[54] Veneziano, R., Shepherd, T., Ratanalert, S., Tao, C., Bathe, M. Asymmetric Polymerase Chain Reaction for synthesis of gene-length single-stranded DNA. Submitted (2017).

[53] Ratanalert, S., Grimm, A., Bathe, M. pyDAEDALUS: Python implementation of the scaffolded DNA origami sequence design algorithm DAEDALUS. Submitted (2017).

[52] Boulais, E., Sawaya, N., Veneziano, R., Andreoni, A., Lin, S., Woodbury, N., Yan, H., Aspuru-Guzik, A., Bathe, M. Programmed coherent coupling in a DNA-based excitonic circuit. Submitted (2017).

[51] Banal, J.L., Kondo, T., Veneziano, R., Bathe, M., Schlau-Cohen, G.S. Photophysics of J-aggregate-mediated energy transfer on DNA. The Journal of Physical Chemistry Letters, in press (2017).

[50] Cunningham, P., Bricker, W., Diaz, S., Medintz, I., Bathe, M., and Melinger, J.S. Optical determination of the electronic coupling and intercalation geometry of Thiazole Orange homodimer in DNA. Journal of Chemical Physics, 147: 055101 (2017).

[49] Pan, K., Bricker, W., Ratanalert, S., Bathe, M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Research 45: 6284 (2017). [ PubMed Article ]

[48] Guo, S-M., Veneziano, R., Gordonov, S., Li, L., Park, D., Kulesa, A.B., Blainey, P.C., Cottrell, J.R., Boyden, E.S., Bathe, M. Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteins. bioRxiv, doi: 10.1101/111625 (2017). [ Article ]

[47] Su, K.C., Barry, Z., Schweizer, N., Maiato, H., Bathe, M., Cheeseman, I. A regulatory switch alters chromosome motions at the metaphase to anaphase transition. Cell Reports, 17: 728 (2016). [ PubMed Article ]

[46] Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M. Designer nanoscale DNA assemblies programmed from the top down. Science, 352: 1534 (2016). [ PubMed Article News ]

[45] Wang, P., Gaitanaros, S., Lee, S., Bathe, M., Shih, W.M., Ke, Y. Programming Self-Assembly of DNA Origami Honeycomb Lattices and Plasmonic Metamaterials. JACS, 138: 7733 (2016). [ PubMed Article ]

[44] Katz, Z.B., English, B.P., Lionnet, T., Yoon, Y.J., Monnier, N., Ovryn, B., Bathe, M., Singer, R.H. Mapping translation ‘hot-spots’ in live cells by tracking single molecules of mRNA and ribosomes. eLife, e10415 (2016). [ PubMed Article ]

[43] Dhakal, S., Adendorff, M., Liu, M., Yan, H., Bathe, M., Walter, N. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale, 8: 3125 (2016). [ PubMed Article ]

[42] Hogstrom, L., Guo, S.M., Murugadoss, K., Bathe, M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length-scales. Journal of The Royal Society Interface, 6: 20150081 (2016). [ PubMed Article ]

[41] Gordonov, S., Hwang, M.K., Wells, A., Gertler, F.B., Lauffenburger, D., Bathe, M. Time-series modeling of live-cell shape dynamics for image-based phenotypic profiling. Integrative Biology, 8: 73 (2016). [ PubMed Article ]

[40] Sedeh, R., Pan, K., Adendorff, M., Hallatschek, O., Bathe, K.J., Bathe, M. Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies. Journal of Chemical Theory & Computation, 12: 261 (2016). [ PubMed Article ]

[39] Monnier, N., Barry, Z., Park, H.Y., Su, K.C., Katz, Z., English, B., Dey, A., Pan, K., Cheeseman, I., Singer, R., Bathe, M. Inferring transient particle transport dynamics in live cells. Nature Methods, 12: 838 (2015). [ PubMed Article ]

[38] Sun, G., Guo, S.M., Teh, C., Korzh, V., Bathe, M., Wohland, T. Bayesian model selection applied to the analysis of FCS data of fluorescent proteins in vitro and in vivo. Analytical Chemistry, 87: 4326 (2015). [ PubMed Article ]

