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Michael T. Woodside, Ph.D. - Publications

Affiliations: 
2001 University of California, Berkeley, Berkeley, CA, United States 
 2013- Physics University of Alberta, Edmonton, Alberta, Canada 
Area:
Protein folding, misfolding and aggregation; RNA folding and function; misfolding diseases; single-molecule approaches to biology
Website:
https://apps.ualberta.ca/directory/person/mwoodsid
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77 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
2023 Devi A, Neupane K, Jung H, Neuman KC, Woodside MT. Non-linear effects in optical trapping of titanium dioxide and diamond nanoparticles. Biophysical Journal. PMID 37496270 DOI: 10.1016/j.bpj.2023.07.018  0.743
2022 Munshi S, Neupane K, Ileperuma SM, Halma MTJ, Kelly JA, Halpern CF, Dinman JD, Loerch S, Woodside MT. Identifying Inhibitors of -1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses. Viruses. 14. PMID 35215770 DOI: 10.3390/v14020177  0.521
2021 Hoffer NQ, Neupane K, Woodside MT. Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34853166 DOI: 10.1073/pnas.2101006118  0.319
2021 Petrosyan R, Narayan A, Woodside MT. Single-Molecule Force Spectroscopy of Protein Folding. Journal of Molecular Biology. 167207. PMID 34418422 DOI: 10.1016/j.jmb.2021.167207  0.322
2020 Kelly JA, Woodside MT, Dinman JD. Programmed -1 Ribosomal Frameshifting in coronaviruses: A therapeutic target. Virology. 554: 75-82. PMID 33387787 DOI: 10.1016/j.virol.2020.12.010  0.516
2020 Kelly JA, Olson AN, Neupane K, Munshi S, Emeterio JS, Pollack L, Woodside MT, Dinman JD. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 32587971 DOI: 10.1101/2020.03.13.991083  0.545
2020 Kelly JA, Olson AN, Neupane K, Munshi S, San Emeterio J, Pollack L, Woodside MT, Dinman JD. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2). The Journal of Biological Chemistry. PMID 32571880 DOI: 10.1074/Jbc.Ac120.013449  0.577
2019 Pyo AGT, Woodside MT. Memory effects in single-molecule force spectroscopy measurements of biomolecular folding. Physical Chemistry Chemical Physics : Pccp. PMID 31663550 DOI: 10.1039/c9cp04197d  0.362
2019 Covino R, Woodside MT, Hummer G, Szabo A, Cossio P. Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics. 151: 154115. PMID 31640370 DOI: 10.1063/1.5118362  0.427
2019 Hoffer NQ, Woodside MT. Probing microscopic conformational dynamics in folding reactions by measuring transition paths. Current Opinion in Chemical Biology. 53: 68-74. PMID 31479831 DOI: 10.1016/J.Cbpa.2019.07.006  0.437
2019 Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT. Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments. Biophysical Journal. PMID 31477241 DOI: 10.1016/J.Bpj.2019.08.013  0.408
2019 Halma MTJ, Ritchie DB, Cappellano TR, Neupane K, Woodside MT. Complex dynamics under tension in a high-efficiency frameshift stimulatory structure. Proceedings of the National Academy of Sciences of the United States of America. PMID 31409714 DOI: 10.1073/Pnas.1905258116  0.428
2019 Hoffer NQ, Neupane K, Pyo AGT, Woodside MT. Measuring the average shape of transition paths during the folding of a single biological molecule. Proceedings of the National Academy of Sciences of the United States of America. PMID 30952784 DOI: 10.1073/Pnas.1816602116  0.387
2019 Halma MT, Ritchie DB, Woodside MT. Force Spectroscopy of the Frameshift Signal from West Nile Virus Reveals Multiple Folding Pathways and Structural Heterogeneity Biophysical Journal. 116: 361a. DOI: 10.1016/J.Bpj.2018.11.1967  0.349
