Pt 7 (July 2022): 817–24. https://doi.org/10.1107/s2059798322005010.
       Full Text
    • Zhou, Ye, Amit Moscovich, and Alberto Bartesaghi. “Data-driven determination of number of discrete conformations in single-particle cryo-EM.” Computer Methods and Programs in Biomedicine 221 (June 2022): 106892. https://doi.org/10.1016/j.cmpb.2022.106892.
       Full Text
    • Simões, Vanessa, Blanche K. Cizubu, Lana Harley, Ye Zhou, Joshua Pajak, Nathan A. Snyder, Jonathan Bouvette, et al. “Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.” Cell Rep 39, no. 8 (May 24, 2022): 110860. https://doi.org/10.1016/j.celrep.2022.110860.
       Full Text  Link to Item
    • Kumar, Shivesh, Raul Zavaliev, Qinglin Wu, Ye Zhou, Jie Cheng, Lucas Dillard, Jordan Powers, et al. “Structural basis of NPR1 in activating plant immunity.” Nature 605, no. 7910 (May 2022): 561–66. https://doi.org/10.1038/s41586-022-04699-w.
       Full Text  Link to Item
    • Williams, Wilton B., R Ryan Meyerhoff, R. J. Edwards, Hui Li, Kartik Manne, Nathan I. Nicely, Rory Henderson, et al. “Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.” Cell 184, no. 11 (May 27, 2021): 2955-2972.e25. https://doi.org/10.1016/j.cell.2021.04.042.
       Full Text  Open Access Copy  Link to Item
    • Bouvette, Jonathan, Hsuan-Fu Liu, Xiaochen Du, Ye Zhou, Andrew P. Sikkema, Juliana da Fonseca Rezende E Mello, Bradley P. Klemm, et al. “Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.” Nat Commun 12, no. 1 (March 30, 2021): 1957. https://doi.org/10.1038/s41467-021-22251-8.
       Full Text  Link to Item
    • Travis, Brady A., Kathryn M. Ramsey, Samantha M. Prezioso, Thomas Tallo, Jamie M. Wandzilak, Allen Hsu, Mario Borgnia, et al. “Structural Basis for Virulence Activation of Francisella tularensis.” Mol Cell 81, no. 1 (January 7, 2021): 139-152.e10. https://doi.org/10.1016/j.molcel.2020.10.035.
       Full Text  Link to Item
    • Huang, Qinwen, Ye Zhou, Xiaochen Du, Reed Chen, Jianyou Wang, Cynthia Rudin, and Alberto Bartesaghi. “Cryo-ZSSR: multiple-image super-resolution based on deep internal learning,” November 22, 2020.
       Link to Item
    • Zhou, Ye, Panagiotis L. Kastritis, Shannon E. Dougherty, Jonathan Bouvette, Allen L. Hsu, Laura Burbaum, Shyamal Mosalaganti, et al. “Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.” Proc Natl Acad Sci U S A 117, no. 36 (September 8, 2020): 22157–66. https://doi.org/10.1073/pnas.2005301117.
       Full Text  Link to Item
    • Bendory, Tamir, Alberto Bartesaghi, and Amit Singer. “Single-particle cryo-electron microscopy: Mathematical theory, computational challenges, and opportunities.” Ieee Signal Processing Magazine 37, no. 2 (March 2020): 58–76. https://doi.org/10.1109/msp.2019.2957822.
       Full Text
    • Henderson, Rory, Maolin Lu, Ye Zhou, Zekun Mu, Robert Parks, Qifeng Han, Allen L. Hsu, et al. “Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.” Nat Commun 11, no. 1 (January 24, 2020): 520. https://doi.org/10.1038/s41467-019-14196-w.
       Full Text  Link to Item
    • Bendory, Tamir, Alberto Bartesaghi, and Amit Singer. “Single-Particle Cryo-Electron Microscopy: Mathematical Theory, Computational Challenges, and Opportunities.” Ieee Signal Process. Mag. 37 (2020): 58–76. https://doi.org/10.1109/MSP.2019.2957822.
       Full Text
    • Zhou, Y., A. Moscovich, T. Bendory, and A. Bartesaghi. “Unsupervised particle sorting for high-resolution single-particle cryo-EM.” Inverse Problems 36, no. 4 (January 1, 2020). https://doi.org/10.1088/1361-6420/ab5ec8.
