publications

2023

Qinwen Huang, Ye Zhou, Hsuan-Fu Liu, Alberto Bartesaghi (2023) Multiple-image super-resolution of cryo-EM micrographs based on deep internal learning, Biological Imaging 1, p. 1-15, doi:10.1017/S2633903X2300003X

Shivesh Kumar, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A. Sciandra, Ning Sui, Rodolfo Zentella, Emily Zahn, Jeffrey Shabanowitz, Donald F. Hunt, Mario J. Borgnia, Alberto Bartesaghi, Tai-ping Sun, Pei Zhou (2023) Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY, Nature Communications 2023 14:1 14(1), p. 1-12, doi:10.1038/s41467-023-37279-1

Erica J. Washington, Ye Zhou, Allen L. Hsu, Matthew Petrovich, Mario J. Borgnia, Alberto Bartesaghi, Richard G. Brennan (2023) Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen Cryptococcus neoformans: a target for novel antifungals, bioRxiv, p. 2023.03.14.530545, doi:10.1101/2023.03.14.530545

2022

Jonathan Bouvette, Qinwen Huang, Amanda A Riccio, William C. Copeland, Alberto Bartesaghi, Mario J. Borgnia (2022) Automated systematic evaluation of cryo-EM specimens with SmartScope, eLife, doi:https://doi.org/10.7554/eLife.80047

Qinwen Huang, Ye Zhou, Hsuan-Fu Liu, Alberto Bartesaghi (2022) Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels, European Conference on Computer Vision (ECCV) 13681, p. 644-660, doi:10.1007/978-3-031-19803-8_38

Qinwen Huang, Ye Zhou, Hsuan-Fu Liu, Alberto Bartesaghi (2022) Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-Electron Microscopy, IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), p. 3246-3255, url

Shivesh Kumar, Raul Zavaliev, Qinglin Wu, Ye Zhou, Jie Cheng, Lucas Dillard, Jordan Powers, John Withers, Jinshi Zhao, Ziqiang Guan, Mario J. Borgnia, Alberto Bartesaghi, Xinnian Dong, Pei Zhou (2022) Structural basis of NPR1 in activating plant immunity, Nature, p. 1-6, doi:10.1038/s41586-022-04699-w

H.-F. Liu, Y. Zhou, A. Bartesaghi, IUCr (2022) High-resolution structure determination using high-throughput electron cryo-tomography, Acta Cryst. D 78(7), p. 2059-7983, International Union of Crystallography, doi:10.1107/S2059798322005010

Priyamvada Acharya Rory Henderson, Ye Zhou, Victoria Stalls, Kevin Wiehe, Kevin O. Saunders, Kshitij Wagh, Kara Anasti, Maggie Barr, Robert Parks, S. Munir Alam, Bette Korber, Barton F. Haynes, Alberto Bartesaghi (2022) Structural basis for breadth development in a HIV-1 neutralizing antibody, bioRxiv, doi:https://doi.org/10.1101/2022.09.14.507935

Vanessa Simões, Blanche K Cizubu, Lana Harley, Gaurav Arya, Alberto Bartesaghi, Gustavo M Silva Correspondence, Ye Zhou, Joshua Pajak, Nathan A Snyder, Jonathan Bouvette, Mario J Borgnia, Gustavo M Silva (2022) Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes, Cell Reports 39(8), p. 110860, doi:10.1016/J.CELREP.2022.110860

Arpine Sokratian, Ye Zhou, Enquan Xu, Elizabeth Viverette, Lucas Dillard, Yuan Yuan, Joshua Y. Li, Ariana Matarangas, Jonathan Bouvette, Mario Borgnia, Alberto Bartesaghi, Andrew West (2022) Structural and functional landscape of α-synuclein fibril conformations amplified from cerebrospinal fluid, bioRxiv, doi:10.1101/2022.07.13.499896

Ye Zhou, Amit Moscovich, Alberto Bartesaghi (2022) Data-driven determination of number of discrete conformations in single-particle cryo-EM, Computer Methods and Programs in Biomedicine 221, p. 106892, doi:10.1016/J.CMPB.2022.106892

2021

Jonathan Bouvette, Qinwen Huang, Alberto Bartesaghi, Mario J. Borgnia (2021) Smartscope: AI-driven grid navigation for high-throughput cryo-EM, 2021 IEEE Applied Imagery Pattern Recognition Workshop (AIPR), p. 1-6, doi:10.1109/AIPR52630.2021.9762104