2019 Petrosyan R, Shubhadeep P, Rezajooei N, Garen C, Woodside MT. Single-Molecule Force Spectroscopy Shows that the Anti-Prion Compound Pentosan Polysulfate Binds Heterogeneously to Folded and Unfolded Prion Protein Biophysical Journal. 116: 193a. DOI: 10.1016/J.Bpj.2018.11.1069  0.388
2018 Pyo AGT, Hoffer NQ, Neupane K, Woodside MT. Transition-path properties for folding reactions in the limit of small barriers. The Journal of Chemical Physics. 149: 115101. PMID 30243275 DOI: 10.1063/1.5046692  0.352
2018 Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT. High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy. Nano Letters. PMID 30234311 DOI: 10.1021/Acs.Nanolett.8B02597  0.642
2018 Neupane K, Hoffer NQ, Woodside MT. Measuring the Local Velocity along Transition Paths during the Folding of Single Biological Molecules. Physical Review Letters. 121: 018102. PMID 30028173 DOI: 10.1103/Physrevlett.121.018102  0.357
2018 Neupane K, Hoffer NQ, Woodside MT. Testing Kinetic Identities Involving Transition-Path Properties Using Single-Molecule Folding Trajectories. The Journal of Physical Chemistry. B. PMID 30004229 DOI: 10.1021/Acs.Jpcb.8B05355  0.389
2018 Foster DAN, Petrosyan R, Pyo AGT, Hoffmann A, Wang F, Woodside MT. Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy. Biophysical Journal. 114: 1657-1666. PMID 29642035 DOI: 10.1016/J.Bpj.2018.02.026  0.381
2018 Hoffer NQ, Neupane K, Woodside MT. Testing Kinetic Identities using Measurements of Transition Paths in Single-Molecule Folding Trajectories Biophysical Journal. 114: 168a-169a. DOI: 10.1016/J.Bpj.2017.11.942  0.38
2018 Sen Mojumdar S, Scholl Z, Sullivan M, Garen C, Woodside MT. Role of Dimer Interface on the Cooperativity and Misfolding in SOD1 Studied by Single Molecule Force Spectroscopy Biophysical Journal. 114: 356a. DOI: 10.1016/J.Bpj.2017.11.1979  0.38
2018 Anand U, Garen C, Woodside MT. Probing the Single Molecule Folding Dynamics of Mammalian Prion Proteins from Species with Different Disease Susceptibility Biophysical Journal. 114: 355a. DOI: 10.1016/J.Bpj.2017.11.1976  0.346
2017 Sen Mojumdar S, N Scholl Z, Dee DR, Rouleau L, Anand U, Garen C, Woodside MT. Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories. Nature Communications. 8: 1881. PMID 29192167 DOI: 10.1038/S41467-017-01996-1  0.769
2017 Ritchie DB, Cappellano TR, Tittle C, Rezajooei N, Rouleau L, Sikkema WK, Woodside MT. Conformational dynamics of the frameshift stimulatory structure in HIV-1. Rna (New York, N.Y.). PMID 28522581 DOI: 10.1261/Rna.061655.117  0.77
2017 Neupane K, Wang F, Woodside MT. Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28115714 DOI: 10.1073/Pnas.1611602114  0.356
2017 Hoffer NQ, Neupane K, Woodside MT. Direct Observation of Transition-State Dynamics during Folding Reactions Biophysical Journal. 112: 166a. DOI: 10.1016/J.Bpj.2016.11.913  0.416
2017 Ritchie DB, Tittle C, Rezajooei N, Rouleau L, Cappellano TR, Sikkema W, Woodside MT. Folding Heterogeneity in HIV-1 Frameshifting Hairpin Biophysical Journal. 112: 368a. DOI: 10.1016/J.Bpj.2016.11.1994  0.722
2016 Neupane K, Woodside MT. Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy. Biophysical Journal. PMID 27369870 DOI: 10.1016/J.Bpj.2016.06.011  0.452
2016 Gupta AN, Neupane K, Rezajooei N, Cortez LM, Sim VL, Woodside MT. Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein. Nature Communications. 7: 12058. PMID 27346148 DOI: 10.1038/Ncomms12058  0.406
