Michael T. Woodside, Ph.D. - Publications

Affiliations: 
2001 University of California, Berkeley, Berkeley, CA 
 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

72 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
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  1
2021 Neupane K, Zhao M, Lyons A, Munshi S, Ileperuma SM, Ritchie DB, Hoffer NQ, Narayan A, Woodside MT. Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers. Nature Communications. 12: 4749. PMID 34362921 DOI: 10.1038/s41467-021-25085-6  1
2021 Zhao M, Woodside MT. Mechanical strength of RNA knot in Zika virus protects against cellular defenses. Nature Chemical Biology. PMID 34253909 DOI: 10.1038/s41589-021-00829-z  1
2021 Yu Wan W, Liu L, Liu X, Wang W, Zahurul Islam M, Dong C, Garen CR, Woodside MT, Gupta M, Mandal M, Rozmus W, Yin Tsui Y. Integration of light scattering with machine learning for label free cell detection. Biomedical Optics Express. 12: 3512-3529. PMID 34221676 DOI: 10.1364/BOE.424357  1
2021 Petrosyan R, Patra S, Rezajooei N, Garen CR, Woodside MT. Unfolded and intermediate states of PrP play a key role in the mechanism of action of an antiprion chaperone. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33619087 DOI: 10.1073/pnas.2010213118  1
2021 Halma MTJ, Ritchie DB, Woodside MT. Conformational Shannon Entropy of mRNA Structures from Force Spectroscopy Measurements Predicts the Efficiency of -1 Programmed Ribosomal Frameshift Stimulation. Physical Review Letters. 126: 038102. PMID 33543960 DOI: 10.1103/PhysRevLett.126.038102  1
2021 Shearer LJ, Petersen NO, Woodside MT. Internalization of α-synuclein oligomers into SH-SY5Y cells. Biophysical Journal. PMID 33515601 DOI: 10.1016/j.bpj.2020.12.031  1
2021 Omar SI, Zhao M, Sekar RV, Moghadam SA, Tuszynski JA, Woodside MT. Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. Plos Computational Biology. 17: e1008603. PMID 33465066 DOI: 10.1371/journal.pcbi.1008603  1
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  1
2020 Neupane K, Munshi S, Zhao M, Ritchie DB, Ileperuma SM, Woodside MT. Anti-Frameshifting Ligand Active against SARS Coronavirus-2 Is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot. Journal of Molecular Biology. PMID 32920049 DOI: 10.1016/J.Jmb.2020.09.006  1
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  1
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  1
2019 Pyo AGT, Woodside MT. Memory effects in single-molecule force spectroscopy measurements of biomolecular folding. Physical Chemistry Chemical Physics : Pccp. PMID 31663550 DOI: 10.1016/J.Bpj.2019.11.1301  1
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  0.01
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  1
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  1
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  1
2019 Dong C, Garen CR, Mercier P, Petersen NO, Woodside MT. Characterizing the inhibition of α-synuclein oligomerisation by a pharmacological chaperone that prevents prion formation by the protein PrP. Protein Science : a Publication of the Protein Society. PMID 31306510 DOI: 10.1002/Pro.3684  1
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  1
2019 Li X, Dong C, Hoffmann M, Garen CR, Cortez LM, Petersen NO, Woodside MT. Early stages of aggregation of engineered α-synuclein monomers and oligomers in solution. Scientific Reports. 9: 1734. PMID 30741954 DOI: 10.1038/S41598-018-37584-6  1
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  1
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  1
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  1
2018 Dong C, Hoffmann M, Li X, Wang M, Garen CR, Petersen NO, Woodside MT. Structural characteristics and membrane interactions of tandem α-synuclein oligomers. Scientific Reports. 8: 6755. PMID 29712958 DOI: 10.1038/S41598-018-25133-0  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Healey MA, Woodside MT, Tuszynski JA. Phase transitions and structure analysis in wild-type, A30P, E46K, and A53T mutants of α-synuclein. European Biophysics Journal : Ebj. PMID 26695014 DOI: 10.1007/S00249-015-1103-0  1
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  1
2015 Sahu KK, Woodside MT, Tuszynski JA. α-Synuclein dimer structures found from computational simulations. Biochimie. 116: 133-40. PMID 26193124 DOI: 10.1016/J.Biochi.2015.07.011  1
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  1
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  1
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  1
2015 Woodside MT. Structure formation in biological molecules as a diffusive process probed by optical tweezers Optical Trapping Applications, Ota 2015 1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Solez K, Bernier A, Crichton J, Graves H, Kuttikat P, Lockwood R, Marovitz WF, Monroe D, Pallen M, Pandya S, Pearce D, Saleh A, Sandhu N, Sergi C, Tuszynski J, ... Woodside M, et al. Bridging the gap between the technological singularity and mainstream medicine: highlighting a course on technology and the future of medicine. Global Journal of Health Science. 5: 112-25. PMID 24171879 DOI: 10.5539/Gjhs.V5N6P112  1
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  1
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  1
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  1
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  1
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  1
2012 Dee DR, Gupta AN, Anikovskiy M, Sosova I, Grandi E, Rivera L, Vincent A, Brigley AM, Petersen NO, Woodside MT. Phthalocyanine tetrasulfonates bind to multiple sites on natively-folded prion protein. Biochimica Et Biophysica Acta. 1824: 826-32. PMID 22480824 DOI: 10.1016/J.Bbapap.2012.03.011  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
1999 Aharonovitz O, Demaurex N, Woodside M, Grinstein S. ATP dependence is not an intrinsic property of Na+/H+ exchanger NHE1: requirement for an ancillary factor. The American Journal of Physiology. 276: C1303-11. PMID 10362593 DOI: 10.1152/Ajpcell.1999.276.6.C1303  1
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  1
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  1
1997 Robertson MA, Woodside M, Foskett JK, Orlowski J, Grinstein S. Muscarinic agonists induce phosphorylation-independent activation of the NHE-1 isoform of the Na+/H+ antiporter in salivary acinar cells. The Journal of Biological Chemistry. 272: 287-94. PMID 8995260 DOI: 10.1074/Jbc.272.1.287  1
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