       Full Text
    • Aguerrebere, C., M. Delbracio, A. Bartesaghi, and G. Sapiro. “A Practical Guide to Multi-Image Alignment.” Icassp, Ieee International Conference on Acoustics, Speech and Signal Processing  Proceedings 2018-April (September 10, 2018): 1927–31. https://doi.org/10.1109/ICASSP.2018.8461588.
       Full Text
    • Kang, Yanyong, Oleg Kuybeda, Parker W. de Waal, Somnath Mukherjee, Ned Van Eps, Przemyslaw Dutka, X Edward Zhou, et al. “Publisher Correction: Cryo-EM structure of human rhodopsin bound to an inhibitory G protein.” Nature 561, no. 7724 (September 2018): E44. https://doi.org/10.1038/s41586-018-0302-0.
       Full Text
    • Matthies, Doreen, Chanhyung Bae, Gilman Es Toombes, Tara Fox, Alberto Bartesaghi, Sriram Subramaniam, and Kenton Jon Swartz. “Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs.” Elife 7 (August 2018): e37558. https://doi.org/10.7554/elife.37558.
       Full Text
    • Bartesaghi, Alberto, Cecilia Aguerrebere, Veronica Falconieri, Soojay Banerjee, Lesley A. Earl, Xing Zhu, Nikolaus Grigorieff, et al. “Atomic Resolution Cryo-EM Structure of β-Galactosidase.” Structure (London, England : 1993) 26, no. 6 (June 2018): 848-856.e3. https://doi.org/10.1016/j.str.2018.04.004.
       Full Text
    • Kang, Yanyong, Oleg Kuybeda, Parker W. de Waal, Somnath Mukherjee, Ned Van Eps, Przemyslaw Dutka, X Edward Zhou, et al. “Cryo-EM structure of human rhodopsin bound to an inhibitory G protein.” Nature 558, no. 7711 (June 2018): 553–58. https://doi.org/10.1038/s41586-018-0215-y.
       Full Text
    • Guo, Tai Wei, Alberto Bartesaghi, Hui Yang, Veronica Falconieri, Prashant Rao, Alan Merk, Edward T. Eng, et al. “Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex.” Cell 171, no. 2 (October 2017): 414-426.e12. https://doi.org/10.1016/j.cell.2017.09.006.
       Full Text
    • Aguerrebere, C., M. Delbracio, A. Bartesaghi, and G. Sapiro. “Fundamental limits in multi-image alignment.” Ieee Transactions on Signal Processing 64, no. 21 (November 1, 2016): 5707–22. https://doi.org/10.1109/TSP.2016.2600517.
       Full Text
    • Frank, Gabriel A., Suneet Shukla, Prashant Rao, Mario J. Borgnia, Alberto Bartesaghi, Alan Merk, Aerfa Mobin, et al. “Cryo-EM Analysis of the Conformational Landscape of Human P-glycoprotein (ABCB1) During its Catalytic Cycle.” Mol Pharmacol 90, no. 1 (July 2016): 35–41. https://doi.org/10.1124/mol.116.104190.
       Full Text  Link to Item
    • Borgnia, Mario J., Soojay Banerjee, Alan Merk, Doreen Matthies, Alberto Bartesaghi, Prashant Rao, Jason Pierson, et al. “Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.” Mol Pharmacol 89, no. 6 (June 2016): 645–51. https://doi.org/10.1124/mol.116.103382.
       Full Text  Link to Item
    • Merk, Alan, Alberto Bartesaghi, Soojay Banerjee, Veronica Falconieri, Prashant Rao, Mindy I. Davis, Rajan Pragani, et al. “Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.” Cell 165, no. 7 (June 2016): 1698–1707. https://doi.org/10.1016/j.cell.2016.05.040.
       Full Text
    • Tran, Erin E. H., Kira A. Podolsky, Alberto Bartesaghi, Oleg Kuybeda, Giovanna Grandinetti, Teddy John Wohlbold, Gene S. Tan, et al. “Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Influenza Vaccine Candidate.” Mbio 7, no. 2 (March 2016): e00257. https://doi.org/10.1128/mbio.00257-16.
       Full Text
    • Matthies, Doreen, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, et al. “Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.” Cell 164, no. 4 (February 11, 2016): 747–56. https://doi.org/10.1016/j.cell.2015.12.055.
