Publications

  • Bates, Jonathan, and Washington Mio. "Density Estimators of Gaussian Type on Closed Riemannian Manifolds." Journal of Mathematical Imaging and Vision (2013): 1-7.
  • Martinez, Diego H. Diaz, Facundo Memoli, and Washington Mio. "Multiscale Covariance Fields, Local Scales, and Shape Transforms." Geometric Science of Information. Springer Berlin Heidelberg, 2013. 794-801.
  • Mander, Luke, Mao Li, Washington Mio, Charless C. Fowlkes, and Surangi W. Punyasena. "Classification of grass pollen through the quantitative analysis of surface ornamentation and texture." Proceedings of the Royal Society B: Biological Sciences 280, no. 1770 (2013): 20131905.
  • D. Diaz Martinez, F. Memoli, W. Mio, Covariance Tensor Fields for Manifold Clustering, submitted in 2014.
  • Muller, Rolf, Jianguo Ma, Zhen Yan, Cindy Grimm, and Washington Mio. "Bioinspiration From Biodiversity in Sensor Design." In ASME 2011 International Mechanical Engineering Congress and Exposition, pp. 825-834. American Society of Mechanical Engineers, 2011.
  • Muller, Rolf, Lvyin Cai, Cindy Grimm, and Washington Mio. "Shape space analysis of structures in bat biosonar." The Journal of the Acoustical Society of America 129, no. 4 (2011): 2507-2507.
  • Jonathan Bates, Washington Mio, Density Estimators of Gaussian Type on Closed Riemannian Manifolds, Journal of Mathematical Imaging and Vision, September 2014, Volume 50, Issue 1-2, pp 53-59
  • A. Cinquin, M. Chiang, A. Paz, S. Hallman, O. Yuan, C. Fowlkes, O. Cinquin "Stochastic cycling balances stem cell self-renewal and senescence"
  • M. Chiang, S. Hallman, C. Fowlkes, O. Cinquin, "In vivo analysis analysis of single cell behavior by three-dimensional spatial cytometry"
  • M. Staller, C. Fowlkes, M. Bragdon, Z. Wunderlich, A. DePace, "A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate", preprint doi: http://dx.doi.org/10.1101/004788
  • C. Fowlkes, K. Eckenrode, M. Bragdon, M. Meyer, Z. Wunderlich, L. Simirenko,C. Hendriks, S. Keranen, C. Henreiquez, M. Biggin, M. Eisen, A. DePace, "A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila," PLoS Genetics, 7(10): e1002346, 2011.
  • J. Hengenius, M. Gribskov, A. Rundell, C. Fowlkes, D. Umulis, "Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosohpila melanogaster Embryo", PLoS ONE 6(11): e26797. doi:10.1371/journal.pone.0026797, 2011.
  • A. Chen, E. Lee, R. Tu, K. Santiago, A. Grosberg, C. Fowlkes, M. Khine, "Integrated Platform for Functional Monitoring of Biomimetic Heart Sheets Derived From Human Pluripotent Stem Cells", Biomaterials 35(2):675-683tex
  • A. Chen, D. Lieu, L. Freschauf, V. Lew, H. Sharma, J. Wang, D. Nguyen, I. Karakikes, R. Hajjar, A. Gopinathan, E. Botvinick, C. Fowlkes, R. Li, M. Khine, "Shrink-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac Derivatives", 10.1002/adma.201103463, Advanced Materials, 2011.
  • J. Luna, J. Ciriza, M. Ojeda-Garcia, M. Kong, A. Herren, D. Lieu, R. Li, C. Fowlkes, M. Khine, K. McCloskey, "Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart Cells", Tissue Engineering: Part C , 17(5), p. 579-588 , 2011
  • Yang G. (2014) Image-based computational tracking and analysis of spindle protein dynamics, in Mitosis: Methods and Protocols, Methods in Molecular Biology, D. Sharp ed., vol. 1136, DOI 10.1007/978-1-4939-0329-0_5, Springer.
  • Gunawardena S., Yang G., and Goldstein L. S. B. (2013) Presenilin controls kinesin-1 and dynein function during AP vesicle transport in vivo, Human Molecular Genetics, vol. 22, pp. 3838-3843.
  • Yang G. (2013) Bioimage informatics for understanding spatiotemporal dynamics of cellular processes, Wiley Interdisciplinary Reviews Systems Biology and Medicine, vol. 5, pp. 367-380. Booth-Gauthier E. A., Alcoser T. A., Yang G., and Dahl K. N. (2012) Force-induced changes in subnuclear movement and rheology, Biophysical Journal, vol. 103, pp. 2423-2431.
