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Programming Structured DNA Assemblies to Probe Biophysical Processes.

Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M.

Annu Rev Biophys. 2019 May 6;48:395-419. doi: 10.1146/annurev-biophys-052118-115259.


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

Kulikov V, Guo SM, Stone M, Goodman A, Carpenter A, Bathe M, Lempitsky V.

PLoS Comput Biol. 2019 May 13;15(5):e1007012. doi: 10.1371/journal.pcbi.1007012. eCollection 2019 May.


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

Shepherd TR, Du RR, Huang H, Wamhoff EC, Bathe M.

Sci Rep. 2019 Apr 16;9(1):6121. doi: 10.1038/s41598-019-42665-1.


Autonomously designed free-form 2D DNA origami.

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

Sci Adv. 2019 Jan 4;5(1):eaav0655. doi: 10.1126/sciadv.aav0655. eCollection 2019 Jan.


Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges.

Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M.

ACS Nano. 2019 Feb 26;13(2):2083-2093. doi: 10.1021/acsnano.8b08671. Epub 2019 Jan 24.


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

Holec PV, Berleant J, Bathe M, Birnbaum ME.

Bioinformatics. 2019 Apr 15;35(8):1318-1325. doi: 10.1093/bioinformatics/bty801.


Molecular model of J-aggregated pseudoisocyanine fibers.

Bricker WP, Banal JL, Stone MB, Bathe M.

J Chem Phys. 2018 Jul 14;149(2):024905. doi: 10.1063/1.5036656.


Normative reference data, determinants, and clinical implications of right atrial reservoir function in women assessed by 2D speckle-tracking echocardiography.

Brand A, Bathe M, Hübscher A, Baldenhofer G, Hättasch R, Seeland U, Oertelt-Prigione S, Rücke M, Regitz-Zagrosek V, Stangl K, Dreger H, Stangl V, Knebel F.

Echocardiography. 2018 Oct;35(10):1542-1549. doi: 10.1111/echo.14092. Epub 2018 Jul 1.


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

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

Sci Rep. 2018 Apr 25;8(1):6548. doi: 10.1038/s41598-018-24677-5.


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

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.

Nat Mater. 2018 Feb;17(2):159-166. doi: 10.1038/nmat5033. Epub 2017 Nov 13.


Photophysics of J-Aggregate-Mediated Energy Transfer on DNA.

Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS.

J Phys Chem Lett. 2017 Dec 7;8(23):5827-5833. doi: 10.1021/acs.jpclett.7b01898. Epub 2017 Nov 16.


Right heart function in impaired left ventricular diastolic function: 2D speckle tracking echocardiography-based and Doppler tissue imaging-based analysis of right atrial and ventricular function.

Brand A, Bathe M, Oertelt-Prigione S, Seeland U, Rücke M, Regitz-Zagrosek V, Stangl K, Knebel F, Stangl V, Dreger H.

Echocardiography. 2018 Jan;35(1):47-55. doi: 10.1111/echo.13745. Epub 2017 Nov 6.


Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA.

Cunningham PD, Bricker WP, Díaz SA, Medintz IL, Bathe M, Melinger JS.

J Chem Phys. 2017 Aug 7;147(5):055101. doi: 10.1063/1.4995431.


Structure and conformational dynamics of scaffolded DNA origami nanoparticles.

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

Nucleic Acids Res. 2017 Jun 20;45(11):6284-6298. doi: 10.1093/nar/gkx378.


A Regulatory Switch Alters Chromosome Motions at the Metaphase-to-Anaphase Transition.

Su KC, Barry Z, Schweizer N, Maiato H, Bathe M, Cheeseman IM.

Cell Rep. 2016 Nov 8;17(7):1728-1738. doi: 10.1016/j.celrep.2016.10.046.


Designer nanoscale DNA assemblies programmed from the top down.

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

Science. 2016 Jun 24;352(6293):1534. doi: 10.1126/science.aaf4388. Epub 2016 May 26.


Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials.

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

J Am Chem Soc. 2016 Jun 22;138(24):7733-40. doi: 10.1021/jacs.6b03966. Epub 2016 Jun 9.


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

Hogstrom LJ, Guo SM, Murugadoss K, Bathe M.

Interface Focus. 2016 Feb 6;6(1):20150081. doi: 10.1098/rsfs.2015.0081.


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

Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG.

Nanoscale. 2016 Feb 7;8(5):3125-37. doi: 10.1039/c5nr07263h.


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

Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH.

Elife. 2016 Jan 13;5. pii: e10415. doi: 10.7554/eLife.10415.


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

Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger DA, Bathe M.

Integr Biol (Camb). 2016 Jan;8(1):73-90. doi: 10.1039/c5ib00283d. Epub 2015 Dec 11.


Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies.

Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M.

J Chem Theory Comput. 2016 Jan 12;12(1):261-73. doi: 10.1021/acs.jctc.5b00965. Epub 2015 Dec 16.


Inferring transient particle transport dynamics in live cells.

Monnier N, Barry Z, Park HY, Su KC, Katz Z, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M.

Nat Methods. 2015 Sep;12(9):838-40. doi: 10.1038/nmeth.3483. Epub 2015 Jul 20.


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

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

Anal Chem. 2015 Apr 21;87(8):4326-33. doi: 10.1021/acs.analchem.5b00022. Epub 2015 Apr 8.


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

Pan K, Kim DN, Zhang F, Adendorff MR, Yan H, Bathe M.