       Full Text  Link to Item
    • Banerjee, Soojay, Alberto Bartesaghi, Alan Merk, Prashant Rao, Stacie L. Bulfer, Yongzhao Yan, Neal Green, et al. “2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.” Science (New York, N.Y.) 351, no. 6275 (February 2016): 871–75. https://doi.org/10.1126/science.aad7974.
       Full Text
    • Bartesaghi, Alberto, Alan Merk, Soojay Banerjee, Doreen Matthies, Xiongwu Wu, Jacqueline L. S. Milne, and Sriram Subramaniam. “2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.” Science (New York, N.Y.) 348, no. 6239 (June 2015): 1147–51. https://doi.org/10.1126/science.aab1576.
       Full Text
    • Meyerson, Joel R., Janesh Kumar, Sagar Chittori, Prashant Rao, Jason Pierson, Alberto Bartesaghi, Mark L. Mayer, and Sriram Subramaniam. “Structural mechanism of glutamate receptor activation and desensitization.” Nature 514, no. 7522 (October 2014): 328–34. https://doi.org/10.1038/nature13603.
       Full Text
    • Tran, Erin E. H., James A. Simmons, Alberto Bartesaghi, Charles J. Shoemaker, Elizabeth Nelson, Judith M. White, and Sriram Subramaniam. “Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.” Journal of Virology 88, no. 18 (September 2014): 10958–62. https://doi.org/10.1128/jvi.00870-14.
       Full Text
    • Bartesaghi, Alberto, Doreen Matthies, Soojay Banerjee, Alan Merk, and Sriram Subramaniam. “Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 32 (August 2014): 11709–14. https://doi.org/10.1073/pnas.1402809111.
       Full Text
    • Bartesaghi, Alberto, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam. “Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.” Nat Struct Mol Biol 20, no. 12 (December 2013): 1352–57. https://doi.org/10.1038/nsmb.2711.
       Full Text  Link to Item
    • Harris, Audray K., Alberto Bartesaghi, Jacqueline L. S. Milne, and Sriram Subramaniam. “HIV-1 envelope glycoprotein trimers display open quaternary conformation when bound to the gp41 membrane-proximal external-region-directed broadly neutralizing antibody Z13e1.” Journal of Virology 87, no. 12 (June 2013): 7191–96. https://doi.org/10.1128/jvi.03284-12.
       Full Text
    • Schauder, David M., Oleg Kuybeda, Jinjin Zhang, Katherine Klymko, Alberto Bartesaghi, Mario J. Borgnia, Mark L. Mayer, and Sriram Subramaniam. “Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain.” Proc Natl Acad Sci U S A 110, no. 15 (April 9, 2013): 5921–26. https://doi.org/10.1073/pnas.1217549110.
       Full Text  Link to Item
    • Kuybeda, Oleg, Gabriel A. Frank, Alberto Bartesaghi, Mario Borgnia, Sriram Subramaniam, and Guillermo Sapiro. “A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography.” J Struct Biol 181, no. 2 (February 2013): 116–27. https://doi.org/10.1016/j.jsb.2012.10.010.
       Full Text  Link to Item
    • Milne, Jacqueline L. S., Mario J. Borgnia, Alberto Bartesaghi, Erin E. H. Tran, Lesley A. Earl, David M. Schauder, Jeffrey Lengyel, Jason Pierson, Ardan Patwardhan, and Sriram Subramaniam. “Cryo-electron microscopy--a primer for the non-microscopist.” Febs J 280, no. 1 (January 2013): 28–45. https://doi.org/10.1111/febs.12078.
       Full Text  Link to Item
    • Bartesaghi, Alberto, Federico Lecumberry, Guillermo Sapiro, and Sriram Subramaniam. “Protein secondary structure determination by constrained single-particle cryo-electron tomography.” Structure (London, England : 1993) 20, no. 12 (December 2012): 2003–13. https://doi.org/10.1016/j.str.2012.10.016.
       Full Text
    • Frank, Gabriel A., Alberto Bartesaghi, Oleg Kuybeda, Mario J. Borgnia, Tommi A. White, Guillermo Sapiro, and Sriram Subramaniam. “Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging.” J Struct Biol 178, no. 2 (May 2012): 165–76. https://doi.org/10.1016/j.jsb.2012.01.004.
