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Mark Bathe, Ph.D. - Publications

Affiliations: 
2009- Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Website:
http://be.mit.edu/directory/mark-bathe
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Year Citation  Score
2023 Chen C, Luo X, Kaplan AEK, Bawendi MG, Macfarlane RJ, Bathe M. Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision. Science Advances. 9: eadh8508. PMID 37566651 DOI: 10.1126/sciadv.adh8508  0.302
2023 Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering Exciton Dynamics with Synthetic DNA Scaffolds. Accounts of Chemical Research. PMID 37345736 DOI: 10.1021/acs.accounts.3c00086  0.737
2023 Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. Nature Reviews. Materials. 8: 123-138. PMID 37206669 DOI: 10.1038/s41578-022-00517-x  0.357
2023 Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nature Communications. 14: 382. PMID 36693871 DOI: 10.1038/s41467-023-36156-1  0.678
2022 Du RR, Cedrone E, Romanov A, Falkovich R, Dobrovolskaia MA, Bathe M. Innate Immune Stimulation Using 3D Wireframe DNA Origami. Acs Nano. PMID 36459697 DOI: 10.1021/acsnano.2c06275  0.306
2022 Hart SM, Banal JL, Castellanos MA, Markova L, Vyborna Y, Gorman J, Häner R, Willard AP, Bathe M, Schlau-Cohen GS. Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds. Chemical Science. 13: 13020-13031. PMID 36425503 DOI: 10.1039/d2sc02759c  0.809
2022 Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M. Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nature Communications. 13: 4935. PMID 35999227 DOI: 10.1038/s41467-022-32662-w  0.816
2022 Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. Acs Nano. PMID 35640255 DOI: 10.1021/acsnano.1c11575  0.326
2022 Wang X, Li S, Jun H, John T, Zhang K, Fowler H, Doye JPK, Chiu W, Bathe M. Planar 2D wireframe DNA origami. Science Advances. 8: eabn0039. PMID 35594345 DOI: 10.1126/sciadv.abn0039  0.684
2022 Wei X, Chen C, Zhao Y, Harazinska E, Bathe M, Hernandez R. Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots. Acs Nano. PMID 35405067 DOI: 10.1021/acsnano.2c01178  0.305
2022 Wang X, Jun H, Bathe M. Programming 2D Supramolecular Assemblies with Wireframe DNA Origami. Journal of the American Chemical Society. PMID 35230115 DOI: 10.1021/jacs.1c11332  0.701
2022 Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS. Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds. The Journal of Physical Chemistry Letters. 13: 1863-1871. PMID 35175058 DOI: 10.1021/acs.jpclett.1c03848  0.695
2021 Adendorff MR, Tang GQ, Millar DP, Bathe M, Bricker WP. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Research. PMID 34935970 DOI: 10.1093/nar/gkab1246  0.785
2021 Banal JL, Bathe M. Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules. Acs Applied Materials & Interfaces. PMID 34652142 DOI: 10.1021/acsami.1c14985  0.735
2021 Jun H, Wang X, Parsons MF, Bricker WP, John T, Li S, Jackson S, Chiu W, Bathe M. Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. Nucleic Acids Research. PMID 34508356 DOI: 10.1093/nar/gkab762  0.828
2021 Knappe GA, Wamhoff EC, Read BJ, Irvine DJ, Bathe M. Covalent Functionalization of DNA Origami Virus-like Particles. Acs Nano. PMID 34490781 DOI: 10.1021/acsnano.1c03158  0.327
2021 Banal JL, Shepherd TR, Berleant J, Huang H, Reyes M, Ackerman CM, Blainey PC, Bathe M. Random access DNA memory using Boolean search in an archival file storage system. Nature Materials. PMID 34112975 DOI: 10.1038/s41563-021-01021-3  0.787
2020 Dobrovolskaia MA, Bathe M. Opportunities and challenges for the clinical translation of structured DNA assemblies as gene therapeutic delivery and vaccine vectors. Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology. e1657. PMID 32672007 DOI: 10.1002/Wnan.1657  0.366
2020 Veneziano R, Moyer TJ, Stone MB, Wamhoff EC, Read BJ, Mukherjee S, Shepherd TR, Das J, Schief WR, Irvine DJ, Bathe M. Role of nanoscale antigen organization on B-cell activation probed using DNA origami. Nature Nanotechnology. PMID 32601450 DOI: 10.1038/S41565-020-0719-0  0.683