  • Reis R. F., Yang G., Szpankowski L., Weaver C., Shah S. B., Robinson J. T., Hays T. S., Danuser G., and Goldstein L. S. B. (2012) Molecular motor function in axonal transport in vivo probed by genetic and computational analysis in Drosophila,Molecular Biology of the Cell, vol. 23, pp. 1700-1714.
  • Chen K.C., Yang G., and Kovacevic J. (2014) Spatial density estimation based segmentation of super-resolution localization microscopy images, Proc. 2014 IEEE International Conference on Image Processing (ICIP), to appear.
  • Chen K.C., Qiu M., Kovacevic J., and Yang G. (2014) Computational image modeling for characterization and analysis of intracellular cargo transport, Proc. of CompIMAGE'14, to appear.
  • Lee H.-C. and Yang G. (2014) Integrating dimension reduction with mean-shift clustering for biological shape classification,Proc. 2014 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 254-257.
  • Chen K.-C. Kovacevic J., and Yang G. (2014) Structure-based determination of imaging length for super-resolution localization microscopy, Proc. 2014 IEEE International Symposium on Biomedical Imaging (ISBI), 991-994.
  • Yang G. and Olivo-Marin J.-C. (2013) Image-based representation and modeling of spatiotemporal cell dynamics, Proc. 2013 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 1198-1201
  • Qiu M. and Yang G. (2013), Drift correction for fluorescence live cell imaging through correlated motion detection, Proc. 2013 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 452-455
  • Chen K.-C., Yu Y., Li R., Lee H.-C., Yang G., and Kovacevic J. (2012), Adaptive active-mask image segmentation for quantitative characterization of mitochondrial morphology, Proc. 2012 IEEE International Conference on Image Processing (ICIP), pp. 2033-2036
  • Qiu M., Lee H.-C., and Yang G. (2012), Nanometer resolution tracking and modeling of bidirectional axonal cargo transport,Proc. 2012 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 992-995
  • Yang G. (2011) Nanometer resolution imaging and tracking of axonal cargo transport in normal and degenerative neurons (invited paper), Proc. 45th Annual Asilomar Conference on Signals, Systems, and Computers, pp. 431-435.
  • Hongfei Cao; Jing Han; Chi-Ren Shyu, "Object behavior mining from mitochondiral shape databases for degenerated nerve disease studies," IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.7,9, 18-21 Dec. 2013, doi: 10.1109/BIBM.2013.6732743
  • Mander, L., J. Rodriguez, P.G. Mueller, S.T. Jackson, and S.W. Punyasena. Identifying the pollen of an extinct spruce species in the Late Quaternary sediments of the Tunica Hills region, southeastern United States. Journal of Quaternary Science.
  • Mander, L. and S.W. Punyasena (in press). On the taxonomic resolution of pollen and spore records of Earth's vegetation. International Journal of Plant Sciences.
  • Han, J.G, H. Cao, A. Barb, S.W. Punyasena, C. Jaramillo, and C-R. Shyu. 2014. A Neotropical Miocene pollen database employing image-based search and semantic modeling. Applications in Plant Sciences. 2(8): 1400030.
  • Mander, L., S.J. Baker, C.M. Belcher, D.S. Haselhorst, J. Rodriguez, J.L. Thorn, S. Tiwari, D.H. Urrego, C.J. Wesseln and S.W. Punyasena. 2014. The accuracy and consistency of grass pollen identification by human analysts compared to recent computational methods. Applications in Plant Sciences. 2(8): 1400031.
  • Mander, L., M. Li, W. Mio, C.C. Fowlkes and S.W. Punyasena. 2013. Identification of grass pollen through the quantitative analysis of surface ornamentation and texture. Proceedings of the Royal Society B 280(1770): 20131905
  • Belcher, C.M, S.W. Punyasena, and M. Sivaguru. 2013. Novel application of confocal laser scanning microscopy and 3D volume rendering toward improving the resolution of the fossil record of charcoal. PLoS ONE 8(8):e72265.
  • Johnsrud, S., H. Yang, A. Nayak, and S.W. Punyasena. 2013. Semi-automated segmentation of pollen grains in microscopic images: A tool for three imaging modes. Grana 52(3): 181-191.
  • Sivaguru M., L. Mander, G. Fried, and S.W. Punyasena. 2012. Capturing the surface texture and shape of pollen: a comparison of microscopy techniques. PLoS ONE 7(6): e39129.
  • Punyasena, S.W., D.K. Tcheng, C. Wesseln, and P. G. Mueller. 2012. Classifying black and white spruce pollen using layered machine learning. New Phytologist 196(3): 937-944.
  • Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR, "An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites", IEEE/ACM Trans. Comput. Biology Bioinform., 2014
  • Hossain, M. Shahriar, Praveen Kumar Reddy Ojili, Cindy Grimm, Rolf Muller, Layne T. Watson, and Naren Ramakrishnan. "Scatter/gather clustering: flexibly incorporating user feedback to steer clustering results." Visualization and Computer Graphics, IEEE Transactions on 18, no. 12 (2012): 2829-2838.
  • Meymand, Sajjad Zeinoddini, Mittu Pannala, and Rolf Muller. "Characterization of the time-variant behavior of a biomimetic beamforming baffle." The Journal of the Acoustical Society of America 133.2 (2013): 1141-1150.
  • Motamedi, Mohammad, and Rolf Muller. "Characterization of the diversity in bat biosonar beampatterns with spherical harmonics power spectra." The Journal of the Acoustical Society of America 135.6 (2014): 3613-3619.
  • Pannala, Mittu, Sajjad Zeinoddini Meymand, and Rolf Muller. "Interplay of static and dynamic features in biomimetic smart ears." Bioinspiration & biomimetics 8.2 (2013): 026008.
  • Caspers, Philip, Alexander Leonessa, and Rolf Mueller. "Eigenbeam analysis of the diversity in bat biosonar beampatterns." The Journal of the Acoustical Society of America 135.4 (2014): 2207-2207.
  • Muller, Rolf, Jianguo Ma, Zhen Yan, Cindy Grimm, and Washington Mio. "Bioinspiration From Biodiversity in Sensor Design." In ASME 2011 International Mechanical Engineering Congress and Exposition, pp. 825-834. American Society of Mechanical Engineers, 2011.
  • Knutsen, Andrew K., Yulin V. Chang, Cindy M. Grimm, Ly Phan, Larry A. Taber, and Philip V. Bayly. "A new method to measure cortical growth in the developing brain." Journal of biomechanical engineering 132, no. 10 (2010): 101004.
  • Heider, Paul, Alain Pierre-Pierre, Ruosi Li, Rolf Mueller, and Cindy Grimm. "Comparing local shape descriptors." The Visual Computer 28, no. 9 (2012): 919-929.
  • Kurtek, Sebastian, Jingyong Su, Cindy Grimm, Michelle Vaughan, Ross Sowell, and Anuj Srivastava. "Statistical analysis of manual segmentations of structures in medical images." Computer Vision and Image Understanding 117, no. 9 (2013): 1036-1050.
  • Ly Phan, Sandra Rugonyi, Cindy Grimm, Visualization techniques for the developing chicken heart. (in preparation to IEEE TRANS. ON VISUALIZATION AND COMPUTER GRAPHICS), 2014
  • Shi, Liang, Sevan Goenezen, Stephen Haller, Monica T. Hinds, Kent L. Thornburg, and Sandra Rugonyi. "Alterations in pulse wave propagation reflect the degree of outflow tract banding in HH18 chicken embryos." American Journal of Physiology-Heart and Circulatory Physiology 305, no. 3 (2013): H386-H396.
  • Yin, Xin, Aiping Liu, Kent L. Thornburg, Ruikang K. Wang, and Sandra Rugonyi. "Extracting cardiac shapes and motion of the chick embryo heart outflow tract from four-dimensional optical coherence tomography images." Journal of biomedical optics 17, no. 9 (2012): 096005-096005.
  • Madeline Midgett, Sevan Goenezen and Sandra Rugonyi, Blood flow dynamics reflect degree of outflow tract banding in Hamburger -Hamilton stage 18 chicken embryos. J. R. Soc. Interface 2014 11, 20140643, published 27 August 2014
  • Li, Peng, Xin Yin, Liang Shi, Sandra Rugonyi, and Ruikang K. Wang. "In vivo functional imaging of blood flow and wall strain rate in outflow tract of embryonic chick heart using ultrafast spectral domain optical coherence tomography." Journal of biomedical optics 17, no. 9 (2012): 0960061-0960068.
  • Yin X, Liu A, Thornburg K, Wang RK, Rugonyi S. Extracting the 3D Cardiac Shape and Motion of the Chick Embryo Heart Outflow Tract from 4D Optical Coherence Tomography Images. Journal of Biomedical Optics 2012;17:096005.
  • Phan L, Knutsen AK, Bayly PV, Rugonyi S, Grimm C. Refining shape correspondence for similar objects using strain. Eurographic Workshop on 3D Retrieval 2011;Sect. 17-24.
  • Shi L, Goenezen S, Haller S, Hinds MT, Thornburg KL, Rugonyi S. Alterations in pulse wave propagation reflect the degree of outflow tract banding in HH18 chicken embryos. American Journal of Physiology - Heart and Circulatory Physiology 2013;305:H386-H96.