       Full Text  Link to Item
    • Tran, Erin E. H., Mario J. Borgnia, Oleg Kuybeda, David M. Schauder, Alberto Bartesaghi, Gabriel A. Frank, Guillermo Sapiro, Jacqueline L. S. Milne, and Sriram Subramaniam. “Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.” Plos Pathog 8, no. 7 (2012): e1002797. https://doi.org/10.1371/journal.ppat.1002797.
       Full Text  Link to Item
    • Meyerson, Joel R., Tommi A. White, Donald Bliss, Amy Moran, Alberto Bartesaghi, Mario J. Borgnia, M Jason V. de la Cruz, et al. “Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.” J Vis Exp, no. 58 (December 1, 2011). https://doi.org/10.3791/2770.
       Full Text  Link to Item
    • White, Tommi A., Alberto Bartesaghi, Mario J. Borgnia, M Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne, and Sriram Subramaniam. “Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-electron tomography.” J Virol 85, no. 23 (December 2011): 12114–23. https://doi.org/10.1128/JVI.05297-11.
       Full Text  Link to Item
    • Harris, Audray, Mario J. Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun Kenneth Kang, et al. “Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.” Proc Natl Acad Sci U S A 108, no. 28 (July 12, 2011): 11440–45. https://doi.org/10.1073/pnas.1101414108.
       Full Text  Link to Item
    • White, Tommi A., Alberto Bartesaghi, Mario J. Borgnia, Joel R. Meyerson, M Jason V. de la Cruz, Julian W. Bess, Rachna Nandwani, et al. “Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.” Plos Pathog 6, no. 12 (December 23, 2010): e1001249. https://doi.org/10.1371/journal.ppat.1001249.
       Full Text  Link to Item
    • Bartesaghi, Alberto, and Sriram Subramaniam. “Membrane protein structure determination using cryo-electron tomography and 3D image averaging.” Current Opinion in Structural Biology 19, no. 4 (August 2009): 402–7. https://doi.org/10.1016/j.sbi.2009.06.005.
       Full Text
    • Liu, Jun, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro, and Sriram Subramaniam. “Molecular architecture of native HIV-1 gp120 trimers.” Nature 455, no. 7209 (September 4, 2008): 109–13. https://doi.org/10.1038/nature07159.
       Full Text  Link to Item
    • Bartesaghi, A., P. Sprechmann, J. Liu, G. Randall, G. Sapiro, and S. Subramaniam. “Classification and 3D averaging with missing wedge correction in biological electron tomography.” Journal of Structural Biology 162, no. 3 (June 2008): 436–50. https://doi.org/10.1016/j.jsb.2008.02.008.
       Full Text
    • Aganj, I., A. Bartesaghi, M. Borgnia, H. Y. Liao, G. Sapiro, and S. Subramaniam. “Regularization for inverting the radon transform with wedge consideration.” 2007 4th Ieee International Symposium on Biomedical Imaging: From Nano to Macro  Proceedings, November 27, 2007, 217–20. https://doi.org/10.1109/ISBI.2007.356827.
       Full Text
    • Bartesaghi, A., P. Sprechmann, G. Randall, G. Sapiro, and S. Subramaniam. “Classification, averaging and reconstruction of macromolecules in electron tomography.” 2007 4th Ieee International Symposium on Biomedical Imaging: From Nano to Macro  Proceedings, November 27, 2007, 244–47. https://doi.org/10.1109/ISBI.2007.356834.
       Full Text
    • Subramaniam, Sriram, Alberto Bartesaghi, Jun Liu, Adam E. Bennett, and Rachid Sougrat. “Electron tomography of viruses.” Current Opinion in Structural Biology 17, no. 5 (October 2007): 596–602. https://doi.org/10.1016/j.sbi.2007.09.009.
       Full Text
    • Sougrat, Rachid, Alberto Bartesaghi, Jeffrey D. Lifson, Adam E. Bennett, Julian W. Bess, Daniel J. Zabransky, and Sriram Subramaniam. “Electron tomography of the contact between T cells and SIV/HIV-1: implications for viral entry.” Plos Pathogens 3, no. 5 (May 2007): e63. https://doi.org/10.1371/journal.ppat.0030063.