2020 Hart SM, Banal JL, Bathe M, Schlau-Cohen GS. Identification of Non-Radiative Decay Pathways in Cy3. The Journal of Physical Chemistry Letters. PMID 32484350 DOI: 10.1021/Acs.Jpclett.0C01201  0.762
2019 Jun H, Wang X, Bricker WP, Bathe M. Automated sequence design of 2D wireframe DNA origami with honeycomb edges. Nature Communications. 10: 5419. PMID 31780654 DOI: 10.1038/S41467-019-13457-Y  0.828
2019 Guo SM, Veneziano R, Gordonov S, Li L, Danielson E, Perez de Arce K, Park D, Kulesa AB, Wamhoff EC, Blainey PC, Boyden ES, Cottrell JR, Bathe M. Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes. Nature Communications. 10: 4377. PMID 31558769 DOI: 10.1038/S41467-019-12372-6  0.673
2019 Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annual Review of Biophysics. 48: 395-419. PMID 31084582 DOI: 10.1146/Annurev-Biophys-052118-115259  0.812
2019 Shepherd TR, Du RR, Huang H, Wamhoff EC, Bathe M. Bioproduction of pure, kilobase-scale single-stranded DNA. Scientific Reports. 9: 6121. PMID 30992517 DOI: 10.1038/S41598-019-42665-1  0.436
2019 Jun H, Zhang F, Shepherd T, Ratanalert S, Qi X, Yan H, Bathe M. Autonomously designed free-form 2D DNA origami. Science Advances. 5: eaav0655. PMID 30613779 DOI: 10.1126/Sciadv.Aav0655  0.821
2019 Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. Acs Nano. PMID 30605605 DOI: 10.1021/Acsnano.8B08671  0.816
2019 Veneziano R, Moyer T, Stone MB, Kumari S, Schief WR, Bathe M, Irvine D. Probing the Role of HIV Antigen Nanoscale Organization on B-Cell Activation with DNA Origami Biophysical Journal. 116: 578a. DOI: 10.1016/J.Bpj.2018.11.3109  0.697
2018 Boulais É, Sawaya NPD, Veneziano R, Andreoni A, Banal JL, Kondo T, Mandal S, Lin S, Schlau-Cohen GS, Woodbury NW, Yan H, Aspuru-Guzik A, Bathe M. Programmed coherent coupling in a synthetic DNA-based excitonic circuit. Nature Materials. 17: 159-166. PMID 31745283 DOI: 10.1038/nmat5033  0.321
2018 Bricker WP, Banal JL, Stone MB, Bathe M. Molecular model of J-aggregated pseudoisocyanine fibers. The Journal of Chemical Physics. 149: 024905. PMID 30007374 DOI: 10.1063/1.5036656  0.763
2018 Veneziano R, Shepherd TR, Ratanalert S, Bellou L, Tao C, Bathe M. In vitro synthesis of gene-length single-stranded DNA. Scientific Reports. 8: 6548. PMID 29695837 DOI: 10.1038/S41598-018-24677-5  0.808
2018 Guo S, Li L, Veneziano R, Gordonov S, Cottrell JR, Bathe M. Multiplexed Imaging of Neuronal Synapses Using Nucleic Acid Probe Exchange Protocol Exchange. DOI: 10.1038/Protex.2018.066  0.655
2017 Boulais É, Sawaya NPD, Veneziano R, Andreoni A, Banal JL, Kondo T, Mandal S, Lin S, Schlau-Cohen GS, Woodbury NW, Yan H, Aspuru-Guzik A, Bathe M. Programmed coherent coupling in a synthetic DNA-based excitonic circuit. Nature Materials. PMID 29180771 DOI: 10.1038/Nmat5033  0.795
2017 Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS. Photophysics of J-Aggregate-Mediated Energy Transfer on DNA. The Journal of Physical Chemistry Letters. 5827-5833. PMID 29144136 DOI: 10.1021/Acs.Jpclett.7B01898  0.806
2017 Cunningham PD, Bricker WP, Díaz SA, Medintz IL, Bathe M, Melinger JS. Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA. The Journal of Chemical Physics. 147: 055101. PMID 28789556 DOI: 10.1063/1.4995431  0.788
2017 Pan K, Bricker WP, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Research. PMID 28482032 DOI: 10.1093/Nar/Gkx378  0.817
2017 Bathe M, Rothemund PWK. DNA Nanotechnology: A foundation for Programmable Nanoscale Materials Mrs Bulletin. 42: 882-888. DOI: 10.1557/Mrs.2017.279  0.455
2017 Bricker W, Pan K, Bathe M. Multi-Scale Structure and Conformational Dynamics of Scaffolded DNA Origami Nanoparticles Biophysical Journal. 112: 70a-71a. DOI: 10.1016/J.Bpj.2016.11.425  0.799
2017 Veneziano R, Bathe M. Structured DNA Nanoparticles for Spatially Controlled Antigen Presentation Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.3183  0.72
