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Engineering couplings for exciton transport using synthetic DNA scaffolds

Stephanie M. Hart, Wei-Jia Chen, James L. Banal, William P. Bricker, Amro Dodin, Larysa Markova, Yuliia Vyborna, Adam P. Willard, Robert Häner, Mark Bathe, Gabriela S. Schlau-Cohen

Chem (2020). doi:


Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging

Eric Danielson, Karen Perez de Arce, Beth Cimini, Eike-Christian Wamhoff, Shantanu Singh, Jeffrey R. Cottrell, Anne E. Carpenter, Mark Bathe

eNeuro (2020). doi:


Structure of the full SARS-CoV-2 RNA genome in infected cells

Tammy C. T. Lan, Matthew F. Allan, Lauren E. Malsick, Stuti Khandwala, Sherry S. Y. Nyeo, Mark Bathe, Anthony Griffiths, Silvi Rouskin

bioRxiv (2020). doi:


Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology

Kirill A. Afonin, Marina A. Dobrovolskaia, George Church, Mark Bathe

ACS Nano (2020).


Opportunities and challenges for the clinical translation of structured DNA assemblies as gene therapeutic delivery and vaccine vectors

Marina A. Dobrovolskaia,  Mark Bathe

WIREs Nanomedicine And Nanobiotechnology (2020).



Rémi Veneziano,  Tyson J. Moyer, Matthew B. Stone,  Sayak Mukherjee, Tyson R. Shepherd,  Jayajit Das, William R. Schief,  Darrell J. Irvine,  Mark Bathe

Nature Nanotechnology (2020).


Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging

Eric Danielson, Karen Perez de Arce, Beth Cimini, Eike-Christian Wamhoff, Shantanu Singh, Jeffrey R. Cottrell, Anne E. Carpenter, Mark Bathe

bioRxiv (2020).


Controlling wireframe DNA origami nuclease degradation with minor groove binders

Eike-Christian Wamhoff, Hellen Huang, Benjamin J. Read, Eric Ginsburg, William R. Schief, Nicholas Farrell, Darrell J. Irvine, Mark Bathe

bioRxiv (2020).



Stephanie M. Hart, James L. Banal, Mark Bathe, and Gabriela S. Schlau-Cohen

J Phys Chem Lett (2020).


Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

Hyungmin Jun, Xiao Wang, William Bricker, Steve Jackson, Mark Bathe

bioRxiv (2020).


Arbitrary Boolean logical search operations on massive molecular file systems

James L. Banal, Tyson R. Shepherd, Joseph D. Berleant, Hellen Huang, Miguel Reyes, Cheri M. Ackerman, Paul Blainey, Mark Bathe

bioRxiv (2020).


Automated sequence design of 2D wireframe DNA origami with honeycomb edges

Hyungmin Jun, Xiao Wang, William P. Bricker & Mark Bathe

Nature Communications, 10: 5419 (2019)


Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes.

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.

Nature Communications, 10: 4377 (2019)


Programming structured DNA assemblies to probe biophysical processes.

Wamhoff, E-C., Banal, J.L., Bricker, T.R., Parsons, M.F., Veneziano, R., Stone, M.B., Jun, H., Wang, X., Bathe, M.

Annual Review of Biophysics, 48: 395 (2019)


Bioproduction of pure, kilobase-scale single-stranded DNA.

Shepherd, T.R., Du, R.,R. Huang, H., Wamhoff, E-C., Bathe, M.

Scientific Reports, 9: 6121 (2019)


DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.

Kulikov, V., Guo, S-M., Stone, M.B., Goodman, A., Carpenter, A., Bathe, M., Lempitsky, V.

PLoS Computational Biology, 15: e1007012 (2019)


Autonomously designed free-form 2D DNA origami.

Jun, H., Zhang, F., Shepherd, T., Ratalanert, S., Qi, X., Yan, H., Bathe, M.

Science Advances, 5: eaav0655 (2019)


Automated sequence design of 3D polyhedral wireframe DNA origami with honeycomb edges.

