DBBS - Biochemistry, Biophysics, and Structural Biology

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  • 2013

    Quantitative evaluation of registration methods for atlas-based Diffuse Optical Tomography

    Wu, X., Eggebrecht, A. T., Culver, J. P., Zhan, Y., Basevi, H. & Dehghani, H., 2013, European Conference on Biomedical Optics, ECBO 2013. Optical Society of America, (Optics InfoBase Conference Papers).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Raman spectroscopic sensing using whispering gallery microresonators

    Edwards, P., Janisch, C., Peng, B., Ozdemir, S. K., Yang, L. & Liu, Z., 2013, Ultrafast Imaging and Spectroscopy. SPIE, 884512. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8845).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Real-time segmentation and tracking of brain metabolic state in ICU EEG recordings of burst suppression

    Westover, M. B., Ching, S., Shafi, M. M., Cash, S. S. & Brown, E. N., 2013, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 7108-7111 4 p. 6611196. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    17 Scopus citations

  • Reflection detection of nanoparticles using whispering gallery microresonators

    Zhu, J., Ozdemir, S. K. & Yang, L., 2013, CLEO: Science and Innovations, CLEO_SI 2013. p. CM2H.5 (CLEO: Science and Innovations, CLEO_SI 2013).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Reflection detection of nanoparticles using whispering gallery microresonators

    Zhu, J., Ozdemir, S. K. & Yang, L., 2013, 2013 Conference on Lasers and Electro-Optics, CLEO 2013. IEEE Computer Society, 6833167. (2013 Conference on Lasers and Electro-Optics, CLEO 2013).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Single-molecule orientation measurements with a quadrated pupil

    Backer, A. S., Backlund, M. P., Lew, M. D. & Moerner, W. E., 2013, Imaging Systems and Applications, ISA 2013. Optical Society of America (OSA), (Optics InfoBase Conference Papers).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access

  • The double-helix point spread function enables precise and accurate measurement of 3D single-molecule localization and orientation

    Backlund, M. P., Lew, M. D., Backer, A. S., Sahl, S. J., Grover, G., Agrawal, A., Piestun, R. & Moerner, W. E., 2013, Single Molecule Spectroscopy and Superresolution Imaging VI. 85900L. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8590).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    33 Scopus citations

  • The effects of extracellular matrix protein insufficiency and treatment on the stiffness of arterial smooth muscle cells

    Espinosa, G., Bennett, L., Gardner, W. & Wagenseil, J., 2013, ASME 2013 Summer Bioengineering Conference, SBC 2013. (ASME 2013 Summer Bioengineering Conference, SBC 2013; vol. 1 B).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • The effects of noise and spatial sampling on identification of material parameters by magnetic resonance elastography

    Connesson, N., Clayton, E. H., Bayly, P. V. & Pierron, F., 2013, Mechanics of Biological Systems and Materials - Proceedings of the 2012 Annual Conference on Experimental and Applied Mechanics. p. 161-168 8 p. (Conference Proceedings of the Society for Experimental Mechanics Series; vol. 5).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Ultrasound sensing using a fiber coupled silica microtoroid resonator encapsulated in a polymer

    Monifi, F., Peng, B., Ozdemir, S. K., Ma, L., Maslov, K., Wang, L. V. & Yang, L., 2013, 2013 IEEE Photonics Conference, IPC 2013. p. 215-216 2 p. 6656511. (2013 IEEE Photonics Conference, IPC 2013).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    14 Scopus citations
  • 2012

    3D dilation and distortion estimated in the living human brain from mr images of propagating shear waves

    Clayton, E. H., Genin, G. M. & Bayly, P. V., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 57-58 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • An on-chip tunable add-drop filter using a microtoroid resonator

    Monifi, F., Ozdemir, S. K., Yang, L. & Friedlein, J., 2012, 2012 IEEE Photonics Conference, IPC 2012. p. 260-261 2 p. 6358591. (2012 IEEE Photonics Conference, IPC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Application of the virtual fields method to magnetic resonance elastography data