2017 Ratanalert S, Veneziano R, Bathe M. DNA Nanoparticles Programmed from the Top Down with Variable Design Motifs Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.172  0.832
2016 Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W, Bathe M. Designer nanoscale DNA assemblies programmed from the top down. Science (New York, N.Y.). PMID 27229143 DOI: 10.1126/Science.Aaf4388  0.837
2016 Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials. Journal of the American Chemical Society. PMID 27224641 DOI: 10.1021/Jacs.6B03966  0.83
2016 Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales. Interface Focus. 6: 20150081. PMID 26855758 DOI: 10.1098/Rsfs.2015.0081  0.304
2016 Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale. PMID 26788713 DOI: 10.1039/C5Nr07263H  0.47
2016 Ratanalert S, Bathe M. Staple-Free DNA Self-Assembly Biophysical Journal. 110: 565. DOI: 10.1016/J.Bpj.2015.11.3026  0.777
2016 Ratanalert S, Veneziano R, Zhang K, Pan K, Zhang F, Chiu W, Yan H, Bathe M. Structure-Based Design, Synthesis, and Characterization of Custom DNA Nanoparticles Biophysical Journal. 110: 565a. DOI: 10.1016/J.Bpj.2015.11.3025  0.821
2016 Adendorff MR, Bathe M. Base-Pair Level Analysis of DNA Four-Way Junction Structure and Dynamics Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.3010  0.417
2016 Barry ZT, Garner E, Bathe M. Heterogeneous Molecular Dynamics Revealed through Live, Single-Cell Imaging Biophysical Journal. 110: 468a. DOI: 10.1016/J.Bpj.2015.11.2504  0.32
2016 Boulais E, Sawaya N, Veneziano R, Andreoni A, Lin S, Woodbury N, Yan H, Aspuru-Guzik A, Bathe M. A DNA-Based Building Block for Designer Excitonic Circuits Biophysical Journal. 110: 313a. DOI: 10.1016/J.Bpj.2015.11.1681  0.775
2016 Pan K, Bathe M. Modeling Secondary Structural Elements in Programmed DNA Assemblies Biophysical Journal. 110: 183a. DOI: 10.1016/J.Bpj.2015.11.1022  0.463
2015 Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M. Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies. Journal of Chemical Theory and Computation. PMID 26636351 DOI: 10.1021/Acs.Jctc.5B00965  0.463
2015 Boulais É, Sun W, Sawaya N, Hakobyan Y, Wang W, Guan A, Pan K, Aspuru-Guzik A, Yin P, Bathe M. Programming Nanophotonic Materials with DNA Biophysical Journal. 108: 605a. DOI: 10.1016/J.Bpj.2014.11.3295  0.493
2015 Guo S, Veneziano R, McConnell RE, Agasti S, Gordonov S, Kulesa T, Gertler FB, Blainey P, Boyden E, Yin P, Bathe M. Quantitative Multiplexed Super-Resolution Neuronal Synapse Imaging using DNA-Paint Biophysical Journal. 108: 477a. DOI: 10.1016/J.Bpj.2014.11.2609  0.714
2015 Adendorff MR, Bathe M. Molecular Dynamics Investigation of Immobile DNA Four-Way Junctions Biophysical Journal. 108: 394a. DOI: 10.1016/J.Bpj.2014.11.2159  0.4
2015 Sedeh R, Pan K, Adendorff M, Hallatschek O, Bathe K, Bathe M. Brownian Dynamics of Folded DNA and Protein Assemblies Biophysical Journal. 108: 232a. DOI: 10.1016/J.Bpj.2014.11.1284  0.416
2015 Pan K, Kim D, Zhang F, Adendorff M, Yan H, Bathe M. Lattice-Free 3D Structure-Prediction of Programmed DNA Assemblies Biophysical Journal. 108: 232a. DOI: 10.1016/J.Bpj.2014.11.1283  0.756
2015 Dhakal S, Liu M, Adendorff MR, Bathe M, Yan H, Walter NG. Mechanical Modulation of Enzyme Activity by Rationally Designed DNA Tweezers: From the Ensemble to the Single-Molecule Level Biophysical Journal. 108: 186a-187a. DOI: 10.1016/J.Bpj.2014.11.1030  0.403
2014 Pan K, Kim DN, Zhang F, Adendorff MR, Yan H, Bathe M. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nature Communications. 5: 5578. PMID 25470497 DOI: 10.1038/Ncomms6578  0.732
2014 Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A, Bathe M, Yin P. Casting inorganic structures with DNA molds. Science (New York, N.Y.). 346: 1258361. PMID 25301973 DOI: 10.1126/Science.1258361  0.42