Jun, H., Shepherd, T.R., Zhang, K., Bricker, W.P., Li, S., Chiu, W., Bathe, M. 

ACS Nano, 13: 2083 (2019)


Roadmap on biological pathways for electronic nanofabrication and materials.

Bathe, M., Chrisey, L.A., Herr, D.J., Lin, Q., Rasic, D., Woolley, A.T., Zadegan, R., Zhirnov, V.V.

Nano Futures, 3: 012001 (2019)


A Bayesian framework for high-throughput T cell receptor pairing.

Holec, P.V., Berleant, J., Bathe, M., Birnbaum, M.E.

Bioinformatics, 149: 024905 (2018)


Molecular model of J-aggregated pseudoisocyanine fibers.

Bricker, W.P., Banal, J.L., Stone, M.B., Bathe, M.

The Journal of Chemical Physics, 149: 024905 (2018)


Multiplexed imaging of neuronal synapses using nucleic acid probe exchange.

Bathe, M., Guo, S-M., Li, L., Veneziano, R., Gordonov, S., Cottrell, J.C.

Protocol Exchange, doi:10.1038/protex.2018.066 (2018)


In vitro synthesis of gene-length single-stranded DNA.

Veneziano, R., Shepherd, T., Ratanalert, S., Bellou, L., Tao, C., Bathe, M.

Scientific Reports, 8: 6548 (2018)


DNA Nanotechnology: A foundation for programmable nanoscale materials.

Bathe, M. and Rothemund, P.

MRS Bulletin, 42: 882 (2017)


Programmed coherent coupling in a synthetic DNA-based excitonic circuit.

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.

Nature Materials, 17: 159 (2018)


Photophysics of J-aggregate-mediated energy transfer on DNA.

Banal, J.L., Kondo, T., Veneziano, R., Bathe, M., Schlau-Cohen, G.S.

The Journal of Physical Chemistry Letters, 8: 5827 (2017)


Optical determination of the electronic coupling and intercalation geometry of Thiazole Orange homodimer in DNA.

Cunningham, P., Bricker, W., Diaz, S., Medintz, I., Bathe, M., and Melinger, J.S.

The Journal of Chemical Physics, 147: 055101 (2017)


Structure and conformational dynamics of scaffolded DNA origami nanoparticles.

Pan, K., Bricker, W., Ratanalert, S., Bathe, M. 

Nucleic Acids Research45: 6284 (2017)


A regulatory switch alters chromosome motions at the metaphase to anaphase transition.

Su, K.C., Barry, Z., Schweizer, N., Maiato, H., Bathe, M., Cheeseman, I.

Cell Reports, 17: 728 (2016)


Designer nanoscale DNA assemblies programmed from the top down.

Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M.

Science, 352: 1534 (2016)


Programming self-assembly of DNA origami honeycomb lattices and plasmonic metamaterials.

Wang, P., Gaitanaros, S., Lee, S., Bathe, M., Shih, W.M., Ke, Y.

JACS, 138: 7733 (2016)


Mapping translation ‘hot-spots’ in live cells by tracking single molecules of mRNA and ribosomes.

Katz, Z.B., English, B.P., Lionnet, T., Yoon, Y.J., Monnier, N., Ovryn, B., Bathe, M., Singer, R.H.

eLife, e10415 (2016)


Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis.

Dhakal, S., Adendorff, M., Liu, M., Yan, H., Bathe, M., Walter, N.

Nanoscale, 8: 3125 (2016)


Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length-scales.

Hogstrom, L., Guo, S.M., Murugadoss, K., Bathe, M.

Journal of The Royal Society Interface, 6: 20150081 (2016)


Time-series modeling of live-cell shape dynamics for image-based phenotypic profiling.

Gordonov, S., Hwang, M.K., Wells, A., Gertler, F.B., Lauffenburger, D., Bathe, M.

Integrative Biology, 8: 73 (2016)


Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies.

Sedeh, R., Pan, K., Adendorff, M., Hallatschek, O., Bathe, K.J., Bathe, M.

