Publications

95

Wamhoff, E-C., Ronsard, L., Feldman, J., Hauser, B.M., Knappe, G.A., Romanov, A., Lam, E., St Denis, K., Balazs, A.B., Schmidt, A., Lingwood, D., Bathe, M. (2022). Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. bioRxiv, doi: 10.1101/2022.08.16.504128

94

Knappe, G.A., Wamhoff, E-C., Bathe, M. (2022). Functionalizing DNA origami to investigate and interact with biological systems. Nature Reviews Materials. https://doi.org/10.1038/s41578-022-00517-x

93

Parsons, M.F., Allan, M.F., Li, S., Shepherd, T.R., Ratanalert, S., Zhang, S., Pullen, K.M., Chiu, W., Rouskin, S., Bathe, M. (2023). 3D RNA-scaffolded wireframe origami. Nature Communications, 14: 382. https://doi.org/10.1038/s41467-023-36156-1

92

Du, R.R., Cedrone, E., Romanov, A., Falkovich, R., Dobrovolskaia, M.A., Bathe, M. (2022). Innate immune stimulation using 3D wireframe DNA origami. ACS Nano, doi 10.1021/acsnano.2c06275

91

Falkovich, R., Danielson, E.W., Perez de Arce, K., Wamhoff, E-C., Cottrell, J.R., Sheng, M., Bathe, M. (2022) Perturbations of a causal synaptic molecular network in autism and schizophrenia revealed with multiplexed imaging. bioRxiv, doi 10.1101/2022.07.11.499330.

90

Chen, C., Wei, X., Parsons, M.F., Guo, J., Banal, J.L., Zhao, Y., Scott, M.N., Schlau-Cohen, G.S., Hernandez, R., Bathe, M. (2022). Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nature Communications, 13: 4935.

89

Wamhoff, E-C., Romanov, A., Huang, H., Read, B.J., Ginsburg, E., Knappe, G.A., Kim, H-M., Farrell, N.P., Irvine, D.J., Bathe, M. (2022). Controlling nuclease degradation of wireframe DNA origami with minor groove binders. ACS Nano, 16: 8954

88

Wang, X., Li, S., Jun, H., John, T., Zhang, K., Fowler, H., Doye, J.P.K., Chiu, W., Bathe, M. (2022). Planar wireframe 2D origami. Science Advances, 8: eabn0039.

87

Lan, T.C.T., Allan, M.F., Malsick, L.E., Woo, J.Z., Zhu, C., Zhang, F., Khandwala, S., Nyeo, S.S.Y., Sun, Y., Guo, J.U., Bathe, M., Näär, A., Griffiths, A., Rouskin, S. (2022). Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nature Communications, 13: 1128.

86

Wei, X., Chen, C., Zhao, Y., Harazinska, E., Bathe, M., Hernandez, R. (2022). Molecular structure of single-stranded DNA on the ZnS surface of quantum dots. ACS Nano, 16: 6666.

85

Wang, X., Jun, H., Bathe, M. (2022). Programming 2D supramolecular assemblies with wireframe DNA origami. Journal of the American Chemical Society, 144: 4403.

84

Hart, S.M., Wang, X., Guo, J., Bathe, M., Schlau-Cohen, G.S. (2022). Tuning optical absorption and emission using strongly coupled dimers in programmable DNA scaffolds. The Journal of Physical Chemistry Letters, 13: 1863.

83

Afonin, K.A., Dobrovolskaia, M.A., Ke, W., Grodzinski, P., Bathe, M. (2022). Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Advanced Drug Delivery Reviews, 181: 114081.

82

Adendorff, M.R., Tang, G.Q., Millar, D.P., Bathe, M., Bricker, W.P. (2022). Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Research, 50: 717.

81

Berleant, J., Sheridan, K., Condon, A., Williams, V.V., Bathe, M. (2021). Isometric Hamming embeddings of weighted graphs. arXiv arXiv:2112.06994.

80

Sheridan, K., Berleant, J., Bathe, M., Condon, A., Williams, V.V. (2021). Factorization and pseudofactorization of weighted graphs. arXiv arXiv:2112.06990.

79

Lavi, R., Bathe, M., Hosoi, A., Mitra, A., Crawley, E. (2021). The NEET ways of thinking: Implementing them at MIT and assessing their efficacy. Advances in Engineering Education.

78

Bathe, M. (2021). Nanoscale 2D and 3D patterning using programmed DNA assemblies. Novel Patterning Technologies 2021,11610: 1161012.

77

Banal, J. and Bathe, M. (2021). Scalable nucleic acid storage and retrieval using barcoded microcapsules. ACS Applied Materials & Interfaces, 13: 49729.