2014 Oh HS, Bryant KF, Nieland TJ, Mazumder A, Bagul M, Bathe M, Root DE, Knipe DM. A targeted RNA interference screen reveals novel epigenetic factors that regulate herpesviral gene expression. Mbio. 5: e01086-13. PMID 24496796 DOI: 10.1128/Mbio.01086-13  0.706
2014 Pan K, Boulais E, Yang L, Bathe M. Structure-based model for light-harvesting properties of nucleic acid nanostructures. Nucleic Acids Research. 42: 2159-70. PMID 24311563 DOI: 10.1093/Nar/Gkt1269  0.504
2013 Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA. H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation. Plos Genetics. 9: e1003725. PMID 23990805 DOI: 10.1371/Journal.Pgen.1003725  0.708
2013 Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Research. 41: 9310-24. PMID 23935119 DOI: 10.1093/Nar/Gkt715  0.75
2013 Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter NG. Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Letters. 13: 728-33. PMID 23356935 DOI: 10.1021/Nl304415B  0.691
2013 Mazumder A, Tummler K, Bathe M, Samson LD. Single-cell analysis of ribonucleotide reductase transcriptional and translational response to DNA damage. Molecular and Cellular Biology. 33: 635-42. PMID 23184665 DOI: 10.1128/Mcb.01020-12  0.745
2013 Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA. Disruption of H2A.Z acidic patch increases chromatin dynamics in a transcription-dependent manner. Plos Genetics. DOI: 10.1371/Journal.Pgen.1003725.G005  0.708
2013 Guo S, Ma X, Bag N, Monnier N, He J, Wohland T, Bathe M. Bayesian Fluorescence Correlation Microscopy to Resolve Heterogeneity in Membrane Protein Dynamics Biophysical Journal. 104: 683a. DOI: 10.1016/J.Bpj.2012.11.3769  0.323
2013 Pan K, Bathe M. Bayesian Reconstruction of Chromatin Conformation from FISH and Hi-C Data Biophysical Journal. 104: 581a. DOI: 10.1016/J.Bpj.2012.11.3228  0.33
2013 Kim D, Adendorff MR, Pan K, Bathe M. Biophysical Modeling of Nucleic Acid Nanostructure Solution Shape and Stability Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.193  0.757
2013 Sharifi Sedeh R, Hallatschek O, Bathe K, Bathe M. Dynamics of High Molecular Weight Macromolecular Assemblies Biophysical Journal. 104: 227a. DOI: 10.1016/J.Bpj.2012.11.1283  0.372
2012 Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends in Cell Biology. 22: 624-33. PMID 23140833 DOI: 10.1016/J.Tcb.2012.10.001  0.354
2012 Kim DN, Kilchherr F, Dietz H, Bathe M. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Research. 40: 2862-8. PMID 22156372 DOI: 10.1093/Nar/Gkr1173  0.75
2012 Diesinger PM, Fritsche M, Pan K, Heermann D, Bathe M. Chromatin Architecture Reconstruction Biophysical Journal. 102: 482a. DOI: 10.1016/J.Bpj.2011.11.2644  0.302
2011 Castro CE, Kilchherr F, Kim DN, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H. A primer to scaffolded DNA origami. Nature Methods. 8: 221-9. PMID 21358626 DOI: 10.1038/Nmeth.1570  0.742
2011 Kim DN, Altschuler J, Strong C, McGill G, Bathe M. Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. Nucleic Acids Research. 39: D451-5. PMID 21051356 DOI: 10.1093/Nar/Gkq1088  0.668
2011 Kim DN, Nguyen CT, Bathe M. Conformational dynamics of supramolecular protein assemblies. Journal of Structural Biology. 173: 261-70. PMID 20854912 DOI: 10.1016/J.Jsb.2010.09.015  0.69
2011 Sedeh R, Fedorov A, Fedorov E, Ono S, Matsumura F, Almo S, Bathe M. Structure, Conformational Dynamics, and Evolutionary Conservation of Human Fascin-1 Biophysical Journal. 100: 34a. DOI: 10.1016/J.Bpj.2010.12.389  0.304
2011 Kim D, Nguyen C, Bathe M. Conformational Dynamics and Allostery of Supramolecular Protein Assemblies: from the Nuclear Pore Complex to GroEL Biophysical Journal. 100: 172a. DOI: 10.1016/J.Bpj.2010.12.1163  0.683
2010 Sedeh RS, Fedorov AA, Fedorov EV, Ono S, Matsumura F, Almo SC, Bathe M. Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein. Journal of Molecular Biology. 400: 589-604. PMID 20434460 DOI: 10.1016/J.Jmb.2010.04.043  0.307
2010 Bathe M, Chang F. Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding. Trends in Microbiology. 18: 38-45. PMID 19959363 DOI: 10.1016/J.Tim.2009.10.002  0.324
