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Publications

109

X Wei, Q Mo, C Chen, M Bathe, R Hernandez (2025).
DNA Origami Nanostructures Observed in Transmission Electron Microscopy Images can be Characterized through Convolutional Neural Networks
arXiv preprint arXiv:2503.10950


scholar


article

108

GA Knappe, J Gorman, AN Bigley, SP Harvey, M Bathe (2025).
Heterovalent Click Reactions on DNA Origami
Bioconjugate Chemistry


scholar


article

107

A Romanov, GA Knappe, L Ronsard, H Suh, M Omer, AP Chapman, VR Lewis, K Spivakovsky, J Canales, B Reizis, RD Tingle, CA Cottrell, T Schiffner, D Lingwood, M Bathe, DJ Irvine (2025).

DNA origami vaccines program antigen-focused germinal centers

bioRxiv, 2025.02. 21.639354

scholar


article

106

X Luo, L Ranno, T Sverko, JY Lee, N Sbalbi, A Jones, C Chen, MG Bawendi, J Hu, RJ Macfarlane, M Bathe (2025).

DNA origami directed integration of colloidal nanophotonic materials with silicon photonics

bioRxiv, 2025.01. 23.634416

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article

105

R Falkovich, S Aryal, J Wang, M Sheng, M Bathe (2024).

Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging.

bioRxiv, 2024.10. 28.620504

scholar


article

104

PC Ofoegbu, GA Knappe, A Romanov, BE Draper, M Bathe, MF Jarrold (2024).

Charge Detection Mass Spectrometry Enables Molecular Characterization of Nucleic Acid Nanoparticles

ACS nano 18 (34), 23301-23309

scholar


article

103

S Rouskin, M Allan, J Aruda, J Plung, S Grote, Y Martin, A de Lajarte, M Bathe (2024).

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA

scholar


article

102

X Wei, C Chen, AV Popov, M Bathe, R Hernandez (2024).

Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures</a

The Journal of Physical Chemistry A 128 (25), 4999-5008

scholar


article

101

HM Kim, M Bathe (2024).
Force-free activation of Notch with DNA origami Trends in Genetics

scholar


article

100

Berleant, J.D., Banal, J.L., Rao, D.K., Bathe, M.(2024).
Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language
medRxiv DOI: https://doi.org/10.1101/2024.04.12.24305660

scholar


article

99

Gorman, J., Hart, S.M., John, T., Castellanos, M.A., Harris, D., Parsons, M.F., Banal, J.L., Willard, A.P., Schlau-Cohen, G.S., Bathe, M. (2024). Sculpting photoproducts with DNA origami. Chem DOI: https://doi.org/10.1016/j.chempr.2024.03.007.


SCHOLAR


article

98

Wamhoff, E-C., Ronsard, L., Feldman, J., Knappe, G.A., Hauser, B.M., Romanov, A., Case, J.B., Sanapala, S., Lam, E.C., St. Denis, K.J., Boucau, J., Barczak, A.K., Balazs, A.B., Diamond, M.S., Schmidt, A.G., Lingwood, D., Bathe, M. (2024). Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. Nature Communications 15: 795.


SCHOLAR


article


NEWS

97

Chen, C., Luo, X., Kaplan, A.E.K., Bawendi, M.G., Macfarlane, R.J., Bathe, M. (2023). Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision. Science Advances, 32: eadh8508.


SCHOLAR


article


NEWS

96

Hart, S.M., Gorman, J., Bathe, M., Schlau-Cohen, G.S. (2023). Engineering exciton dynamics with synthetic DNA scaffolds. Accounts of Chemical Research, 56: 2051.


SCHOLAR


article

95

Falkovich, R., Danielson, E.W., Perez de Arce, K., Wamhoff, E-C., Strother, J., Lapteva, A.P., Sheng, M., Cottrell, J.R., Bathe, M. (2023). A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging. Cell Reports, 42: 112430.


SCHOLAR


article

94

Wamhoff, E-C., Knappe, G.A., Burds, A.A., Du, R.R., Neun, B., Difilipppantonio, S., Sanders, C., Edmondson, E., Matta, J.L., Dobrovolskaia, M., Bathe, M. (2023). Evaluation of non-modified wireframe DNA origami for acute toxicity and biodistribution in mice. ACS Applied Bio Materials, 6: 1960.


scholar


article

93

Sheridan, K., Berleant, J., Bathe, M., Condon, A., Williams, V.V.,  (2023). Factorization and pseudofactorization of weighted graphs. Discrete Applied Mathematics, 337: 81.


scholar


article

92

Berleant, J., Sheridan, K., Condon, A., Williams, V.V., Bathe, M. (2023). Isometric Hamming embeddings of weighted graphs. Discrete Applied Mathematics, 332: 119.


scholar


article

91

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. 


SCHOLAR


ARTICLE

90

Knappe, G.A., Wamhoff, E-C., Bathe, M. (2023). Functionalizing DNA origami to investigate and interact with biological systems. Nature Reviews Materials, 8: 123.


scholar


article

89

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, 16: 20340.


PubMED


article

88

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.


SCHOLAR


article

87

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.


SCHOLAR


article

86

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.


PubMed


article

85

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.


PubMed


article

84

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.


PubMed


article

83

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


PubMed


article

82

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.


PubMed


article

81

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.


PubMed


article

80

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.


PubMed


article

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.


article

78

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


article

77

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


PubMed


article

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.


PubMed


article

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.


PubMed


article

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.


PubMed


article

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.


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Article


MIT News


News & Views


Tech Review

72

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


pubmed


Article

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.


Article

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.


pubmed


Article

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.


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Article

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.


pubmed


Article

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.


pubmed


Article

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.


pubmed


Article


MIT News

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.


Article

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.


Article

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.


Pubmed


Article


MIT news


NIH Directors Blog

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article


MIT NEWS

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.


Pubmed


Article

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.


Article

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.


Pubmed


article

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.


Pubmed


article

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.


Protocol

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.


Pubmed


article

52

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


article

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.


Pubmed


Article


MIT News


Newsweek

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.


Pubmed


Article

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.


Pubmed


Article

48

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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article


MIT News

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.


Pubmed


Article

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.


Pubmed


Article

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. 


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article


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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

25

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


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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article


MIT News

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.


Pubmed


Article

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.


Pubmed


Article

16

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


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

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.


Pubmed


Article

12

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


Pubmed


Article

11

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


Pubmed


Article

10

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


Pubmed


Article

9

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


Pubmed


Article

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.


Pubmed


Article

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.


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Article

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.


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Article

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.


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AIP

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.


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Article

3

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


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Article

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.


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Article

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.


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Article