    Pierron, F., Bayly, P. V. & Namani, R., 2012, Applications of Imaging Techniques to Mechanics of Materials and Structures - Proceedings of the 2010 Annual Conference on Experimental and Appied Mechanics. p. 135-142 8 p. (Conference Proceedings of the Society for Experimental Mechanics Series; vol. 4).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    3 Scopus citations

  • A quantitative spatial comparison of high-density diffuse optical tomography and fMRI cortical mapping

    Eggebrecht, A. T., White, B. R., Ferradal, S. L., Zhan, Y., Snyder, A. Z., Dehghani, H. & Culver, J. P., 2012, Biomedical Optics, BIOMED 2012. Optical Society of America (OSA), p. BSu4A.2 (Biomedical Optics, BIOMED 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access

  • Artificial tissue bioreactor (ATB) for biological and imaging applications

    Whitehead, T. D., Nemanich, S. T. & Shoghi, K. I., 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. p. 2420-2423 4 p. 6346452. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Cellular membrane tether retraction: Experiment and model

    Shao, J. Y. & Liu, B., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 1163-1164 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Comparison of dynamic mechanical testing and MR elastography of biomaterials

    Clayton, E. H., Okamoto, R. J., Wilson, K. S., Namani, R. & Bayly, P. V., 2012, Applications of Imaging Techniques to Mechanics of Materials and Structures - Proceedings of the 2010 Annual Conference on Experimental and Appied Mechanics. p. 143-150 8 p. (Conference Proceedings of the Society for Experimental Mechanics Series; vol. 4).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Confidence intervals for estimation of the concentration and brightness of multiple diffusing species

    Abney, T. M., Wakatsuki, T., Elson, E. L. & Genin, G., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 673-674 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Confidence intervals for estimation of the concentration and brightness of multiple diffusing species

    Rong, X., Pryse, K. M., Whisler, J. A., Jiang, Y., McConnaughey, W. B., Melnykov, A., Genin, G. M. & Elson, E. L., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 791-792 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Encapsulation of a microtoroid resonator side-coupled to a fiber taper into a polymer matrix

    Monifi, F., Ozdemir, S. K., Yang, L. & Friedlein, J., 2012, 2012 IEEE Photonics Conference, IPC 2012. p. 632-633 2 p. 6358780. (2012 IEEE Photonics Conference, IPC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Exploring semi-supervised coreference resolution of medical concepts using semantic and temporal features

    Raghavan, P., Fosler-Lussier, E. & Lai, A. M., 2012, Proceedings of the 2012 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. Association for Computational Linguistics (ACL), p. 731-741 11 p. (NAACL HLT 2012 - 2012 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Proceedings of the Conference).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    9 Scopus citations

  • Fiber taper based Raman spectroscopic sensing

    Edwards, P. S., Janisch, C. T., He, L., Zhu, J., Yang, L. & Liu, Z., 2012, 2012 IEEE Photonics Conference, IPC 2012. p. 501-502 2 p. 6358712. (2012 IEEE Photonics Conference, IPC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    3 Scopus citations

  • Functional connectivity mapping in hospitalized infants using diffuse optical tomography

    Ferradal, S. L., Liao, S. M., Eggebrecht, A. T., Inder, T. E. & Culver, J. P., 2012, Biomedical Optics, BIOMED 2012. Optical Society of America (OSA), p. BSu4A.7 (Biomedical Optics, BIOMED 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Hybrid photonic molecules

    Peng, B., Ozdemir, S. K., Zhu, J. & Yang, L., 2012, 2012 Conference on Lasers and Electro-Optics, CLEO 2012. 6326723. (2012 Conference on Lasers and Electro-Optics, CLEO 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Hybrid photonic molecules

    Peng, B., Ozdemir, S. K., Zhu, J. & Yang, L., 2012, Quantum Electronics and Laser Science Conference, QELS 2012. (Optics InfoBase Conference Papers).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Hybrid photonic molecules