2009 Bathe M. Towards a Molecular Understanding of Actin Bundle Stability and Mechanics Biophysical Journal. 96: 3-7. DOI: 10.1016/J.Bpj.2008.12.2894  0.311
2008 Bathe M, Heussinger C, Claessens MM, Bausch AR, Frey E. Cytoskeletal bundle mechanics. Biophysical Journal. 94: 2955-64. PMID 18055529 DOI: 10.1529/Biophysj.107.119743  0.301
2008 Bathe M. A finite element framework for computation of protein normal modes and mechanical response. Proteins. 70: 1595-609. PMID 17975833 DOI: 10.1002/Prot.21708  0.303
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation. Biophysical Journal. 89: 2357-71. PMID 16055525 DOI: 10.1529/Biophysj.105.067918  0.744
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophysical Journal. 88: 3870-87. PMID 15805173 DOI: 10.1529/Biophysj.104.058800  0.764
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Effects of chemical composition on chondroitin sulfate osmotic pressure and aggrecan conformation Proceedings of the 2005 Summer Bioengineering Conference. 2005: 667-668.  0.583
2004 Bathe M, Grodzinsky AJ, Tidor B, Rutledge GC. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. The Journal of Chemical Physics. 121: 7557-61. PMID 15485214 DOI: 10.1063/1.1808411  0.75
2003 Bathe M, Rutledge GC. Inverse Monte Carlo procedure for conformation determination of macromolecules. Journal of Computational Chemistry. 24: 876-90. PMID 12692797 DOI: 10.1002/Jcc.10246  0.53
2003 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Towards a multi-scale model of cartilage: Coarse-graining glycosaminoglycans Computational Fluid and Solid Mechanics 2003. 1626-1630. DOI: 10.1016/B978-008044046-0.50396-1  0.667
Low-probability matches (unlikely to be authored by this person)
2012 Guo SM, He J, Monnier N, Sun G, Wohland T, Bathe M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data II: application to simulated and in vitro data. Analytical Chemistry. 84: 3880-8. PMID 22455375 DOI: 10.1021/Ac2034375  0.292
2015 Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger DA, Bathe M. Time series modeling of live-cell shape dynamics for image-based phenotypic profiling. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 26658688 DOI: 10.1039/C5Ib00283D  0.283
2015 Barry Z, Monnier N, Park HY, Su K, Katz Z, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M. Bayesian Classification of Mrna and Kinetochore Transport Dynamics Biophysical Journal. 108: 164a-165a. DOI: 10.1016/J.Bpj.2014.11.907  0.282
2012 He J, Guo SM, Bathe M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data I: theory. Analytical Chemistry. 84: 3871-9. PMID 22423978 DOI: 10.1021/Ac2034369  0.281
2011 He J, Bathe M. Objective, Bayesian Analysis of Fluorescence Correlation Spectroscopy Data Biophysical Journal. 100: 175a. DOI: 10.1016/J.Bpj.2010.12.1177  0.28
2023 Wamhoff EC, Knappe GA, Burds AA, Du RR, Neun BW, Difilippantonio S, Sanders C, Edmondson EF, Matta JL, Dobrovolskaia MA, Bathe M. Evaluation of non-modified wireframe DNA origami for acute toxicity and biodistribution in mice. Biorxiv : the Preprint Server For Biology. PMID 36909507 DOI: 10.1101/2023.02.25.530026  0.279
2015 Sun G, Guo SM, Teh C, Korzh V, Bathe M, Wohland T. Bayesian model selection applied to the analysis of fluorescence correlation spectroscopy data of fluorescent proteins in vitro and in vivo. Analytical Chemistry. 87: 4326-33. PMID 25815704 DOI: 10.1021/Acs.Analchem.5B00022  0.276
2011 Bransford P, Kamm R, Bathe M. Probing F-actin Stability and Mechanics using Structure-Based Computational Modeling Biophysical Journal. 100: 299a. DOI: 10.1016/J.Bpj.2010.12.1834  0.274
2023 Wamhoff EC, Knappe GA, Burds AA, Du RR, Neun BW, Difilippantonio S, Sanders C, Edmondson EF, Matta JL, Dobrovolskaia MA, Bathe M. Evaluation of Nonmodified Wireframe DNA Origami for Acute Toxicity and Biodistribution in Mice. Acs Applied Bio Materials. PMID 37040258 DOI: 10.1021/acsabm.3c00155  0.273