       Full Text
    • Yatziv, L., A. Bartesaghi, and G. Sapiro. “O(N) implementation of the fast marching algorithm.” Journal of Computational Physics 212, no. 2 (March 1, 2006): 393–99. https://doi.org/10.1016/j.jcp.2005.08.005.
       Full Text
    • Mohan, A., A. Bartesaghi, and G. Sapiro. “Constrained regularization of digital terrain elevation data.” Ieee Geoscience and Remote Sensing Letters 3, no. 1 (January 1, 2006): 59–62. https://doi.org/10.1109/LGRS.2005.856702.
       Full Text
    • Bartesaghi, A., and G. Sapiro. “Tracking of moving objects under severe and total occlusions.” Proceedings  International Conference on Image Processing, Icip 1 (December 1, 2005): 301–4. https://doi.org/10.1109/ICIP.2005.1529747.
       Full Text
    • Bartesaghi, Alberto, Guillermo Sapiro, and Sriram Subramaniam. “An energy-based three-dimensional segmentation approach for the quantitative interpretation of electron tomograms.” Ieee Transactions on Image Processing : A Publication of the Ieee Signal Processing Society 14, no. 9 (September 2005): 1314–23. https://doi.org/10.1109/tip.2005.852467.
       Full Text
    • Bartesaghi, A., G. Sapiro, T. Malzbender, and D. Gelb. “Three-dimensional shape rendering from multiple images.” Graphical Models 67, no. 4 (July 1, 2005): 332–46. https://doi.org/10.1016/j.gmod.2005.02.002.
       Full Text
    • Bartesaghi, A., G. Sapiro, S. Lee, J. Lefman, S. Wahl, J. Orenstein, and S. Subramaniam. “A new approach for 3D segmentation of cellular tomograms obtained using three-dimensional electron microscopy.” 2004 2nd Ieee International Symposium on Biomedical Imaging: Macro to Nano 1 (December 1, 2004): 5–8.
    • Bartesaghi, A., G. Sapiro, T. Malzbender, and D. Gelb. “Non-photorealistic rendering from multiple images.” Proceedings  International Conference on Image Processing, Icip 4 (December 1, 2004): 2403–6. https://doi.org/10.1109/ICIP.2004.1421585.
       Full Text
    • Bartesaghi, A., and G. Sapiro. “A system for the generation of curves on 3D brain images.” Human Brain Mapping 14, no. 1 (September 2001): 1–15. https://doi.org/10.1002/hbm.1037.
       Full Text

  • Conference Papers

    • Huang, Q., Y. Zhou, H. F. Liu, and A. Bartesaghi. “Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-Electron Microscopy.” In Proceedings  2022 Ieee/Cvf Winter Conference on Applications of Computer Vision, Wacv 2022, 3260–69, 2022. https://doi.org/10.1109/WACV51458.2022.00332.
       Full Text
    • Huang, Q., Y. Zhou, H. F. Liu, and A. Bartesaghi. “Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13681 LNCS:644–60, 2022. https://doi.org/10.1007/978-3-031-19803-8_38.
       Full Text
    • Bouvette, Jonathan, Mario Borgnia, Hsuan-Fu Liu, Alberto Bartesaghi, Roel Schaaper, Bradley Klemm, Andrew Sikkema, et al. “Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.” In Acta Crystallographica Section a Foundations and Advances, 77:a209–a209. International Union of Crystallography (IUCr), 2021. https://doi.org/10.1107/s0108767321097907.
       Full Text
    • Bouvette, J., Q. Huang, A. Bartesaghi, and M. J. Borgnia. “Smartscope: AI-driven grid navigation for high-throughput cryo-EM.” In Proceedings  Applied Imagery Pattern Recognition Workshop, Vol. 2021-October, 2021. https://doi.org/10.1109/AIPR52630.2021.9762104.
       Full Text
    • Huang, Q., Y. Zhou, and A. Bartesaghi. “Joint Model for Image Denoising and Detection of Proteins Imaged by Cryo-EM.” In Proceedings  Applied Imagery Pattern Recognition Workshop, Vol. 2021-October, 2021. https://doi.org/10.1109/AIPR52630.2021.9762098.
       Full Text
    • Bartesaghi, Alberto. “Streamlining Workflows for Structure Determination by Single Particle Cryo-EM.” In Biophysical Journal, 116:11a-11a. Elsevier BV, 2019. https://doi.org/10.1016/j.bpj.2018.11.100.