Jonathan Bouvette, Hsuan-Fu Liu, Xiaochen Du, Ye Zhou, Andrew P. Sikkema, Juliana da Fonseca Rezende e Mello, Bradley P. Klemm, Rick Huang, Roel M. Schaaper, Mario J. Borgnia, Alberto Bartesaghi (2021) Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography, Nature Communications 12(1), p. 1957, doi:10.1038/s41467-021-22251-8

Qinwen Huang, Ye Zhou, Alberto Bartesaghi (2021) Joint Model for Image Denoising and Detection of Proteins Imaged by Cryo-EM, 2021 IEEE Applied Imagery Pattern Recognition Workshop (AIPR), p. 1-8, doi:10.1109/AIPR52630.2021.9762098

Qinwen Huang, Ye Zhou, Hsuan-Fu Liu, Alberto Bartesaghi (2021) Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-EM, Machine Learning in Structural Biology Workshop at the 35th Conference on Neural Information Processing Systems (NeurIPS), pdf

Wilton B. Williams, R. Ryan Meyerhoff, R.J. Edwards, Hui Li, Kartik Manne, Nathan I. Nicely, Rory Henderson, Ye Zhou, Katarzyna Janowska, Katayoun Mansouri, Sophie Gobeil, Tyler Evangelous, Bhavna Hora, Madison Berry, A. Yousef Abuahmad, Jordan Sprenz, Margaret Deyton, Victoria Stalls, Megan Kopp, Allen L. Hsu, Mario J. Borgnia, Guillaume Stewart-Jones, Matthew S. Lee, Naomi Bronkema, M. Anthony Moody, Kevin Wiehe, Todd Bradley, S. Munir Alam, Robert J. Parks, Andrew Foulger, Thomas Oguin, Sampa Santra, John Perfect, Joseph R. Francica, Geoffrey M. Lynn, Baptiste Aussedat, William E. Walkowicz, Richard Laga, Garnett Kelsoe, Kevin O. Saunders, Daniela Fera, Peter D. Kwong, Robert A. Seder, Alberto Bartesaghi, George M. Shaw, Priyamvada Acharya, Barton F. Haynes (2021) Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies, Cell, doi:10.1016/j.cell.2021.04.042

2020

Tamir Bendory, Alberto Bartesaghi, Amit Singer (2020) Single-Particle Cryo-Electron Microscopy: Mathematical Theory, Computational Challenges, and Opportunities, IEEE Signal Processing Magazine 37(2), p. 58-76, doi:10.1109/MSP.2019.2957822

Rory Henderson, Maolin Lu, Ye Zhou, Zekun Mu, Robert Parks, Qifeng Han, Allen L. Hsu, Elizabeth Carter, Scott C. Blanchard, R J Edwards, Kevin Wiehe, Kevin O. Saunders, Mario J. Borgnia, Alberto Bartesaghi, Walther Mothes, Barton F. Haynes, Priyamvada Acharya, S. Munir Alam (2020) Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements, Nature Communications 11(1), p. 520, doi:10.1038/s41467-019-14196-w

Qinwen Huang, Ye Zhou, Xiaochen Du, Reed Chen, Jianyou Wang, Cynthia Rudin, Alberto Bartesaghi (2020) Cryo-ZSSR: multiple-image super-resolution based on deep internal learning, Workshop at the 34th Conference on Neural Information Processing Systems (NeurIPS 2020), url

Brady A. Travis, Kathryn M. Ramsey, Samantha M. Prezioso, Thomas Tallo, Jamie M. Wandzilak, Allen Hsu, Mario Borgnia, Alberto Bartesaghi, Simon L. Dove, Richard G. Brennan, Maria A. Schumacher (2020) Structural Basis for Virulence Activation of Francisella tularensis, Molecular Cell 81(1), p. P139-152.E10, doi:10.1016/j.molcel.2020.10.035

Ye Zhou, Panagiotis L. Kastritis, Shannon E. Dougherty, Jonathan Bouvette, Allen L. Hsu, Laura Burbaum, Shyamal Mosalaganti, Stefan Pfeffer, Wim J. H. Hagen, Friedrich Förster, Mario J. Borgnia, Christine Vogel, Martin Beck, Alberto Bartesaghi, Gustavo M. Silva (2020) Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress, PNAS 117(36), p. 22157-22166, doi:10.1073/pnas.2005301117