  • Midgett M, Goenezen S, Rugonyi S. Blood flow dynamics reflect degree of outflow tract banding in Hamburger-Hamilton stage 18 chicken embryos. Journal of the Royal Society Interface 2014;11:20140643.
  • Zelaya J, Goenezen S, Dargon P, Azarbal A-F, Rugonyi S. Improving the Efficiency of Abdominal Aortic Aneurysm Wall Stress Computations. PLoS ONE 2014;9:e101353.
  • Liu, Aiping, Xin Yin, Liang Shi, Peng Li, Kent L. Thornburg, Ruikang Wang, and Sandra Rugonyi. "Biomechanics of the chick embryonic heart outflow tract at HH18 using 4D optical coherence tomography imaging and computational modeling." PloS one 7, no. 7 (2012): e40869.
  • Midgett M, Rugonyi S. Congenital heart malformations induced by hemodynamic altering surgical interventions. Frontiers in Physiology 2014;5.
  • Keller BB. Embryonic cardiovascular function, coupling and maturation: a species view. In: Burggren WW, Keller BB, eds. Development of Cardiovascular Systems. Cambridge, MA: University Press; 1998.
  • Clark EB, Rosenquist GC. Spectrum of cardiovascular anomalies following cardiac loop constriction in the chick embryo. Birth Defects: Original Article Series 1978;XIV:431-42.
  • Bergwerff M, DeRuiter MC, Poelmann RE, Gittenberger-de Groot AC. Onset of elastogenesis and downregulation of smooth muscle actin as distinguishing phenomena in artery differentiation in the chick embryo. Anat Embryol (Berl) 1996;194:545?57.
  • B. Kong, C. Fowlkes, "Fast Convolutional Sparse Coding", UCI Technical Report, May 2014 http://www.ics.uci.edu/~fowlkes/papers/kf_fcsc_techreport_2014.pdf
  • A. Chen, E. Lee, R. Tu, K. Santiago, A. Grosberg, C. Fowlkes, M. Khine, "Integrated Platform for Functional Monitoring of Biomimetic Heart Sheets Derived From Human Pluripotent Stem Cells", Biomaterials 35(2):675-683, http://www.ics.uci.edu/~fowlkes/papers/chen_et_al_biomaterials_2013.pdf
  • L. Mander, M. Li, W. Mio, C. Fowlkes, S. Punyasena, "Classification of grass pollen through the quantitative analysis of surface ornamentation and texture", Proc. R. Soc. B. 2013 280 (1770) http://www.ics.uci.edu/~fowlkes/papers/mlmfp_pollen.pdf
  • J. Yarkony, A. Ihler, C. Fowlkes, "Fast Planar Correlation Clustering for Image Segmentation'', Proc. of ECCV, Firenze, Italy (Oct. 2012). arXiv:1208.0378v1 http://www.ics.uci.edu/~fowlkes/papers/yif-eccv12-extended.pdf
  • X. Zhu, C. Vondrick, D. Ramanan, C. Fowlkes, "Do we need more training data or better models for object detection?", Proc. of BMVC, Surrey, UK (Sept. 2012). http://www.ics.uci.edu/~fowlkes/papers/zvrf-bmvc12.pdf
  • C. Fowlkes, K. Eckenrode, M. Bragdon, M. Meyer, Z. Wunderlich, L. Simirenko, C. Hendriks, S. Keranen, C. Henreiquez, M. Biggin, M. Eisen, A. DePace, "A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila," PLoS Genetics, 7(10): e1002346, 2011. http://www.ics.uci.edu/~fowlkes/papers/FowlkesDePace_PLoSGen2011.pdf
  • J. Hengenius, M. Gribskov, A. Rundell, C. Fowlkes, D. Umulis, "Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosohpila melanogaster Embryo", PLoS ONE 6(11): e26797. doi:10.1371/journal.pone.0026797, 2011. http://www.ics.uci.edu/~fowlkes/papers/Hengenuius_et_al_PLoSone2011.pdf
  • A. Chen, D. Lieu, L. Freschauf, V. Lew, H. Sharma, J. Wang, D. Nguyen, I. Karakikes, R. Hajjar, A. Gopinathan, E. Botvinick, C. Fowlkes, R. Li, M. Khine, "Shrink-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac Derivatives", 10.1002/adma.201103463, Advanced Materials, 2011. http://www.ics.uci.edu/~fowlkes/papers/Chen_et_al_AdvMat2011.pdf
  • J. Luna, J. Ciriza, M. Ojeda-Garcia, M. Kong, A. Herren, D. Lieu, R. Li, C. Fowlkes, M. Khine, K. McCloskey, "Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart Cells", Tissue Engineering: Part C , 17(5), p. 579-588 , 2011 http://www.ics.uci.edu/~fowlkes/papers/Luna_et_al_TEC2011.pdf