[37] Zhou, Z., Munteanu, E.L., He, J., Ursell, T., Bathe, M., Huang, K.C., Chang, F. The contractile ring coordinates curvature dependent septum assembly during fission yeast cytokinesis. Molecular Biology of the Cell, 26: 78 (2015). [ PubMed Article ]

[36] Pan, K., Kim, D.N., Zhang, F., Adendorff, M., Yan, H., Bathe, M. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nature Communications, 5: 5578 (2014). [ PubMed Article News ]

[35] Klingner, C., Cherian, A.V., Diesinger, P.M., Aufschnaiter, R., Maghelli, N., Keil, T., Beck, G., Tolic-Norrelykke, I., Bathe, M., and Wedlich-Soldner, R. An isotropic acto-myosin network promotes organization of the apical cell cortex in epithelial cells. The Journal of Cell Biology, 207: 107 (2014). [ PubMed Article ]

[34] Sun, W., Boulais, E., Hakobyan, Y., Wang, W., Guan, A., Bathe, M., Yin, P. Casting inorganic structures with DNA molds. Science 346: 717 (2014). [ PubMed Article ]

[33] Mori, M., Somogyi, K., Kondo, H., Monnier, N., Falk, H., Machado, P., Bathe, M., Nedelec, F., and Lenart, P. An Arp2/3 nucleated F-actin shell fragments nuclear membranes at nuclear envelope breakdown. Current Biology, 24: 1421 (2014). [ PubMed Article ]

[32] Oh, H.S., Bryant, K.F., Nieland, T., Mazumder, A., Bagul, M., Bathe, M., Root, D.E. and Knipe, D.M. Targeted RNAi Screen Reveals Novel Epigenetic Factors that Regulate Herpesviral Gene Expression in U2OS Osteosarcoma Cells. mBio, 5: e01086 (2014). [ PubMed Article ]

[31] Guo, S.M., 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 (2014). [ PubMed Article ]

[30] Pan, K., Boulais, E., Yang, L., Bathe, M. Structure-based model for light-harvesting properties of nucleic acid nanostructures. Nucleic Acids Research, 42: 2159 (2014). [ PubMed Article ]

[29] Subramanian, V., Mazumder, A., Surface, L.E., Butty, V., Fields, P.A., Alwan, A., Torrey, L., Thai, K.K., Levine, S., Bathe, M., Boyer, L. H2A.Z acidic patch couples chromatin dynamics to regulation of developmental gene expression programs during lineage commitment. PLoS Genetics, 9: e1003725 (2013). [ PubMed Article ]

[28] Mazumder, A., Pesudo, L.Q., McRee, S., Bathe, M., Samson, L. 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 (2013). [ PubMed Article ]

[27] Johnson-Buck, A., Nangreave, J., Kim, D.N., Bathe, M., Yan, H., Walter, N. Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Letters, 13: 728 (2013). [ PubMed Article ]

[26] Mazumder, A., Tummler, K., Bathe, M., Samson, L.D. Single-cell analysis of RNR transcriptional and translational response to DNA damage. Molecular & Cellular Biology, 33: 635 (2013). [ PubMed Article ]

[25] Krishnan, Y., Bathe, M. Designer nucleic acids to probe and program the cell. Trends in Cell Biology, 22: 624 (2012). [ PubMed Article ]

[24] Schmidt, J.C., Arthanari, H., Boeszoermenyi, A., Dashkevich, N.M., Wilson-Kubalek, E., Monnier, N., Markus, M., Oberer, M., Milligan, R., Bathe, M., Wagner, G., Grishchuk, E.L., Cheeseman, I.M. The kinetochore-bound Ska1 complex tracks depolymerizing microtubules by binding to curved protofilaments. Developmental Cell, 23: 968 (2012). [ PubMed Article ]

[23] Monnier, N., Guo, S.M., Mori, M., He, J., Lenart, P., Bathe, M. Bayesian approach to MSD-based analysis of particle motion in live cells. Biophysical Journal, 103: 616 (2012). [ PubMed Article ]

[22] Guo, S.M., 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 (2012). [ PubMed Article ]

[21] He, J., Guo, S.M., Bathe, M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data I: Theory. Analytical Chemistry, 84: 3871 (2012). [ PubMed Article ]

[20] Kim, D.N., Kilchherr, F., Dietz, H., Bathe, M. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Research, 40: 2862 (2012). [ PubMed Article ]