2016 Dee DR, Woodside MT. Comparing the energy landscapes for native folding and aggregation of PrP. Prion. 0. PMID 27191683 DOI: 10.1080/19336896.2016.1173297  0.391
2016 Neupane K, Foster DA, Dee DR, Yu H, Wang F, Woodside MT. Direct observation of transition paths during the folding of proteins and nucleic acids. Science (New York, N.Y.). 352: 239-242. PMID 27124461 DOI: 10.1126/Science.Aad0637  0.399
2016 Neupane K, Manuel AP, Woodside MT. Protein folding trajectories can be described quantitatively by one-dimensional diffusion over measured energy landscapes Nature Physics. DOI: 10.1038/Nphys3677  0.349
2016 Sen Mojumdar S, Dee DR, Rouleau L, Anand U, Garen C, Woodside MT. Multiple Intermediates in the Folding of Superoxide Dismutase 1 Revealed by Single Molecule Force Spectroscopy Biophysical Journal. 110: 497a. DOI: 10.1016/J.Bpj.2015.11.2657  0.429
2016 Neupane KP, Manuel AP, Lambert J, Woodside M. Testing the Physical Theory of Folding as Diffusive Motion over an Energy Landscape using Transition Path Analysis of Single-Molecule Folding Trajectories Biophysical Journal. 110: 194a. DOI: 10.1016/J.Bpj.2015.11.1080  0.403
2015 Neupane K, Manuel AP, Lambert J, Woodside MT. Transition-Path Probability as a Test of Reaction-Coordinate Quality Reveals DNA Hairpin Folding Is a One-Dimensional Diffusive Process. The Journal of Physical Chemistry Letters. 6: 1005-10. PMID 26262860 DOI: 10.1021/Acs.Jpclett.5B00176  0.325
2015 Ritchie DB, Woodside MT. Probing the structural dynamics of proteins and nucleic acids with optical tweezers. Current Opinion in Structural Biology. 34: 43-51. PMID 26189090 DOI: 10.1016/J.Sbi.2015.06.006  0.426
2015 Yu H, Dee DR, Liu X, Brigley AM, Sosova I, Woodside MT. Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 26109573 DOI: 10.1073/Pnas.1419197112  0.394
2015 Manuel AP, Lambert J, Woodside MT. Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories. Proceedings of the National Academy of Sciences of the United States of America. 112: 7183-8. PMID 26039984 DOI: 10.1073/Pnas.1419490112  0.418
2015 Neupane KP, Gupta AN, Rezajooei N, Woodside MT. Anti-Prion Ligand Binding Promotes Native PrP Folding Over Misfolding at the Single Molecule Level Biophysical Journal. 108: 204a. DOI: 10.1016/J.Bpj.2014.11.1127  0.386
2014 Engel MC, Ritchie DB, Foster DA, Beach KS, Woodside MT. Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform. Physical Review Letters. 113: 238104. PMID 25526163 DOI: 10.1103/Physrevlett.113.238104  0.385
2014 Woodside MT, Lambert J, Beach KS. Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements. Biophysical Journal. 107: 1647-53. PMID 25296317 DOI: 10.1016/J.Bpj.2014.08.007  0.432
2014 Woodside MT, Block SM. Reconstructing folding energy landscapes by single-molecule force spectroscopy. Annual Review of Biophysics. 43: 19-39. PMID 24895850 DOI: 10.1146/Annurev-Biophys-051013-022754  0.629
2014 Solanki A, Neupane K, Woodside MT. Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein α-synuclein. Physical Review Letters. 112: 158103. PMID 24785077 DOI: 10.1103/Physrevlett.112.158103  0.456
2014 Neupane K, Solanki A, Sosova I, Belov M, Woodside MT. Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy. Plos One. 9: e86495. PMID 24475132 DOI: 10.1371/Journal.Pone.0086495  0.402
2014 Ritchie DB, Soong J, Sikkema WK, Woodside MT. Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot. Journal of the American Chemical Society. 136: 2196-9. PMID 24446874 DOI: 10.1021/Ja410344B  0.752