Journal of Chemical Theory & Computation, 12: 261 (2016)


Inferring transient particle transport dynamics in live cells.

Monnier, N., Barry, Z., Park, H.Y., Su, K.C., Katz, Z., English, B., Dey, A., Pan, K., Cheeseman, I., Singer, R., Bathe, M.

Nature Methods, 12: 838 (2015)


Bayesian model selection applied to the analysis of FCS data of fluorescent proteins in vitro and in vivo.

Sun, G., Guo, S.M., Teh, C., Korzh, V., Bathe, M., Wohland, T.

Analytical Chemistry, 87: 4326 (2015)


The contractile ring coordinates curvature dependent septum assembly during fission yeast cytokinesis.

Zhou, Z., Munteanu, E.L., He, J., Ursell, T., Bathe, M., Huang, K.C., Chang, F. 

Molecular Biology of the Cell, 26: 78 (2015)


Lattice-free prediction of three-dimensional structure of programmed DNA assemblies.

Pan, K., Kim, D.N., Zhang, F., Adendorff, M., Yan, H., Bathe, M.

Nature Communications, 5: 5578 (2014)


An isotropic acto-myosin network promotes organization of the apical cell cortex in epithelial cells.

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.

The Journal of Cell Biology, 207: 107 (2014)


Casting inorganic structures with DNA molds.

Sun, W., Boulais, E., Hakobyan, Y., Wang, W., Guan, A., Bathe, M., Yin, P. 

Science 346: 717 (2014)


An Arp2/3 nucleated F-actin shell fragments nuclear membranes at nuclear envelope breakdown.

Mori, M., Somogyi, K., Kondo, H., Monnier, N., Falk, H., Machado, P., Bathe, M., Nedelec, F., and Lenart, P.

Current Biology, 24: 1421 (2014)


Targeted RNAi screen reveals novel epigenetic factors that regulate herpesviral gene expression in U2OS osteosarcoma cells.

Oh, H.S., Bryant, K.F., Nieland, T., Mazumder, A., Bagul, M., Bathe, M., Root, D.E. and Knipe, D.M.

mBio, 5: e01086 (2014)


Bayesian total internal reflection fluorescence correlation spectroscopy reveals hIAPP-induced plasma membrane domain organization in live cells.

Guo, S.M., Bag, N., Mishra, A., Wohland, T., Bathe, M.

Biophysical Journal, 106: 190 (2014)


Structure-based model for light-harvesting properties of nucleic acid nanostructures.

Pan, K., Boulais, E., Yang, L., Bathe, M.

Nucleic Acids Research, 42: 2159 (2014)


H2A.Z acidic patch couples chromatin dynamics to regulation of developmental gene expression programs during lineage commitment.

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.

PLoS Genetics, 9: e1003725 (2013)


Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae.

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

Nucleic Acids Research, 41: 9310 (2013)


Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards.

Johnson-Buck, A., Nangreave, J., Kim, D.N., Bathe, M., Yan, H., Walter, N.

Nano Letters, 13: 728 (2013)


Single-cell analysis of RNR transcriptional and translational response to DNA damage.

Mazumder, A., Tummler, K., Bathe, M., Samson, L.D.

Molecular & Cellular Biology, 33: 635 (2013)


Designer nucleic acids to probe and program the cell.

Krishnan, Y., Bathe, M.

Trends in Cell Biology, 22: 624 (2012)


The kinetochore-bound Ska1 complex tracks depolymerizing microtubules by binding to curved protofilaments.

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.

Developmental Cell, 23: 968 (2012)


Bayesian approach to MSD-based analysis of particle motion in live cells.

Monnier, N., Guo, S.M., Mori, M., He, J., Lenart, P., Bathe, M.

Biophysical Journal, 103: 616 (2012)


Bayesian approach to the analysis of fluorescence correlation spectroscopy data II: Application to simulated and in vitro data.

Guo, S.M., He, J., Monnier, N., Sun, G., Wohland, T., Bathe, M.