       Full Text
    • Tran, Erin, Kira Podolsky, Alberto Bartesaghi, Oleg Kuybeda, Giovanna Grandinetti, Teddy John Wohlbold, Gene Tan, et al. “Cryo-EM Tomographic Analysis of a Universal Influenza Virus Vaccine Candidate.” In Biophysical Journal, 112:577a-577a. Elsevier BV, 2017. https://doi.org/10.1016/j.bpj.2016.11.3105.
       Full Text
    • Borgnia, Mario J., Soojay Banerjee, Alberto Bartesaghi, Doreen Matthies, Prashant Rao, Alan Merk, Jason Pierson, Jacqueline L. Milne, and Sriram Subramaniam. “Using cryo-EM to Untangle the Conformational Landscape of a Small Allosterically-Regulated Complex.” In Biophysical Journal, 110:22a-22a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.179.
       Full Text
    • Matthies, Doreen, Olivier Dalmas, Mario Borgnia, Pawel Dominik, Alan Merk, Prashant Rao, Bharat Reddy, et al. “Structures of the Mg2+ Channel Cora in the Open State by Cryo Electron Microscopy.” In Biophysical Journal, 110:291a-291a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.1574.
       Full Text
    • Matthies, Doreen, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, et al. “Single-Particle Cryo-EM Studies of a 200-kDa Magnesium Ion Channel Reveal Large Structural Changes Upon Gating.” In Biophysical Journal, 110:10a-10a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.109.
       Full Text
    • Borgnia, Mario J., Soojay Banerjee, Prashant Rao, Alberto Bartesaghi, Allan Merk, Jason Pierson, Sriram Subramaniam, and Jacqueline Milne. “Localization of Small Ligands in a Metabolic Protein Complex using Cryo-Electron Microscopy.” In Biophysical Journal, 108:514a-514a. Elsevier BV, 2015. https://doi.org/10.1016/j.bpj.2014.11.2818.
       Full Text
    • Matthies, Doreen, Alberto Bartesaghi, Alan Merk, Soojay Banerjee, and Sriram Subramaniam. “Residue Specific Radiation Damage of Protein Structures using High-Resolution Cryo-Electron Microscopy.” In Biophysical Journal, 108:190a-190a. Elsevier BV, 2015. https://doi.org/10.1016/j.bpj.2014.11.1052.
       Full Text
    • Meyerson, Joel R., Janesh Kumar, Sagar Chittori, Prashant Rao, Jason Pierson, Alberto Bartesaghi, Mark L. Mayer, and Sriram Subramaniam. “Structural Mechanism of Glutamate Receptor Activation and Desensitization.” In Biophysical Journal, 108:287a-287a. Elsevier BV, 2015. https://doi.org/10.1016/j.bpj.2014.11.1568.
       Full Text
    • Yoo, T. S., B. C. Lowekamp, O. Kuybeda, K. Narayan, G. A. Frank, A. Bartesaghi, M. Borgnia, S. Subramaniam, G. Sapiro, and M. J. Ackerman. “Accelerating discovery in 3D microanalysis: Leveraging open source software and deskside high performance computing.” In Microscopy and Microanalysis, 20:774–75, 2014. https://doi.org/10.1017/S1431927614005595.
       Full Text
    • Bartesaghi, Alberto, Jason Pierson, Prashant Rao, Soojay Banerjee, Mario Borgnia, Lingbo Yu, Lesley Earl, Michael Alink, Jacqueline Milne, and Sriram Subramaniam. “Structure Determination of Small Macromolecular Complexes by Cryo-Electron Microscopy.” In Biophysical Journal, 106:601a-601a. Elsevier BV, 2014. https://doi.org/10.1016/j.bpj.2013.11.3329.
       Full Text
    • Bartesaghi, Alberto, Jason Pierson, David Schauder, Mario Borgnia, and Sriram Subramaniam. “Automated Workflows for Structure Determination by Single-Particle Cryo-EM at Sub-Nanometer Resolutions.” In Biophysical Journal, 104:352a-352a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1955.