2014 Woodside M. Diverse Transient Structures in Small Oligomers of α-Synuclein Probed by Single-Molecule Force Spectroscopy Biophysical Journal. 106: 5a. DOI: 10.1016/J.Bpj.2013.11.059  0.435
2013 Hoffmann A, Neupane K, Woodside MT. Single-molecule assays for investigating protein misfolding and aggregation. Physical Chemistry Chemical Physics : Pccp. 15: 7934-48. PMID 23612887 DOI: 10.1039/C3Cp44564J  0.362
2013 Yu H, Dee DR, Woodside MT. Single-molecule approaches to prion protein misfolding. Prion. 7: 140-6. PMID 23357831 DOI: 10.4161/Pri.23303  0.429
2013 Yu H, Dee D, Liu X, Brigley AM, Sosova I, Woodside MT. Multistep Pathway to Stable Misfolded Structures Observed in Single Prion Protein Dimers by Force Spectroscopy Biophysical Journal. 104: 167a-168a. DOI: 10.1016/J.Bpj.2012.11.943  0.426
2013 Neupane K, Yu H, Ritchie D, Gupta AN, Liu X, Foster DA, Wang F, Sosova I, Brigley AM, Woodside MT. Transition Path Times for the Folding of Nucleic Acids and Proteins Determined from Experimentally-Reconstructed Energy Landscape Profiles Biophysical Journal. 104: 165a. DOI: 10.1016/J.Bpj.2012.11.932  0.415
2012 Neupane K, Ritchie DB, Yu H, Foster DA, Wang F, Woodside MT. Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories. Physical Review Letters. 109: 068102. PMID 23006308 DOI: 10.1103/Physrevlett.109.068102  0.383
2012 Ritchie DB, Foster DA, Woodside MT. Programmed -1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding. Proceedings of the National Academy of Sciences of the United States of America. 109: 16167-72. PMID 22988073 DOI: 10.1073/Pnas.1204114109  0.407
2012 Yu H, Gupta AN, Liu X, Neupane K, Brigley AM, Sosova I, Woodside MT. Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates. Proceedings of the National Academy of Sciences of the United States of America. 109: 14452-7. PMID 22908253 DOI: 10.1073/Pnas.1206190109  0.412
2012 Yu H, Liu X, Neupane K, Gupta AN, Brigley AM, Solanki A, Sosova I, Woodside MT. Direct observation of multiple misfolding pathways in a single prion protein molecule. Proceedings of the National Academy of Sciences of the United States of America. 109: 5283-8. PMID 22421432 DOI: 10.1073/Pnas.1107736109  0.442
2012 Ritchie DB, Foster DA, Woodside MT. Frameshifting Efficiency is not Determined by the Mechanical Stability of RNA Pseudoknots Biophysical Journal. 102: 646a. DOI: 10.1016/J.Bpj.2011.11.3516  0.427
2012 Neupane KP, Solanki A, Sosova I, Belov M, Woodside M. Force Spectroscopy of α-Synuclein Oligomers Reveals Rapid Formation of Stable Structures Biophysical Journal. 102: 629a-630a. DOI: 10.1016/J.Bpj.2011.11.3429  0.37
2012 Woodside MT, Hoffmann A. Folding Dynamics and Kinetic Schemes from Signal-Pair Correlation Analysis of Single-Molecule Trajectories Biophysical Journal. 102: 387a. DOI: 10.1016/J.Bpj.2011.11.2115  0.388
2011 Hoffmann A, Woodside MT. Signal-pair correlation analysis of single-molecule trajectories. Angewandte Chemie (International Ed. in English). 50: 12643-6. PMID 22057589 DOI: 10.1002/Anie.201104033  0.328
2011 Neupane K, Yu H, Foster DA, Wang F, Woodside MT. Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Research. 39: 7677-87. PMID 21653559 DOI: 10.1093/Nar/Gkr305  0.462
2011 Gupta AN, Vincent A, Neupane K, Yu H, Wang F, Woodside MT. Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements Nature Physics. 7: 631-634. DOI: 10.1038/Nphys2022  0.394
2011 Yu H, Liu X, Brigley AM, Solanki A, Gupta AN, Sosova I, Woodside MT. Force Spectroscopy of Mammalian Prion Protein Folding and Misfolding Biophysical Journal. 100: 23a. DOI: 10.1016/J.Bpj.2010.12.332  0.416