    Peng, B., Ozdemir, S. K., Zhu, J. & Yang, L., 2012, CLEO: Applications and Technology, CLEO_AT 2012. Optical Society of America (OSA), p. JW4A.93 (CLEO: Applications and Technology, CLEO_AT 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Identification of a transversely isotropic material model for white matter in the brain

    Feng, Y., Okamoto, R. J., Namani, R., Genin, G. M. & Bayly, P. V., 2012, ASME 2012 International Mechanical Engineering Congress and Exposition, IMECE 2012. p. 787-794 8 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Interfacial phases on giant unilamellar vesicles

    Jiang, Y., Genin, G. M., Singamaneni, S. & Elson, E. L., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 705-706 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Learning to temporally order medical events in clinical text

    Raghavan, P., Fosler-Lussier, E. & Lai, A. M., 2012, 50th Annual Meeting of the Association for Computational Linguistics, ACL 2012 - Proceedings of the Conference. p. 70-74 5 p. (50th Annual Meeting of the Association for Computational Linguistics, ACL 2012 - Proceedings of the Conference; vol. 2).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    12 Scopus citations

  • Magnetic resonance elastography of the mouse vitreous humor in vivo

    Clayton, E. H., Wang, Q., Song, S. K., Okamoto, R. J. & Bayly, P. V., 2012, Applications of Imaging Techniques to Mechanics of Materials and Structures - Proceedings of the 2010 Annual Conference on Experimental and Appied Mechanics. p. 129-133 5 p. (Conference Proceedings of the Society for Experimental Mechanics Series; vol. 4).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Measurement of brain biomechanics in vivo by magnetic resonance imaging

    Bayly, P. V., Clayton, E. H., Feng, Y., Abney, T., Namani, R., Okamoto, R. J. & Genin, G. M., 2012, Applications of Imaging Techniques to Mechanics of Materials and Structures - Proceedings of the 2010 Annual Conference on Experimental and Appied Mechanics. p. 117-128 12 p. (Conference Proceedings of the Society for Experimental Mechanics Series; vol. 4).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    6 Scopus citations

  • Medical event coreference resolution using the UMLS metathesaurus and temporal reasoning

    Raghavan, P., Brew, C., Fosler-Lussier, E. & Lai, A. M., 2012, IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. p. 465-472 8 p. (IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Mode splitting based single particle size measurement in water

    Kim, W., Ozdemir, S. K., Zhu, J. & Yang, L., 2012, CLEO: Science and Innovations, CLEO_SI 2012. Optical Society of America (OSA), p. CTu2L.1 (CLEO: Science and Innovations, CLEO_SI 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Mode splitting based single particle size measurement in water

    Kim, W., Ozdemir, S. K., Zhu, J. & Yang, L., 2012, 2012 Conference on Lasers and Electro-Optics, CLEO 2012. 6326072. (2012 Conference on Lasers and Electro-Optics, CLEO 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Multi-modal in cellulo evaluation of NPR-C targeted C-ANF-peptide and C-ANF-comb nanoparticles

    Shokeen, M., Pressly, E., Connal, L., Liu, Y., Hawker, C. J., Woodard, P. K., Anderson, C. J., Achilefu, S. & Welch, M. J., 2012, Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications IV. 82330U. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8233).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • On-chip whispering-gallery-mode lasers for sensing applications

    He, L., Ozdemir, S. K., Zhu, J., Kim, W. & Yang, L., 2012, Laser Resonators, Microresonators, and Beam Control XIV. 82361B. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8236).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Optimal control in molecular-level gene manipulation

    Yu, J. & Li, J. S., 2012, WCICA 2012 - Proceedings of the 10th World Congress on Intelligent Control and Automation. p. 4978-4983 6 p. 6359422. (Proceedings of the World Congress on Intelligent Control and Automation (WCICA)).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Optimizing statistical analysis for DOT to image rapid brain function events