76

Jun, H., Wang, X., Parsons, M. F., Bricker, W. P., John T., Li, S., Jackson, S., Chiu, W., Bathe, M., (2021). Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. Nucleic Acids Research, 49: 10265.

75

Knappe, G.A., Wamhoff, E.C., Read, B. J., Irvine, D. J., Bathe, M. (2021) In situ covalent functionalization of DNA origami virus-like particles. ACS Nano, 15: 14316.

74

Tomov, M. L., O’Neil, A., Abbasi, H. S., Cimini, B. A., Carpenter, A. E., Rubin, L. L., Bathe, M. (2021). Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications Biology, 4: 786.

73

Banal, J.L., Shepherd, T. Y., Berleant, J., Huang, H., Reyes, M., Ackerman, C.M., Blainey, P. C., Bathe, M. (2021). Random access DNA memory using Boolean search in an archival file storage system. Nature Materials, 20: 1272.

72

Bathe, M., Hernandez, R., Komiyama, T., Machiraju, R. and Neogi, S. (2021). Autonomous Computing Materials. ACS Nano, 15: 3586.

71

Hart, S.M., Chen, W.J., Banal, J.L., Bricker, W.P., Dodin, A., Markova, L., Vyborna, Y., Willard, A.P., Häner, R., Bathe, M., Schlau-Cohen, G. S. (2020). Engineering couplings for exciton transport using synthetic DNA scaffolds. Chem, 7: 752.

70

Danielson, E., Perez de Arce, K., Cimini, B., Wamhoff, E. C., Singh, S., Cottrell, J. R., Carpenter, A. E., Bathe, M. (2020). Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. eNeuro, 8: ENEURO.0286-20.2020.

69

Afonin, K. A., Dobrovolskaia, M. A., Church, G., Bathe, M. (2020). Opportunities, barriers, and a strategy for overcoming translational challenges to therapeutic nucleic acid nanotechnology. ACS Nano, 14: 9221.

68

Dobrovolskaia, M.A., Bathe, M. (2020). Opportunities and challenges for the clinical translation of structured DNA assemblies as gene therapeutic delivery and vaccine vectors. WIREs Nanomedicine and Nanobiotechnology, 13: e1657.

67

Pisharady, K.P., Eberly, L.E., Cheong, I., Manousakis, G., Guliani, G., Clark, H.B., Bathe, M., Walk, D., Lenglet, C. (2020). Tract-specific analysis improves sensitivity of spinal cord diffusion MRI to cross-sectional and longitudinal changes in amyotrophic lateral sclerosis. Communications Biology, 3: 370.

66

Veneziano, R., Moyer, T. J., Stone, M. B., Mukherjee, S. Shepherd, T.R., Das, J., Schief, W.R., Irvine, D. J., Bathe, M. (2020). Role of nanoscale antigen organization on B-cell activation probed using DNA origami. Nature Nanotechnology, 15: 716.

65

Hart, S. M., Banal, J. L., Bathe, M., and Schlau-Cohen, G.S. (2020). Identification of non-radiative decay pathways in cy3. The Journal of Physical Chemistry Letters, 11: 5000.

64

Jun, H., Wang, X., Bricker, W.P., & Bathe, M. (2019). Automated sequence design of 2D wireframe DNA origami with honeycomb edges. Nature Communications, 10: 5419.

63

Guo, S-M., Veneziano, R., Gordonov, S., Li, L., Danielson, E., Perez de Arce, K., Park, D., Kulesa, A.B., Wamhoff, E-C., Blainey, P.C., Boyden, E.S., Cottrell, J.R., Bathe, M. (2019). Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes. Nature Communications, 10: 4377.

62

Wamhoff, E-C., Banal, J.L., Bricker, T.R., Parsons, M.F., Veneziano, R., Stone, M.B., Jun, H., Wang, X., Bathe, M. (2019). Programming structured DNA assemblies to probe biophysical processes. Annual Review of Biophysics, 48: 395.

61

Shepherd, T.R., Du, R.,R. Huang, H., Wamhoff, E-C., Bathe, M. (2019). Bioproduction of pure, kilobase-scale single-stranded DNA. Scientific Reports, 9: 6121.

60

Kulikov, V., Guo, S-M., Stone, M.B., Goodman, A., Carpenter, A., Bathe, M., Lempitsky, V. (2019). DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Computational Biology, 15: e1007012.

59

Jun, H., Zhang, F., Shepherd, T., Ratalanert, S., Qi, X., Yan, H., Bathe, M. (2019). Autonomously designed free-form 2D DNA origami. Science Advances, 5: eaav0655.

