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Elizabeth Villa, Ph.D. - Publications

Affiliations: 
2008 Biophysics University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
 2008-2014 Molecular Structural Biology Max Planck Institute of Biochemistry 
 2014- Biological Sciences University of California, San Diego, La Jolla, CA 
Area:
theoretical biophysics, cryo-EM, structural cell biology, neurodegenerative disease, imaging, microbiology
Website:
villalab.ucsd.edu
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Young LN, Sherrard A, Zhou H, Shaikh F, Hutchings J, Riggi M, Rosen MK, Giraldez AJ, Villa E. ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms. Biorxiv : the Preprint Server For Biology. PMID 39416124 DOI: 10.1101/2024.10.12.617288  0.318
2024 Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, ... ... Villa E, et al. The molecular architecture of the nuclear basket. Cell. PMID 39127037 DOI: 10.1016/j.cell.2024.07.020  0.624
2024 Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, ... ... Villa E, et al. The Molecular Architecture of the Nuclear Basket. Biorxiv : the Preprint Server For Biology. PMID 38586009 DOI: 10.1101/2024.03.27.587068  0.628
2024 Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. Biorxiv : the Preprint Server For Biology. PMID 38260487 DOI: 10.1101/2023.12.31.573409  0.557
2021 Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, ... ... Villa E, et al. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. PMID 34982960 DOI: 10.1016/j.cell.2021.12.015  0.69
2021 Lu S, Ye Q, Singh D, Cao Y, Diedrich JK, Yates JR, Villa E, Cleveland DW, Corbett KD. The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nature Communications. 12: 502. PMID 33479198 DOI: 10.1038/s41467-020-20768-y  0.55
2020 Yu H, Lu S, Gasior K, Singh D, Vazquez-Sanchez S, Tapia O, Toprani D, Beccari MS, Yates JR, Da Cruz S, Newby JM, Lafarga M, Gladfelter AS, Villa E, Cleveland DW. HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science (New York, N.Y.). PMID 33335017 DOI: 10.1126/science.abb4309  0.534
2020 Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature. PMID 32814344 DOI: 10.1038/S41586-020-2673-2  0.327
2020 Watanabe R, Buschauer R, Böhning J, Audagnotto M, Lasker K, Lu TW, Boassa D, Taylor S, Villa E. The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell. PMID 32783917 DOI: 10.1016/J.Cell.2020.08.004  0.334
2020 Lu S, Ye Q, Singh D, Villa E, Cleveland DW, Corbett KD. The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Biorxiv : the Preprint Server For Biology. PMID 32766587 DOI: 10.1101/2020.07.30.228023  0.549
2020 Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nature Protocols. PMID 32405053 DOI: 10.1038/S41596-020-0320-X  0.626
2020 Bianchi DM, Breuer M, Lam V, Poddar A, Wise KS, Hutchison CA, Smith HO, Villa E, Ha T, Glass JI, Luthey-Schulten Z. Modeling the Lipid Metabolism of a Genetically Minimal Cell Biophysical Journal. 118: 346a. DOI: 10.1016/J.Bpj.2019.11.1999  0.413
2019 Khanna K, Lopez-Garrido J, Zhao Z, Watanabe R, Yuan Y, Sugie J, Pogliano K, Villa E. The molecular architecture of engulfment during sporulation. Elife. 8. PMID 31282858 DOI: 10.7554/Elife.45257  0.367
2019 Chaikeeratisak V, Khanna K, Nguyen KT, Sugie J, Egan ME, Erb ML, Vavilina A, Nonejuie P, Nieweglowska E, Pogliano K, Agard DA, Villa E, Pogliano J. Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria. Cell. 177: 1771-1780.e12. PMID 31199917 DOI: 10.1016/J.Cell.2019.05.032  0.314
2018 Lopez-Garrido J, Ojkic N, Khanna K, Wagner FR, Villa E, Endres RG, Pogliano K. Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology. Cell. 172: 758-770.e14. PMID 29425492 DOI: 10.1016/J.Cell.2018.01.027  0.337
2017 Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z. Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. The Journal of Physical Chemistry. B. PMID 28291359 DOI: 10.1021/Acs.Jpcb.7B00672  0.544
2017 Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JK, Vavilina A, Newton GL, Buschauer R, Pogliano K, Villa E, Agard DA, Pogliano J. Assembly of a nucleus-like structure during viral replication in bacteria. Science (New York, N.Y.). 355: 194-197. PMID 28082593 DOI: 10.1126/Science.Aal2130  0.364