2006 Claessens MM, Bathe M, Frey E, Bausch AR. Actin-binding proteins sensitively mediate F-actin bundle stiffness. Nature Materials. 5: 748-53. PMID 16921360 DOI: 10.1038/Nmat1718  0.273
2012 Monnier N, Guo SM, Mori M, He J, Lénárt P, Bathe M. Bayesian approach to MSD-based analysis of particle motion in live cells. Biophysical Journal. 103: 616-26. PMID 22947879 DOI: 10.1016/J.Bpj.2012.06.029  0.272
2011 Diesinger P, Cherian A, Klingner C, Wedlich-Soldner R, Bathe M. Structure and Dynamics of Epithelial Cell Cortical Actomyosin Networks Biophysical Journal. 100: 446a. DOI: 10.1016/J.Bpj.2010.12.2630  0.271
2009 Sedeh RS, Bathe M, Bathe K. Accelerated Subspace Iteration Method for Protein Normal Mode Analysis Biophysical Journal. 96: 407a-408a. DOI: 10.1016/J.Bpj.2008.12.2078  0.271
2020 Afonin KA, Dobrovolskaia MA, Church G, Bathe M. Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology. Acs Nano. PMID 32706238 DOI: 10.1021/Acsnano.0C04753  0.266
2010 Sedeh RS, Bathe M, Bathe KJ. The subspace iteration method in protein normal mode analysis. Journal of Computational Chemistry. 31: 66-74. PMID 19408277 DOI: 10.1002/Jcc.21250  0.265
2019 Kulikov V, Guo SM, Stone M, Goodman A, Carpenter A, Bathe M, Lempitsky V. DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. Plos Computational Biology. 15: e1007012. PMID 31083649 DOI: 10.1371/Journal.Pcbi.1007012  0.265
2014 Mori M, Somogyi K, Kondo H, Monnier N, Falk HJ, Machado P, Bathe M, Nédélec F, Lénárt P. An Arp2/3 nucleated F-actin shell fragments nuclear membranes at nuclear envelope breakdown in starfish oocytes. Current Biology : Cb. 24: 1421-8. PMID 24909322 DOI: 10.1016/J.Cub.2014.05.019  0.265
2014 Guo SM, Bag N, Mishra A, Wohland T, Bathe M. Bayesian total internal reflection fluorescence correlation spectroscopy reveals hIAPP-induced plasma membrane domain organization in live cells. Biophysical Journal. 106: 190-200. PMID 24411251 DOI: 10.1016/J.Bpj.2013.11.4458  0.264
2003 Kaazempur-Mofrad MR, Bathe M, Karcher H, Younis HF, Seong HC, Shim EB, Chan RC, Hinton DP, Isasi AG, Upadhyaya A, Powers MJ, Griffith LG, Kamm RD. Role of simulation in understanding biological systems Computers and Structures. 81: 715-726. DOI: 10.1016/S0045-7949(02)00481-9  0.263
2015 Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F. The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis. Molecular Biology of the Cell. 26: 78-90. PMID 25355954 DOI: 10.1091/Mbc.E14-10-1441  0.262
2011 Strehle D, Schnauss J, Heussinger C, Alvarado J, Bathe M, Käs J, Gentry B. Transiently crosslinked F-actin bundles. European Biophysics Journal : Ebj. 40: 93-101. PMID 20734192 DOI: 10.1007/S00249-010-0621-Z  0.261
2014 Klingner C, Cherian AV, Fels J, Diesinger PM, Aufschnaiter R, Maghelli N, Keil T, Beck G, Toli?-Nørrelykke IM, Bathe M, Wedlich-Soldner R. Isotropic actomyosin dynamics promote organization of the apical cell cortex in epithelial cells. The Journal of Cell Biology. 207: 107-21. PMID 25313407 DOI: 10.1083/Jcb.201402037  0.26
2015 Monnier N, Barry Z, Park HY, Su KC, Katz Z, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M. Inferring transient particle transport dynamics in live cells. Nature Methods. 12: 838-40. PMID 26192083 DOI: 10.1038/Nmeth.3483  0.254
2022 Wamhoff EC, Ronsard L, Feldman J, Hauser BM, Knappe GA, Romanov A, Lam E, St Denis K, Balazs AB, Schmidt A, Lingwood D, Bathe M. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. Biorxiv : the Preprint Server For Biology. PMID 36032975 DOI: 10.1101/2022.08.16.504128  0.252
2013 Monnier N, Guo S, Dey A, Bathe M. Bayesian Inference to Discriminate Motion Models from Particle Trajectories Biophysical Journal. 104: 510a. DOI: 10.1016/J.Bpj.2012.11.2816  0.251
2012 Diesinger PM, Mori NMM, Lenart P, Bathe M. F-Actin Mediated Chromosome Transport Biophysical Journal. 102: 238a. DOI: 10.1016/J.Bpj.2011.11.1311  0.249