    Hassanpour, M., White, B. R., Eggebrecht, A. T., Ferradal, S. & Culver, J. P., Dec 1 2012, Biomedical Optics, BIOMED 2012. p. Bsu3A.71 (Biomedical Optics, BIOMED 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Quantum multi-channel decoupling

    Liu, P. L., Li, S. & Tarn, T. J., 2012, WCICA 2012 - Proceedings of the 10th World Congress on Intelligent Control and Automation. p. 2286-2290 5 p. 6358255. (Proceedings of the World Congress on Intelligent Control and Automation (WCICA)).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Shear wave propagation of the ferret brain at multiple frequencies in vivo

    Feng, Y., Chang, Y., Okamoto, R. J. & Bayly, P. V., 2012, ASME 2012 International Mechanical Engineering Congress and Exposition, IMECE 2012. p. 779-785 7 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Similarity-based appearance-prior for fitting a subdivision mesh in gene expression images

    Le, Y. H., Kurkure, U., Paragios, N., Ju, T., Carson, J. P. & Kakadiaris, I. A., 2012, Medical Image Computing and Computer-Assisted Intervention, MICCAI2012 - 15th International Conference, Proceedings. Ayache, N., Delingette, H., Golland, P. & Mori, K. (eds.). Springer Verlag, p. 577-584 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7510 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    5 Scopus citations

  • Spectrally constrained functional diffuse optical tomography of the adult brain

    Zhan, Y., Eggebrecht, A., Culver, J. & Dehghani, H., 2012, Digital Holography and Three-Dimensional Imaging, DH 2012. p. JM3A.68 (Digital Holography and Three-Dimensional Imaging, DH 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • Spectrally constrained functional diffuse optical tomography of the adult brain

    Zhan, Y., Eggebrecht, A., Culver, J. & Dehghani, H., 2012, Biomedical Optics, BIOMED 2012. Optical Society of America (OSA), p. JM3A.68 (Biomedical Optics, BIOMED 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    1 Scopus citations

  • Synthesis of optimal ensemble controls for linear systems using the singular value decomposition

    Zlotnik, A. & Li, S., 2012, 2012 American Control Conference, ACC 2012. Institute of Electrical and Electronics Engineers Inc., p. 5849-5854 6 p. 6315297. (Proceedings of the American Control Conference).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    20 Scopus citations

  • Targeting biological sensing with commercial SERS substrates

    Farrell, M. E., Singamaneni, S. & Pellegrino, P. M., 2012, Advanced Environmental, Chemical, and Biological Sensing Technologies IX. 836602. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8366).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    6 Scopus citations

  • Temporal classification of medical events

    Raghavan, P., Fosler-Lussier, E. & Lai, A. M., 2012, BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings. Association for Computational Linguistics (ACL), p. 29-37 9 p. (BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    13 Scopus citations

  • The apparent flexural rigidity of the flagellar axoneme depends on resistance to inter-doublet sliding

    Xu, G., Wilson, K. S., Okamoto, R. J., Shao, J. Y., Dutcher, S. K. & Bayly, P. V., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 397-398 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • The role of singular control in frictionless atom cooling in a harmonic trapping potential

    Stefanatos, D. & Li, S., 2012, 2012 American Control Conference, ACC 2012. Institute of Electrical and Electronics Engineers Inc., p. 5061-5066 6 p. 6314974. (Proceedings of the American Control Conference).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    2 Scopus citations

  • Viscoelastic properties of living human brain by local frequency estimation applied to distortional wave fields

    Clayton, E. H., Genin, G. M. & Bayly, P. V., 2012, ASME 2012 Summer Bioengineering Conference, SBC 2012. p. 531-532 2 p. (ASME 2012 Summer Bioengineering Conference, SBC 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  • 2011

    A geometric study of v-style pop-ups: Theories and algorithms

    Li, X. Y., Ju, T., Gu, Y. & Hu, S. M., Jul 2011, Proceedings of ACM SIGGRAPH 2011, SIGGRAPH 2011. 4 ed. Vol. 30. 98

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    Open Access
    43 Scopus citations