58

Jun, H., Shepherd, T.R., Zhang, K., Bricker, W.P., Li, S., Chiu, W., Bathe, M. (2019). Automated sequence design of 3D polyhedral wireframe DNA origami with honeycomb edges. ACS Nano, 13: 2083.

57

Bathe, M., Chrisey, L.A., Herr, D.J., Lin, Q., Rasic, D., Woolley, A.T., Zadegan, R., Zhirnov, V.V. (2019). Roadmap on biological pathways for electronic nanofabrication and materials. Nano Futures, 3: 012001.

56

Holec, P.V., Berleant, J., Bathe, M., Birnbaum, M.E. (2018). A Bayesian framework for high-throughput T cell receptor pairing. Bioinformatics, 149: 024905.

55

Bricker, W.P., Banal, J.L., Stone, M.B., Bathe, M. (2018). Molecular model of J-aggregated pseudoisocyanine fibers. The Journal of Chemical Physics, 149: 024905.

54

Bathe, M., Guo, S-M., Li, L., Veneziano, R., Gordonov, S., Cottrell, J.C. (2018). Multiplexed imaging of neuronal synapses using nucleic acid probe exchange. Protocol Exchange, doi:10.1038/protex.2018.066.

53

Veneziano, R., Shepherd, T., Ratanalert, S., Bellou, L., Tao, C., Bathe, M. (2018). In vitro synthesis of gene-length single-stranded DNA. Scientific Reports, 8: 6548.

52

Bathe, M. and Rothemund, P. (2017). DNA Nanotechnology: A foundation for programmable nanoscale materials. MRS Bulletin, 42: 882.

51

Boulais, E., Sawaya, N., Veneziano, R., Andreoni, A., Banal, J.L., Kondo, T., Mandal, S., Lin, S., Schlau-Cohen, G.S., Woodbury, N., Yan, H., Aspuru-Guzik, A., Bathe, M. (2018). Programmed coherent coupling in a synthetic DNA-based excitonic circuit. Nature Materials, 17: 159.

50

Banal, J.L., Kondo, T., Veneziano, R., Bathe, M., Schlau-Cohen, G.S. (2017). Photophysics of J-aggregate-mediated energy transfer on DNA. The Journal of Physical Chemistry Letters, 8: 5827.

49

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

48

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

47

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

46

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

45

Wang, P., Gaitanaros, S., Lee, S., Bathe, M., Shih, W.M., Ke, Y. (2016). Programming self-assembly of DNA origami honeycomb lattices and plasmonic metamaterials. JACS, 138: 7733.

44

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

43

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

42

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

41

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

40

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

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. (2015). Inferring transient particle transport dynamics in live cells. Nature Methods, 12: 838.

38

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

37

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

36

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

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. (2014). An isotropic acto-myosin network promotes organization of the apical cell cortex in epithelial cells. The Journal of Cell Biology, 207: 107.

34

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

33

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

32

Oh, H.S., Bryant, K.F., Nieland, T., Mazumder, A., Bagul, M., Bathe, M., Root, D.E. and Knipe, D.M. (2014). Targeted RNAi screen reveals novel epigenetic factors that regulate herpesviral gene expression in U2OS osteosarcoma cells. mBio, 5: e01086.

31

Guo, S.M., Bag, N., Mishra, A., Wohland, T., Bathe, M. (2014). Bayesian total internal reflection fluorescence correlation spectroscopy reveals hIAPP-induced plasma membrane domain organization in live cells. Biophysical Journal, 106: 190.

30

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

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. (2013). H2A.Z acidic patch couples chromatin dynamics to regulation of developmental gene expression programs during lineage commitment. PLoS Genetics, 9: e1003725.

28

Mazumder, A., Pesudo, L.Q., McRee, S., Bathe, M., Samson, L. (2013). 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.

27

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

26

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

25

Krishnan, Y., Bathe, M. (2013). Designer nucleic acids to probe and program the cell. Trends in Cell Biology, 22: 624.

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. (2012). The kinetochore-bound Ska1 complex tracks depolymerizing microtubules by binding to curved protofilaments. Developmental Cell, 23: 968.

23

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

22

Guo, S.M., He, J., Monnier, N., Sun, G., Wohland, T., Bathe, M. (2012). Bayesian approach to the analysis of fluorescence correlation spectroscopy data II: Application to simulated and in vitro data. Analytical Chemistry, 84: 3880.

21

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

20

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

19

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

18

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

17

Kim, D.N., Altschuler, J., Strong, C., McGill, G., Bathe, M. (2011). Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. Nucleic Acids Research, 39: D451.

16

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

15

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

14

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

13

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

12

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

11

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

10

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

9

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

8

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

7

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

6

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

5

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

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. (2003). Role of simulation in understanding biological systems. Computers & Structures, 81: 715.

3

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

2

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

1

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