Analytical Chemistry, 84: 3880 (2012)


Bayesian approach to the analysis of fluorescence correlation spectroscopy data I: Theory.

He, J.Guo, S.M.Bathe, M.

Analytical Chemistry, 84: 3871 (2012)


Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures.

Kim, D.N., Kilchherr, F., Dietz, H., Bathe, M.

Nucleic Acids Research, 40: 2862 (2012)


A primer to scaffolded DNA origami.

Castro, C.E., Kilchherr, F., Kim, D.N., Lin Shiao, E., Wauer, T., Wortmann, P., Bathe, M., Dietz, H.

Nature Methods, 8: 221 (2011)


Intracellular transport by an anchored homogeneously contracting F-actin meshwork.

Mori, M., Monnier, N., Daigle, N., Bathe, M., Ellenberg, J., Lenart, P.

Current Biology, 21: 606 (2011)


Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Kim, D.N., Altschuler, J., Strong, C., McGill, G., Bathe, M.

Nucleic Acids Research, 39: D451 (2011)


Conformational dynamics of supramolecular protein assemblies.

Kim, D.N.Nguyen, C.T.Bathe, M.

Journal of Structural Biology, 173: 261 (2011)


Transiently crosslinked F-actin bundles.

Strehle, D., Schnauss, J., Heussinger, C., Alvarado, J., Bathe, M., Kaes, J., Gentry, B.

European Biophysical Journal, 40: 93 (2011)


Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein.

Sedeh, R.S., Fedorov, A.A., Fedorov, E.V., Ono, S., Matsumura, F., Almo, S.C., Bathe, M.

Journal of Molecular Biology, 400: 589 (2010)


Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding.

Bathe, M., Chang, F.C.

Trends in Microbiology, 18: 38 (2010)


The subspace iteration method in protein normal mode analysis.

Sedeh, R., Bathe, M., Bathe, K.J.

Journal of Computational Chemistry, 31: 66 (2010)


Cytoskeletal bundle mechanics.

Bathe, M., Heussinger, C., Claessens, M.M.A.E., Bausch, A.R., and Frey, E.

Biophysical Journal, 94: 2955 (2008)


A Finite Element framework for computation of protein normal modes and mechanical response.

Bathe, M.

Proteins: Structure, Function, and Bioinformatics, 70: 1595 (2008)


Statistical mechanics of wormlike bundles.

Heussinger, C., Bathe, M., and Frey, E.

Physical Review Letters: 99: Art. No. 048101 (2007)


Actin-binding proteins sensitively mediate F-actin bundle stiffness.

Claessens, M.M.A.E., Bathe, M., Frey, E., and Bausch, A.R.

Nature Materials, 5: 748 (2006)


Osmotic pressure of aqueous chondroitin sulfate solution: A molecular modeling investigation.

Bathe, M., Rutledge, G.C., Grodzinsky, A.J., and Tidor, B.

Biophysical Journal, 89: 2357 (2005)


A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid.

Bathe, M., Rutledge, G.C., Grodzinsky, A.J., and Tidor, B.

Biophysical Journal, 88: 3870 (2005)


Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution.

Bathe, M., Grodzinsky, A.J., Tidor, B., and Rutledge, G.C.

Journal of Chemical Physics, 121: 7557 (2004)


Role of simulation in understanding biological systems.

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.

Computers & Structures, 81: 715 (2003)


Inverse Monte Carlo procedure for conformation determination of macromolecules.

Bathe, M. and Rutledge, G.C.

Journal of Computational Chemistry, 24: 876 (2003)


Neutrophil transit times through pulmonary capillaries: The effects of capillary geometry and fMLP-stimulation.

Bathe, M., Shirai, A., Doerschuk, C.M., and Kamm, R.D.

Biophysical Journal, 83: 1917 (2002)


A fluid-structure interaction finite element analysis of pulsatile blood flow through a compliant stenotic artery.

Bathe, M. and Kamm, R.D.

Journal of Biomechanical Engineering, 121: 361 (1999)