2017 Villa E, Watanabe R, Buschauer R, Khanna K, Lam V. Opening windows into the cell: bringing structure to cell biology using cryo-electron microscopy Acta Crystallographica Section a Foundations and Advances. 73: a417-a417. DOI: 10.1107/S0108767317095939  0.354
2017 Villa E, Watanabe R, Buschauer R, Khanna K, Lam V, Singla J, Alber F. Revealing the Native Molecular Architecture of the Nuclear Periphery using Cryo-Focused-Ion-Beam Milling, Light Microscopy and Electron Tomography Microscopy and Microanalysis. 23: 1248-1249. DOI: 10.1017/S1431927617006900  0.328
2016 Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R, Cuellar LK, Förster F, Hyman AA, Plitzko JM, Baumeister W. Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science (New York, N.Y.). 351: 969-72. PMID 26917770 DOI: 10.1126/Science.Aad8857  0.557
2015 Engel BD, Schaffer M, Cuellar LK, Villa E, Plitzko JM, Baumeister W. Correction: Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. Elife. 4. PMID 26367339 DOI: 10.7554/Elife.11383  0.496
2015 Plaschka C, Larivière L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature. 518: 376-80. PMID 25652824 DOI: 10.1038/Nature14229  0.506
2015 Engel BD, Schaffer M, Kuhn Cuellar L, Villa E, Plitzko JM, Baumeister W. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. Elife. 4. PMID 25584625 DOI: 10.7554/Elife.04889  0.563
2014 Villa E, Lasker K. Finding the right fit: chiseling structures out of cryo-electron microscopy maps. Current Opinion in Structural Biology. 25: 118-25. PMID 24814094 DOI: 10.1016/J.Sbi.2014.04.001  0.405
2014 Villa E, Schaffer M, Engel B, Plitzko J, Baumeister W. Structural cell biology: Preparing specimens for cryo-electron tomography using focused-ion-beam milling Microscopy and Microanalysis. 20: 1222-1223. DOI: 10.1017/S1431927614007843  0.49
2013 Jasnin M, Asano S, Gouin E, Hegerl R, Plitzko JM, Villa E, Cossart P, Baumeister W. Three-dimensional architecture of actin filaments in Listeria monocytogenes comet tails. Proceedings of the National Academy of Sciences of the United States of America. 110: 20521-6. PMID 24306931 DOI: 10.1073/Pnas.1320155110  0.489
2013 Villa E, Schaffer M, Plitzko JM, Baumeister W. Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography. Current Opinion in Structural Biology. 23: 771-7. PMID 24090931 DOI: 10.1016/J.Sbi.2013.08.006  0.509
2013 Armache JP, Anger AM, Márquez V, Franckenberg S, Fröhlich T, Villa E, Berninghausen O, Thomm M, Arnold GJ, Beckmann R, Wilson DN. Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution. Nucleic Acids Research. 41: 1284-93. PMID 23222135 DOI: 10.1093/Nar/Gks1259  0.417
2013 Schaffer M, Villa E, Engel B, Fukuda Y, Laugks T, Rigort A, Schüler M, Schwarz A, Bäuerlein F, Mahami J, Baumeister W, Plitzko J. Reproducibility in Focused Ion Beam sample preparation - a Key Requirement for Cryo-Electron Tomography of Eukaryotic Cells Microscopy and Microanalysis. 19: 876-877. DOI: 10.1017/S1431927613006375  0.48
2013 Plitzko J, Villa E, Engel B, Fukuda Y, Laugks T, Schaffer M, Schwarz A, Baeuerlein F, Mahamid J, Fitting Kourkoutis L, Rigort A, Baumeister W. Doing Structural Biology in situ - Prospects and Challenges Microscopy and Microanalysis. 19: 424-425. DOI: 10.1017/S143192761300411X  0.492
2013 Villa E, Schaffer M, Rigort A, Bauerlein F, Plitzko J, Baumeister W. Opening Windows into the Cell: Focused Ion Beam Micromachining of Eukaryotic Cells for Cryo-Electron Tomography Biophysical Journal. 104: 353a-354a. DOI: 10.1016/J.Bpj.2012.11.1961  0.564
2012 Beck F, Unverdorben P, Bohn S, Schweitzer A, Pfeifer G, Sakata E, Nickell S, Plitzko JM, Villa E, Baumeister W, Förster F. Near-atomic resolution structural model of the yeast 26S proteasome. Proceedings of the National Academy of Sciences of the United States of America. 109: 14870-5. PMID 22927375 DOI: 10.1073/Pnas.1213333109  0.559
2012 Rigort A, Villa E, Bäuerlein FJ, Engel BD, Plitzko JM. Integrative approaches for cellular cryo-electron tomography: correlative imaging and focused ion beam micromachining. Methods in Cell Biology. 111: 259-81. PMID 22857933 DOI: 10.1016/B978-0-12-416026-2.00014-5  0.354
2012 Schönegge AM, Villa E, Förster F, Hegerl R, Peters J, Baumeister W, Rockel B. The structure of human tripeptidyl peptidase II as determined by a hybrid approach Structure. 20: 593-603. PMID 22483107 DOI: 10.1016/J.Str.2012.01.025  0.566