[19] Castro, C.E., Kilchherr, F., Kim, D.N., Lin Shiao, E., Wauer, T., Wortmann, P., Bathe, M., Dietz, H. A primer to scaffolded DNA origami. Nature Methods, 8: 221 (2011). [ PubMed Article News ]

[18] Mori, M., Monnier, N., Daigle, N., Bathe, M., Ellenberg, J., Lenart, P. Intracellular transport by an anchored homogeneously contracting F-actin meshwork. Current Biology, 21: 606 (2011). [PubMed Article ]

[17] Kim, D.N., 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 (2011). [ PubMed Article ]

[16] Kim, D.N., Nguyen, C.T., Bathe, M. Conformational dynamics of supramolecular protein assemblies. Journal of Structural Biology, 173: 261 (2011). [ PubMed Article ]

[15] Strehle, D., Schnauss, J., Heussinger, C., Alvarado, J., Bathe, M., Kaes, J., Gentry, B. Transiently crosslinked F-actin bundles. European Biophysical Journal, 40: 93 (2011). [ PubMed Article ]

[14] Sedeh, R.S., Fedorov, A.A., Fedorov, E.V., Ono, S., Matsumura, F., Almo, S.C., Bathe, M. Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein. Journal of Molecular Biology, 400: 589 (2010). [ PubMed Article ]

[13] Bathe, M., Chang, F.C. Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding. Trends in Microbiology, 18: 38 (2010). [ PubMed Article ]

[12] Sedeh, R., Bathe, M., Bathe, K.J. The subspace iteration method in protein normal mode analysis. Journal of Computational Chemistry, 31: 66 (2010). [ PubMed Article ]


[11] Bathe, M., Heussinger, C., Claessens, M.M.A.E., Bausch, A.R., and Frey, E. Cytoskeletal bundle mechanics. Biophysical Journal, 94: 2955 (2008). [ PubMed Article ]

[10] Bathe, M. A Finite Element framework for computation of protein normal modes and mechanical response. Proteins: Structure, Function, and Bioinformatics, 70: 1595 (2008). [PubMed Article ]

[9] Heussinger, C., Bathe, M., and Frey, E. Statistical mechanics of wormlike bundles. Physical Review Letters: 99: Art. No. 048101 (2007). [ PubMed Article ]

[8] Claessens, M.M.A.E., Bathe, M., Frey, E., and Bausch, A.R. Actin-binding proteins sensitively mediate F-actin bundle stiffness. Nature Materials, 5: 748 (2006). [ PubMed Article ]

[7] Bathe, M., Rutledge, G.C., Grodzinsky, A.J., and Tidor, B. Osmotic pressure of aqueous chondroitin sulfate solution: A molecular modeling investigation. Biophysical Journal, 89: 2357 (2005). [ PubMed Article ]

[6] Bathe, M., Rutledge, G.C., Grodzinsky, A.J., and Tidor, B. A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophysical Journal, 88: 3870 (2005). [ PubMed Article ]

[5] Bathe, M., Grodzinsky, A.J., Tidor, B., and Rutledge, G.C. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. Journal of Chemical Physics, 121: 7557 (2004). [ PubMed Article ]

[4] Kaazempur-Mofrad, M.R., Bathe, M., Karcher, H., Younis, H.F., Seong, H.C., Shim, E.B., Chan, R.C., Hinton, D.P., Isasi, A.G., Upadhyaya, A., Powers, M.J., Griffith, L.G., and Kamm, R.D. Role of simulation in understanding biological systems. Computers & Structures, 81: 715 (2003). [ PubMed Article ]

[3] Bathe, M. and Rutledge, G.C. Inverse Monte Carlo procedure for conformation determination of macromolecules. Journal of Computational Chemistry, 24: 876 (2003). [ PubMed Article ]

[2] Bathe, M., Shirai, A., Doerschuk, C.M., and Kamm, R.D. Neutrophil transit times through pulmonary capillaries: The effects of capillary geometry and fMLP-stimulation. Biophysical Journal, 83: 1917 (2002). [ PubMed Article ]

[1] Bathe, M. and Kamm, R.D. A fluid-structure interaction finite element analysis of pulsatile blood flow through a compliant stenotic artery. Journal of Biomechanical Engineering, 121: 361 (1999). [ PubMed Article ]

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