2011 Monnier N, Mori M, Daigle N, Ellenberg J, Lenart P, Bathe M. Quantitative Image Analysis and Modeling of Actin-Dependent Chromosome Transport in Starfish Oocytes Biophysical Journal. 100: 445a. DOI: 10.1016/J.Bpj.2010.12.2625  0.248
2007 Heussinger C, Bathe M, Frey E. Statistical mechanics of semiflexible bundles of wormlike polymer chains. Physical Review Letters. 99: 048101. PMID 17678408 DOI: 10.1103/Physrevlett.99.048101  0.248
2014 Bag N, Guo S, Mishra A, Bathe M, Wohland T. Bayesian Analysis of Imaging FCS Investigates the Interaction of Monomeric HIAPP with Live Cell Membrane Biophysical Journal. 106: 295a. DOI: 10.1016/J.Bpj.2013.11.1718  0.244
2011 Mori M, Monnier N, Daigle N, Bathe M, Ellenberg J, Lénárt P. Intracellular transport by an anchored homogeneously contracting F-actin meshwork. Current Biology : Cb. 21: 606-11. PMID 21439825 DOI: 10.1016/J.Cub.2011.03.002  0.241
2012 Schmidt JC, Arthanari H, Boeszoermenyi A, Dashkevich NM, Wilson-Kubalek EM, Monnier N, Markus M, Oberer M, Milligan RA, Bathe M, Wagner G, Grishchuk EL, Cheeseman IM. The kinetochore-bound Ska1 complex tracks depolymerizing microtubules and binds to curved protofilaments. Developmental Cell. 23: 968-80. PMID 23085020 DOI: 10.1016/J.Devcel.2012.09.012  0.236
2016 Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes. Elife. 5. PMID 26760529 DOI: 10.7554/Elife.10415  0.232
2002 Bathe M, Shirai A, Doerschuk CM, Kamm RD. Neutrophil transit times through pulmonary capillaries: the effects of capillary geometry and fMLP-stimulation. Biophysical Journal. 83: 1917-33. PMID 12324412 DOI: 10.1016/S0006-3495(02)73955-6  0.232
2015 Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Author response: Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes Elife. DOI: 10.7554/Elife.10415.028  0.231
1999 Bathe M, Kamm RD. A fluid--structure interaction finite element analysis of pulsatile blood flow through a compliant stenotic artery. Journal of Biomechanical Engineering. 121: 361-9. PMID 10464689 DOI: 10.1115/1.2798332  0.227
2024 Wamhoff EC, Ronsard L, Feldman J, Knappe GA, Hauser BM, Romanov A, Case JB, Sanapala S, Lam EC, Denis KJS, Boucau J, Barczak AK, Balazs AB, Diamond MS, Schmidt AG, ... ... Bathe M, et al. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. Nature Communications. 15: 795. PMID 38291019 DOI: 10.1038/s41467-024-44869-0  0.224
2018 Holec PV, Berleant J, Bathe M, Birnbaum ME. A Bayesian framework for high-throughput T cell receptor pairing. Bioinformatics (Oxford, England). PMID 30215679 DOI: 10.1093/Bioinformatics/Bty801  0.222
2016 Su KC, Barry Z, Schweizer N, Maiato H, Bathe M, Cheeseman IM. A Regulatory Switch Alters Chromosome Motions at the Metaphase-to-Anaphase Transition. Cell Reports. 17: 1728-1738. PMID 27829144 DOI: 10.1016/J.Celrep.2016.10.046  0.207
2022 Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SSY, Sun Y, Guo JU, Bathe M, Näär A, Griffiths A, Rouskin S. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nature Communications. 13: 1128. PMID 35236847 DOI: 10.1038/s41467-022-28603-2  0.155
2021 Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Advanced Drug Delivery Reviews. 181: 114081. PMID 34915069 DOI: 10.1016/j.addr.2021.114081  0.152
2021 Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications Biology. 4: 786. PMID 34168275 DOI: 10.1038/s42003-021-02276-x  0.127
2010 Kim DN, Sedeh RS, Nguyen CT, Bathe M. Finite element framework for mechanics and dynamics of supramolecular protein assemblies Proceedings of the Asme 1st Global Congress On Nanoengineering For Medicine and Biology 2010, Nemb2010. 315-316.  0.122
2016 Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales Interface Focus. 6. DOI: 10.1098/rsfs.2015.0081  0.117
2021 Bathe M, Hernandez R, Komiyama T, Machiraju R, Neogi S. Autonomous Computing Materials. Acs Nano. PMID 33636971 DOI: 10.1021/acsnano.0c09556  0.112