2019

Ye Zhou, Amit Moscovich, Tamir Bendory, Alberto Bartesaghi (2019) Unsupervised particle sorting for high-resolution single-particle cryo-EM, Inverse Problems, doi:10.1088/1361-6420/ab5ec8

2018

A Bartesaghi, C Aguerrebere, V Falconieri, S Banerjee, LA Earl, X Zhu, N Grigorieff, JLS Milne, G Sapiro, X Wu, S Subramaniam (2018) Atomic Resolution Cryo-EM Structure of β-Galactosidase, Structure 26(6), doi:10.1016/j.str.2018.04.004

Y Kang, O Kuybeda, PW de Waal, S Mukherjee, N Van Eps, P Dutka, XE Zhou, A Bartesaghi, S Erramilli, T Morizumi, X Gu, Y Yin, P Liu, Y Jiang, X Meng, G Zhao, K Melcher, OP Ernst, AA Kossiakoff, S Subramaniam, HE Xu (2018) Cryo-EM structure of human rhodopsin bound to an inhibitory G protein, Nature 558, p. 553-558, doi:10.1038/s41586-018-0215-y

Doreen Matthies, Chanhyung Bae, Gilman ES Toombes, Tara Fox, Alberto Bartesaghi, Sriram Subramaniam, Kenton Jon Swartz (2018) Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs, eLife 7(e37558), doi:10.7554/eLife.37558

2017

TW Guo, A Bartesaghi, H Yang, V Falconieri, P Rao, A Merk, ET Eng, AM Raczkowski, T Fox, LA Earl, DJ Patel, S Subramaniam (2017) Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex, Cell 171(2), p. 414-426.e12, doi:10.1016/j.cell.2017.09.006

2016

C Aguerrebere, M Delbracio, A Bartesaghi, G Sapiro (2016) Fundamental Limits in Multi-Image Alignment, IEEE Transactions on Signal Processing 64(21), p. 5707-5722, doi:10.1109/TSP.2016.2600517

S Banerjee, A Bartesaghi, A Merk, P Rao, SL Bulfer, Y Yan, N Green, B Mroczkowski, RJ Neitz, P Wipf, V Falconieri, RJ Deshaies, JLS Milne, D Huryn, M Arkin, S Subramaniam (2016) 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition, Science 351(6275), p. 871-875, doi:10.1126/science.aad7974

MJ Borgnia, S Banerjee, A Merk, D Matthies, A Bartesaghi, P Rao, J Pierson, LA Earl, V Falconieri, S Subramaniam, JLS Milne (2016) Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase, Molecular Pharmacology 89(6), p. 645-651, doi:10.1124/mol.116.103382

GA Frank, S Shukla, P Rao, MJ Borgnia, A Bartesaghi, A Merk, A Mobin, L Esser, LA Earl, MM Gottesman, D Xia, SV Ambudkar, S Subramaniam (2016) Cryo-EM Analysis of the Conformational Landscape of Human P-glycoprotein (ABCB1) During its Catalytic Cycle, Molecular Pharmacology 90(1), p. 35-41, doi:10.1124/mol.116.104190

A Merk, A Bartesaghi, S Banerjee, V Falconieri, P Rao, MI Davis, R Pragani, MB Boxer, LA Earl, JLS Milne, S Subramaniam (2016) Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery, Cell 165(7), p. 1698-1707, doi:10.1016/j.cell.2016.05.040

EEH Tran, KA Podolsky, A Bartesaghi, O Kuybeda, G Grandinetti, TJ Wohlbold, GS Tan, R Nachbagauer, P Palese, F Krammer, S Subramaniam (2016) Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Influenza Vaccine Candidate, mBio 7(2), p. e00257-16, doi:10.1128/mBio.00257-16

2015

Alberto Bartesaghi, Alan Merk, Soojay Banerjee, Doreen Matthies, Xiongwu Wu, Jacqueline L.S. Milne, Sriram Subramaniam (2015) 2.2 å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor, Science 348(6239), p. 1147-1151, doi:10.1126/science.aab1576

2014

A Bartesaghi, D Matthies, S Banerjee, A Merk, S Subramaniam (2014) Structure of B-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy, Proceedings of the National Academy of Sciences 111(32), p. 11709-11714, doi:10.1073/pnas.1402809111