Nat Commun. 2014 Dec 3;5:5578. doi: 10.1038/ncomms6578.


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

Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F.

Mol Biol Cell. 2015 Jan 1;26(1):78-90. doi: 10.1091/mbc.E14-10-1441. Epub 2014 Oct 29.


Isotropic actomyosin dynamics promote organization of the apical cell cortex in epithelial cells.

Klingner C, Cherian AV, Fels J, Diesinger PM, Aufschnaiter R, Maghelli N, Keil T, Beck G, Tolić-Nørrelykke IM, Bathe M, Wedlich-Soldner R.

J Cell Biol. 2014 Oct 13;207(1):107-21. doi: 10.1083/jcb.201402037.


Casting inorganic structures with DNA molds.

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

Science. 2014 Nov 7;346(6210):1258361. doi: 10.1126/science.1258361. Epub 2014 Oct 9.


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

Mori M, Somogyi K, Kondo H, Monnier N, Falk HJ, Machado P, Bathe M, Nédélec F, Lénárt P.

Curr Biol. 2014 Jun 16;24(12):1421-1428. doi: 10.1016/j.cub.2014.05.019. Epub 2014 Jun 5.


A targeted RNA interference screen reveals novel epigenetic factors that regulate herpesviral gene expression.

Oh HS, Bryant KF, Nieland TJ, Mazumder A, Bagul M, Bathe M, Root DE, Knipe DM.

MBio. 2014 Feb 4;5(1):e01086-13. doi: 10.1128/mBio.01086-13.


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

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

Biophys J. 2014 Jan 7;106(1):190-200. doi: 10.1016/j.bpj.2013.11.4458.


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

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

Nucleic Acids Res. 2014 Feb;42(4):2159-70. doi: 10.1093/nar/gkt1269. Epub 2013 Dec 5.


H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation.

Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA.

PLoS Genet. 2013;9(8):e1003725. doi: 10.1371/journal.pgen.1003725. Epub 2013 Aug 22.


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

Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD.

Nucleic Acids Res. 2013 Nov;41(20):9310-24. doi: 10.1093/nar/gkt715. Epub 2013 Aug 9.


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

Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter NG.

Nano Lett. 2013 Feb 13;13(2):728-33. doi: 10.1021/nl304415b. Epub 2013 Jan 31.


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

Mazumder A, Tummler K, Bathe M, Samson LD.

Mol Cell Biol. 2013 Feb;33(3):635-42. doi: 10.1128/MCB.01020-12. Epub 2012 Nov 26.


Designer nucleic acids to probe and program the cell.

Krishnan Y, Bathe M.

Trends Cell Biol. 2012 Dec;22(12):624-33. doi: 10.1016/j.tcb.2012.10.001. Epub 2012 Nov 8. Review.


The kinetochore-bound Ska1 complex tracks depolymerizing microtubules and binds to curved protofilaments.

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.

Dev Cell. 2012 Nov 13;23(5):968-80. doi: 10.1016/j.devcel.2012.09.012. Epub 2012 Oct 18. Erratum in: Dev Cell. 2012 Nov 13;23(5):1081.


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

Monnier N, Guo SM, Mori M, He J, Lénárt P, Bathe M.

Biophys J. 2012 Aug 8;103(3):616-26. doi: 10.1016/j.bpj.2012.06.029.


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

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

Anal Chem. 2012 May 1;84(9):3880-8. doi: 10.1021/ac2034375. Epub 2012 Apr 15.


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

He J, Guo SM, Bathe M.

Anal Chem. 2012 May 1;84(9):3871-9. doi: 10.1021/ac2034369. Epub 2012 Apr 15.


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

Kim DN, Kilchherr F, Dietz H, Bathe M.

Nucleic Acids Res. 2012 Apr;40(7):2862-8. doi: 10.1093/nar/gkr1173. Epub 2011 Dec 10.


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

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

Curr Biol. 2011 Apr 12;21(7):606-11. doi: 10.1016/j.cub.2011.03.002.


A primer to scaffolded DNA origami.

Castro CE, Kilchherr F, Kim DN, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H.

Nat Methods. 2011 Mar;8(3):221-9. doi: 10.1038/nmeth.1570.


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

Kim DN, Altschuler J, Strong C, McGill G, Bathe M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D451-5. doi: 10.1093/nar/gkq1088. Epub 2010 Nov 3.


Conformational dynamics of supramolecular protein assemblies.

Kim DN, Nguyen CT, Bathe M.

J Struct Biol. 2011 Feb;173(2):261-70. doi: 10.1016/j.jsb.2010.09.015. Epub 2010 Sep 18.


Transiently crosslinked F-actin bundles.

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

Eur Biophys J. 2011 Jan;40(1):93-101. doi: 10.1007/s00249-010-0621-z. Epub 2010 Aug 24.


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

Sedeh RS, Fedorov AA, Fedorov EV, Ono S, Matsumura F, Almo SC, Bathe M.

J Mol Biol. 2010 Jul 16;400(3):589-604. doi: 10.1016/j.jmb.2010.04.043. Epub 2010 Apr 29.


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

Bathe M, Chang F.

Trends Microbiol. 2010 Jan;18(1):38-45. doi: 10.1016/j.tim.2009.10.002. Epub 2009 Dec 1. Review.


The subspace iteration method in protein normal mode analysis.

Sedeh RS, Bathe M, Bathe KJ.

J Comput Chem. 2010 Jan 15;31(1):66-74. doi: 10.1002/jcc.21250.


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