2015 Monnier N, Barry Z, Park HY, Su KC, Katz Z, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M. Inferring transient particle transport dynamics in live cells Nature Methods. DOI: 10.1038/nmeth.3483  0.106
2020 Danielson E, Perez de Arce K, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. Eneuro. PMID 33355295 DOI: 10.1523/ENEURO.0286-20.2020  0.103
2023 Falkovich R, Danielson EW, Perez de Arce K, Wamhoff EC, Strother J, Lapteva AP, Sheng M, Cottrell JR, Bathe M. A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging. Cell Reports. 42: 112430. PMID 37099425 DOI: 10.1016/j.celrep.2023.112430  0.097
2016 Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Mapping translation ’hot-spots’ in live cells by tracking single molecules of mRNA and ribosomes Elife. 5. DOI: 10.7554/eLife.10415.001  0.083
2014 Dörnhöfer A, Bathe M, Heuler P, Kraus M. Safety concept for structural durability of HV batteries | Absicherungskonzept für die Betriebsfestigkeit von HV-Speicherbatterien Materialpruefung/Materials Testing. 56: 550-558. DOI: 10.3139/120.110596  0.078
1999 Müller-Hülsbeck S, Bathe M, Grimm J, Heller M. Enhancement of in vitro effectiveness for hydrodynamic thrombectomy devices. Simultaneous high-pressure rt-PA application. Investigative Radiology. 34: 536-42. PMID 10434186 DOI: 10.1097/00004424-199908000-00007  0.073
2011 Moffat J, Bathe M, Frewer L. The Hybrid War Model: A complex adaptive model of complex urban conflict Journal of Simulation. 5: 58-68. DOI: 10.1057/jos.2010.2  0.066
2000 Kamm RD, McVittie AK, Bathe M. On the role of continuum models in mechanobiology American Society of Mechanical Engineers, Applied Mechanics Division, Amd. 242: 1-11.  0.065
1999 Müller-Hülsbeck S, Schwarzenberg H, Bathe M, Lüsse S, Hutzelmann A, Heller M. In vitro effectiveness study for hydrodynamic thrombectomy devices of the second generation. Investigative Radiology. 34: 477-84. PMID 10399638 DOI: 10.1097/00004424-199907000-00006  0.062
1996 Rogers RV, Zuda M, Mykytka E, Bartlett D, Bathe M. Modeling and simulation education: is there a need for graduate degrees in modeling and simulation? Winter Simulation Conference Proceedings. 1401-1406.  0.06
2000 Kamm R, Bathe M, McVittie A. Predicting intracellular stress using continuum computational models Annals of Biomedical Engineering. 28: S-89.  0.057
2010 Ioiart R, Searle J, Bathe M. Three techniques to improve the quality of DIS based crowd simulations 2010 International Simulation Multi-Conference. 151-156.  0.042
1984 Bathe M, Vagle S, Saunders GA, Lambson EF. Ultrasonic wave velocities in the structure II clathrate hydrate THF·17H2O Journal of Materials Science Letters. 3: 904-906. DOI: 10.1007/BF00719584  0.039
2023 Berleant J, Sheridan K, Condon A, Williams VV, Bathe M. Isometric Hamming embeddings of weighted graphs. Discrete Applied Mathematics (Amsterdam, Netherlands : 1988). 332: 119-128. PMID 37982050 DOI: 10.1016/j.dam.2023.02.005  0.038
2023 Sheridan K, Berleant J, Bathe M, Condon A, Williams VV. Factorization and pseudofactorization of weighted graphs. Discrete Applied Mathematics (Amsterdam, Netherlands : 1988). 337: 81-105. PMID 37213330 DOI: 10.1016/j.dam.2023.04.019  0.034
2020 Pisharady PK, Eberly LE, Cheong I, Manousakis G, Guliani G, Clark HB, Bathe M, Walk D, Lenglet C. Tract-specific analysis improves sensitivity of spinal cord diffusion MRI to cross-sectional and longitudinal changes in amyotrophic lateral sclerosis. Communications Biology. 3: 370. PMID 32651439 DOI: 10.1038/s42003-020-1093-z  0.034
1977 Bathe M. Engen's splint; experience with a flexor hinge splint for tetraplegics | ENGEN-SCHIENE, ERFAHRUNGEN MIT EINER FLEXOR-HINDGE-SCHIENE FUR TETRAPLEGIKER Beschaftigungstherapie Und Rehabilitation. 16: 182-183.  0.014
1977 Bathe M. Treatment of patients with spinal paralysis in the Conradie Hospital (South Africa) | BEHANDLUNG VON QUERSCHNITTGELAHMTEN IM CONRADIE HOSPITAL IN SUDAFRIKA Beschaftigungstherapie Und Rehabilitation. 16: 233-234.  0.01
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