JR Meyerson, J Kumar, S Chittori, P. Rao, J Pierson, A Bartesaghi, ML Mayer, S Subramaniam (2014) Structural mechanism of glutamate receptor activation and desensitization, Nature 514(7522), p. 328-334, doi:10.1038/nature13603

EEH Tran, JA Simmons, A Bartesaghi, CJ Shoemaker, E Nelson, JM White, S Subramaniam (2014) Spatial Localization of the Ebola Virus Glycoprotein Mucin-Like Domain Determined by Cryo-Electron Tomography, Journal of Virology 88(18), p. 10958-10962, doi:10.1128/JVI.00870-14

TS Yoo, BC Lowekamp, O Kuybeda, K Narayan, GA Frank, A Bartesaghi, M Borgnia, S Subramaniam, G Sapiro, MJ Ackerman (2014) Accelerating Discovery in 3D Microanalysis: Leveraging Open Source Software and Deskside High Performance Computing, Microsc. Microanal 20

2013

A Bartesaghi, A Merk, MJ Borgnia, JLS Milne, S Subramaniam (2013) Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy., Nature structural & molecular biology 20(12), p. 1352-7, doi:10.1038/nsmb.2711

AK Harris, A Bartesaghi, JLS Milne, S Subramaniam (2013) 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(12), p. 7191-6, doi:10.1128/JVI.03284-12

O Kuybeda, GA Frank, A Bartesaghi, MJ Borgnia, S Subramaniam, G Sapiro (2013) A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography, Journal of Structural Biology 181(2), p. 116-127, doi:10.1016/j.jsb.2012.10.010

JLS Milne, MJ Borgnia, A Bartesaghi, EEH Tran, LA Earl, DM Schauder, J Lengyel, J Pierson, A Patwardhan, S Subramaniam (2013) Cryo-electron microscopy - A primer for the non-microscopist, FEBS Journal 280(1), p. 28-45, doi:10.1111/febs.12078

DM Schauder, O Kuybeda, J Zhang, K Klymko, A Bartesaghi, MJ Borgnia, ML Mayer, S Subramaniam (2013) Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain., Proceedings of the National Academy of Sciences of the United States of America 110(15), p. 5921-6, doi:10.1073/pnas.1217549110

2012

A Bartesaghi, F Lecumberry, G Sapiro, S Subramaniam (2012) Protein secondary structure determination by constrained single-particle cryo-electron tomography, Structure 20(12), p. 2003-2013, doi:10.1016/j.str.2012.10.016

GA Frank, A Bartesaghi, O Kuybeda, MJ Borgnia, TA White, G Sapiro, S Subramaniam (2012) Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging, Journal of Structural Biology 178(2), p. 165-176, doi:10.1016/j.jsb.2012.01.004

EEH Tran, MJ Borgnia, O Kuybeda, DM Schauder, A Bartesaghi, GA Frank, G Sapiro, JLS Milne, S Subramaniam (2012) Structural mechanism of trimeric HIV-1 envelope glycoprotein activation, PLoS Pathogens 8(7), p. 37, doi:10.1371/journal.ppat.1002797

2011

A Harris, MJ Borgnia, D Shi, A Bartesaghi, H He, R Pejchal, YK Kang, R Depetris, AJ Marozsan, RW Sanders, PJ Klasse, JLS Milne, I.A. Wilson, WC Olson, JP Moore, S Subramaniam (2011) Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures., Proceedings of the National Academy of Sciences of the United States of America 108(28), p. 11440-11445, doi:10.1073/pnas.1101414108

JR Meyerson, TA White, D Bliss, A Moran, A Bartesaghi, MJ Borgnia, MJV de la Cruz, D Schauder, LM Hartnell, R Nandwani, M Dawood, B Kim, JH Kim, J Sununu, L Yang, S Bhatia, C Subramaniam, DE Hurt, L Gaudreault, S Subramaniam (2011) Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging, Journal of Visualized Experiments(58), doi:10.3791/2770

TA White, A Bartesaghi, MJ Borgnia, MJV de la Cruz, R Nandwani, JA Hoxie, JW Bess, JD Lifson, JLS Milne, S Subramaniam (2011) Three-Dimensional Structures of Soluble CD4-Bound States of Trimeric Simian Immunodeficiency Virus Envelope Glycoproteins Determined by Using Cryo-Electron Tomography, Journal of Virology 85(23), p. 12114-12123, doi:10.1128/JVI.05297-11