2011 Vincent A, Gupta AN, Neupane K, Yu H, Woodside M. Experimental Validation of Free Energy Landscape Reconstructions from Non-Equilibrium Single-Molecule Pulling Experiments Biophysical Journal. 100: 484a. DOI: 10.1016/J.Bpj.2010.12.2836  0.443
2011 Neupane KP, Yu H, Foster DA, Wang F, Woodside MT. Force Spectroscopy of Add Adenine Riboswitch Aptamer Folding Reveals Multiple Intermediate and Misfolded States Biophysical Journal. 100: 483a. DOI: 10.1016/J.Bpj.2010.12.2830  0.42
2008 Woodside MT, García-García C, Block SM. Folding and unfolding single RNA molecules under tension. Current Opinion in Chemical Biology. 12: 640-6. PMID 18786653 DOI: 10.1016/J.Cbpa.2008.08.011  0.625
2008 Greenleaf WJ, Frieda KL, Foster DA, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science (New York, N.Y.). 319: 630-3. PMID 18174398 DOI: 10.1126/Science.1151298  0.723
2007 Greenleaf WJ, Woodside MT, Block SM. High-resolution, single-molecule measurements of biomolecular motion. Annual Review of Biophysics and Biomolecular Structure. 36: 171-90. PMID 17328679 DOI: 10.1146/Annurev.Biophys.36.101106.101451  0.681
2007 Greenleaf WJ, Frieda KL, Abbondanzieri EA, Woodside MT, Block SM. High-resolution, single-molecule optical trapping measurements of transcription with basepair accuracy: Instrumentation and methods Proceedings of Spie - the International Society For Optical Engineering. 6644. DOI: 10.1117/12.739631  0.751
2006 Woodside MT, Anthony PC, Behnke-Parks WM, Larizadeh K, Herschlag D, Block SM. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (New York, N.Y.). 314: 1001-4. PMID 17095702 DOI: 10.1126/Science.1133601  0.611
2006 Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proceedings of the National Academy of Sciences of the United States of America. 103: 6190-5. PMID 16606839 DOI: 10.1073/Pnas.0511048103  0.617
2005 Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM. Passive all-optical force clamp for high-resolution laser trapping. Physical Review Letters. 95: 208102. PMID 16384102 DOI: 10.1103/Physrevlett.95.208102  0.759
2002 Woodside MT, McEuen PL. Scanned probe imaging of single-electron charge states in nanotube quantum dots. Science (New York, N.Y.). 296: 1098-101. PMID 12004123 DOI: 10.1126/Science.1069923  0.551
2001 Woodside MT, Vale C, McEuen PL, Kadow C, Maranowski KD, Gossard AC. Imaging interedge-state scattering centers in the quantum Hall regime Physical Review B - Condensed Matter and Materials Physics. 64: 413101-413104. DOI: 10.1103/Physrevb.64.041310  0.548
2001 McEuen PL, Park J, Bachtold A, Woodside M, Fuhrer MS, Bockrath M, Shi L, Majumdar A, Kim P. Nanotube nanoelectronics Annual Device Research Conference Digest. 107-110.  0.432
2000 Woodside MT, Vale C, McCormick KL, McEuen PL, Kadow C, Maranowski KD, Gossard AC. Scanned potential microscopy of edge states in a quantum Hall liquid Physica E: Low-Dimensional Systems and Nanostructures. 6: 238-241. DOI: 10.1016/S1386-9477(99)00115-0  0.507
1999 McCormick KL, Woodside MT, Huang M, Wu M, McEuen PL, Duruoz C, Harris JS. Scanned potential microscopy of edge and bulk currents in the quantum Hall regime Physical Review B - Condensed Matter and Materials Physics. 59: 4654-4657. DOI: 10.1103/Physrevb.59.4654  0.546
1998 McCormick KL, Woodside MT, Huang M, McEuen PL, Duruoz CI, Harris JS. Scanned potential microscopy of a two-dimensional electron gas Physica B: Condensed Matter. 249: 79-83. DOI: 10.1016/S0921-4526(98)00071-4  0.551
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