2012 Rigort A, Bäuerlein FJ, Villa E, Eibauer M, Laugks T, Baumeister W, Plitzko JM. Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America. 109: 4449-54. PMID 22392984 DOI: 10.1073/Pnas.1201333109  0.511
2012 Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proceedings of the National Academy of Sciences of the United States of America. 109: 1380-7. PMID 22307589 DOI: 10.1073/Pnas.1120559109  0.541
2011 Becker T, Armache JP, Jarasch A, Anger AM, Villa E, Sieber H, Motaal BA, Mielke T, Berninghausen O, Beckmann R. Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome. Nature Structural & Molecular Biology. 18: 715-20. PMID 21623367 DOI: 10.1038/Nsmb.2057  0.39
2011 Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, Schulten K. Applications of the molecular dynamics flexible fitting method. Journal of Structural Biology. 173: 420-7. PMID 20932910 DOI: 10.1016/J.Jsb.2010.09.024  0.796
2011 Plitzko J, Rigort A, Baeuerlein F, Laugks T, Villa E, Baumeister W. Hybrid Imaging-Novel Approaches and Recent Advances in Correlative Microscopy Microscopy and Microanalysis. 17: 964-965. DOI: 10.1017/S1431927611005691  0.454
2010 Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proceedings of the National Academy of Sciences of the United States of America. 107: 19748-53. PMID 20980660 DOI: 10.1073/Pnas.1009999107  0.424
2010 Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, et al. Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proceedings of the National Academy of Sciences of the United States of America. 107: 19754-9. PMID 20974910 DOI: 10.1073/Pnas.1010005107  0.397
2010 Förster F, Villa E. Integration of cryo-EM with atomic and protein-protein interaction data. Methods in Enzymology. 483: 47-72. PMID 20888469 DOI: 10.1016/S0076-6879(10)83003-4  0.453
2010 Ben-Harush K, Maimon T, Patla I, Villa E, Medalia O. Visualizing cellular processes at the molecular level by cryo-electron tomography. Journal of Cell Science. 123: 7-12. PMID 20016061 DOI: 10.1242/Jcs.060111  0.385
2009 Sener M, Hsin J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides. Chemical Physics. 357: 188-197. PMID 20161332 DOI: 10.1016/J.Chemphys.2009.01.003  0.778
2009 Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science (New York, N.Y.). 326: 1412-5. PMID 19933110 DOI: 10.1126/Science.1177662  0.747
2009 Gumbart J, Trabuco LG, Schreiner E, Villa E, Schulten K. Regulation of the protein-conducting channel by a bound ribosome. Structure (London, England : 1993). 17: 1453-64. PMID 19913480 DOI: 10.1016/J.Str.2009.09.010  0.779
2009 Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophysical Journal. 97: 321-9. PMID 19580770 DOI: 10.1016/J.Bpj.2009.04.031  0.776
2009 Trabuco LG, Villa E, Schreiner E, Harrison CB, Schulten K. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods (San Diego, Calif.). 49: 174-80. PMID 19398010 DOI: 10.1016/J.Ymeth.2009.04.005  0.784
2009 Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proceedings of the National Academy of Sciences of the United States of America. 106: 1063-8. PMID 19122150 DOI: 10.1073/Pnas.0811370106  0.771
2008 Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure (London, England : 1993). 16: 673-83. PMID 18462672 DOI: 10.1016/J.Str.2008.03.005  0.793
2008 Villa E, Trabuco L, Mitra K, Sengupta J, Frank J, Schulten K. Merging data from cryo-EM and X-ray crystallography to reveal biomolecular function Acta Crystallographica Section a Foundations of Crystallography. 64: C47-C47. DOI: 10.1107/S0108767308098498  0.539
2006 Gao M, Sotomayor M, Villa E, Lee EH, Schulten K. Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics : Pccp. 8: 3692-706. PMID 16896432 DOI: 10.1039/B606019F  0.714
2005 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26: 1781-802. PMID 16222654 DOI: 10.1002/Jcc.20289  0.715
2005 Villa E, Balaeff A, Schulten K. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences of the United States of America. 102: 6783-8. PMID 15863616 DOI: 10.1073/Pnas.0409387102  0.748
2004 Villa E, Balaeff A, Mahadevan L, Schulten K. Multiscale Method for Simulating Protein-DNA Complexes Multiscale Modeling & Simulation. 2: 527-553. DOI: 10.1137/040604789  0.742
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