2010

TA White, A Bartesaghi, MJ Borgnia, JR Meyerson, MJV De la Cruz, JW Bess, R Nandwani, JA Hoxie, JD Lifson, JLS Milne, S Subramaniam (2010) Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: Strain- dependent variation in quaternary structure, PLoS Pathogens 6(12), doi:10.1371/journal.ppat.1001249

2009

A Bartesaghi, S Subramaniam (2009) Membrane protein structure determination using cryo-electron tomography and 3D image averaging, Curr. Opin. Struct. Biol. 19(4), p. 402-407, doi:10.1016/j.sbi.2009.06.005

2008

A Bartesaghi, P Sprechmann, J Liu, G Randall, G Sapiro, S Subramaniam (2008) Classification and 3D averaging with missing wedge correction in biological electron tomography, Journal of Structural Biology 162(3), p. 436-450, doi:10.1016/j.jsb.2008.02.008

J Liu, A Bartesaghi, MJ Borgnia, G Sapiro, S Subramaniam (2008) Molecular architecture of native HIV-1 gp120 trimers., Nature 455(7209), p. 109-113, doi:10.1038/nature07159

2007

I Aganj, A Bartesaghi, M Borgnia, HY Liao, G Sapiro, S Subramaniam (2007) Regularization for inverting the radon transform with wedge consideration, 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, p. 217-220, IEEE, doi:10.1109/ISBI.2007.356827

R Sougrat, A Bartesaghi, JD Lifson, AE Bennett, JW Bess, DJ Zabransky, S Subramaniam (2007) Electron tomography of the contact between T cells and SIV/HIV-1: Implications for viral entry, PLoS Pathogens 3(5), p. 0571-0581, doi:10.1371/journal.ppat.0030063

S Subramaniam, A Bartesaghi, J Liu, AE Bennett, R Sougrat (2007) Electron tomography of viruses, Current Opinion in Structural Biology 17(5), p. 596-602, doi:10.1016/j.sbi.2007.09.009

2006

A Bartesaghi, M Nadar (2006) Segmentation of Anatomical Structure from DT-MRI, 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano, 2006., p. 61-64, IEEE, doi:10.1109/ISBI.2006.1624852

A Mohan, A Bartesaghi, G Sapiro (2006) Constrained regularization of digital terrain elevation data, IEEE Geoscience and Remote Sensing Letters 3(1), p. 59-62, doi:10.1109/LGRS.2005.856702

L Yatziv, A Bartesaghi, G Sapiro (2006) O(N) implementation of the fast marching algorithm, Journal of Computational Physics 212(2), p. 393-399, doi:10.1016/j.jcp.2005.08.005

2005

A Bartesaghi, G Sapiro (2005) Tracking of moving objects under severe and total occlusions, IEEE International Conference on Image Processing, p. I-301, IEEE, doi:10.1109/ICIP.2005.1529747

A Bartesaghi, G Sapiro, T Malzbender, D Gelb (2005) Three-dimensional shape rendering from multiple images, Graphical Models 67(4), p. 332-346, doi:10.1016/j.gmod.2005.02.002

A Bartesaghi, G Sapiro, S Subramaniam (2005) An energy-based three-dimensional segmentation approach for the quantitative interpretation of electron tomograms, IEEE Transactions on Image Processing 14(9), p. 1314-1323, doi:10.1109/TIP.2005.852467

2004

A Bartesaghi, G Sapiro, S Lee, J Lefman, S Wahl, J Orenstein, S Subramaniam (2004) A new approach for 3D segmentation of cellular tomograms obtained using three-dimensional electron microscopy, 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano 2, p. 5-8, IEEE, doi:10.1109/ISBI.2004.1398460

A Bartesaghi, G Sapiro, T Malzbender, D Gelb (2004) Non-photorealistic rendering from multiple images, Proceedings - International Conference on Image Processing, ICIP 4, p. 2403-2406, doi:10.1109/ICIP.2004.1421585

2001

A Bartesaghi, A Fernández, A Gómez (2001) Performance Evaluation of an Automatic Fingerprint Classification Algorithm Adapted to a Vucetich Based Classification System, p. 259-265, Springer, Berlin, Heidelberg

A Bartesaghi, G Sapiro (2001) A system for the generation of curves on 3D brain images, Human Brain Mapping 14(1), p. 1-15, doi:10.1002/hbm.1037