Mark Bathe, Ph.D. - Publications

2009- Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 

70 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
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  0.52
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  0.6
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  0.6
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  1
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  0.6
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  1
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  0.48
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  0.52
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  1
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  1
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  0.6
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  1
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  0.6
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  0.6
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  0.6
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  1
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  1
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  0.6
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  1
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  1
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  0.48
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  1
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  1
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  1
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  1
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
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  1
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  1
2000 Kamm R, Bathe M, McVittie A. Predicting intracellular stress using continuum computational models Annals of Biomedical Engineering. 28: S-89.  1
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.  1
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  1
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