       Full Text
    • Borgnia, Mario J., Alberto Bartesaghi, Erin Tran, Jacqueline L. S. Milne, and Sriram Subramaniam. “9 Å Structure of Trimeric HIV-1 Envelope Glycoprotein in an Activated State.” In Biophysical Journal, 104:350a-350a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1946.
       Full Text
    • Frank, Gabriel A., Oleg Kuybeda, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro, and Sriram Subramaniam. “Computational Separation of Conformational Heterogeneity using Cryo-Electron Tomography and 3D Sub-Volume Averaging.” In Biophysical Journal, 104:350a-351a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1947.
       Full Text
    • Schauder, David M., Oleg Kuybeda, Jinjin Zhang, Katherine Klymko, Alberto Bartesaghi, Mario J. Borgnia, Mark L. Mayer, and Sriram Subramaniam. “Glutamate Receptor Desensitization Mediated by Changes in Quaternary Structure of the Ligand Binding Domain.” In Biophysical Journal, 104:352a-352a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1953.
       Full Text
    • Tran, Erin E. H., Oleg Kuybeda, Alberto Bartesaghi, Jacqueline L. S. Milne, and Sriram Subramaniam. “Binding of Neutralizing Antibodies Results in Distinct Quaternary Conformations of Trimeric HIV-1 Envelope Glycoproteins.” In Biophysical Journal, 104:352a-352a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1952.
       Full Text
    • Bartesaghi, Alberto, Pablo Sprechmann, Gregory Randall, Guillermo Sapiro, and Sriram Subramaniam. “A framework for classification and averaging of 3D tomographic volumes.” In Biophysical Journal, 509A-509A. BIOPHYSICAL SOCIETY, 2007.
       Link to Item
    • Bartesaghi, A., and M. Nadar. “Segmentation of anatomical structure from DT-MRI.” In 2006 3rd Ieee International Symposium on Biomedical Imaging: From Nano to Macro  Proceedings, 2006:61–64, 2006.
    • Bartesaghi, A., and G. Sapiro. “Tracking of moving objects under severe and total occlusions.” In 2005 International Conference on Image Processing (Icip), Vols 1 5, 249–52. IEEE, 2005.
       Link to Item
    • Bartesaghi, A., A. Fernández, and A. Gómez. “Performance evaluation of an automatic fingerprint classification algorithm adapted to a Vucetich based classification system.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2091 LNCS:259–65, 2001. https://doi.org/10.1007/3-540-45344-x_38.
       Full Text
    • Guerreschi, F., M. Incerti, A. Bartesaghi, R. Rigoni, and R. Cattaneo. “Correction of monoplanar and biplanar axial deviations of lower limbs with Ilizarov method.” In Minerva Ortopedica E Traumatologica, 42:405–11, 1991.
    • Incerti, M., A. Villa, R. Rigoni, A. Bartesaghi, and F. Guerreschi. “Indications for G. A. Ilizarov's astragalarcalcaneal curvilinear osteotomy.” In Chirurgia Del Piede, 15:147–51, 1991.

  • Preprints

    • Sokratian, Arpine, Ye Zhou, Enquan Xu, Elizabeth Viverette, Lucas Dillard, Yuan Yuan, Joshua Y. Li, et al. “Structural and functional landscape of α-synuclein fibril conformations amplified from cerebrospinal fluid.” Cold Spring Harbor Laboratory, July 13, 2022. https://doi.org/10.1101/2022.07.13.499896.
       Full Text
• Teaching & Mentoring
• 

  Recent Courses

  • COMPSCI 362: Introduction to Computational Imaging 2023
  • BIOCHEM 393: Research Independent Study 2022
  • BIOCHEM 562: High-Resolution Cryo-Electron Microscopy Image Analysis 2022
  • BIOCHEM 593: Research Independent Study 2022
  • CBB 562: High-Resolution Cryo-Electron Microscopy Image Analysis 2022
  • COMPSCI 562: High-Resolution Cryo-Electron Microscopy Image Analysis 2022
  • BIOCHEM 393: Research Independent Study 2021
  • BIOCHEM 593: Research Independent Study 2021
  • BIOCHEM 690: Advanced Topics in Biochemistry 2021
  • COMPSCI 290: Topics in Computer Science 2021
  • COMPSCI 393: Research Independent Study 2021
  • COMPSCI 590: Advanced Topics in Computer Science 2021

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.