Contact Information

The IGERT Program
Winston Chung Hall Room 216
University of California, Riverside
900 University Avenue
Riverside, CA 92521-0425

Tel: (951)-827-3954

Participating Ph.D. Programs:
Electrical and Computer Engineering
Bioengineering
Computer Science and Engineering
Cell, Molecular and Development Biology
Botany & Plant Sciences
Nematology
Plant Pathology and Microbiology
Biomedical Sciences
Psychology
Biology
Entomology
Mechanical Engineering
Chemical & Environmental Engineering

IGERT on Video Bioinformatics Fellows Publications

Edited Books

• B. Bhanu and P. Talbot, "Video Bioinformatics - From Live Imaging to Knowledge", Springer 2016. ISBN: 978-3-319-23723-7.

Journals

• Harrison*, R. E., Gorham, R. D., Morikis, "Synergy of Putative Binding Modes in the Factor H (CCP 19-20) and C3d Complex" Biophysical Journal, 2016.
• Bays*, B., Turk-Browne, N., Seitz, A., "Dissociable behavioral outcomes of visual statistical learning," Visual Cognition, 2016.
• C. Zhang, M. Brown, W. Van de Ven, Z. Zhang, B. Wu, M. Young, L. Synek, D. Borchardt, R. Harrison, S. Pan, N. Luo, Y. Huang, Y. Ghang, N. Ung, R. Li, J. Isley, D. Morikis, J. Song, W. Guo, R. Hooley, C. Chang, Z. Yang, V. Zarsky, G. Muday, G. Hicks, and N. Raikhel, "Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis,” Proceedings of the National Academy of Sciences, vol. 113, no. 1, pp. E41–E50, Jan. 2016.
• K. Mkrtchyan, A. Chakraborty, and A. Roy-Chowdhury,"Optimal landmark selection for registration of 4D confocal image stacks in arabidopsis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016
• A. Tambo and B. Bhanu, “Segmentation of pollen tube growth videos using dynamic bi-modal fusion and seam carving,” IEEE Trans. on Image Processing, (in Press), 2016.
• A. Zahedi, V. On, S. Lin, B.C. Bays, E. Omaiye, B. Bhanu and P. Talbot, “Evaluating cell processes, quality, and biomarkers in pluripotent stem cells using video bioinformatics” Plos One, 2016.
• Cabrera*, I.E., Pacentine, I., Lim, A., Guerrero, N., Krystofova, S., Li, L., Michkov, A., Servin, J., Ahrendt, S., Carrillo, A., Davidson, L., Barsoum, A., Cao, J., Castillo, R., Chen, W., Dinkchian,A., Kim, S., Kitada, S., Lai, T., Mach, A., Malekyan, C., Moua, T., Torres, C., Yamamoto, A., Borkovich, K., "Global analysis of G protein coupled receptor genes in the filamentous fungus, Nuerospora crassa," G3 (Genes, Genomics, Genetics), 2015.
• X. Guan, B. Bhanu, P. Talbot and J-H Weng, “Extraction of blebs in human embryonic stem cell videos,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015.
• A.L. Tambo, B. Bhanu, N. Ung, N. Thakoor, N. Luo and Z. Yang, “Understanding pollen tube growth dynamics using the unscented Kalman filter,” Pattern Recognition Letters, 2015.
• Bianchi*, A., Bhanu, B., and Obenaus, A. (2015, January). Dynamic low-level context for the detection of mild traumatic brain injury. IEEE Transactions on Biomedical Engineering, 62(1).
• Cruz*, A., Bhanu, B., and Thakoor, N. (2015). Background suppressing Gabor energy filtering. Pattern Recognition Letters, 52, 40-47.
• Cruz*, A., Bhanu, B. and Thakoor,N. (2014, December), Vision and attention theory based sampling for continuous facial emotion recognition. IEEE Transactions on Affective Computing, 5(4), pp. 418-431.
• Eberle*, M., Hsu, M., Rodriguez*, C., Szu, J., Oliveira*, M., Binder, D., & Park, B. (2015). Localization of cortical tissue optical changes during seizure activity in vivo with opticalcoherence tomography. Biomedical Optics Express, 6(5), 1812-1827. doi:10.1364/BOE.6.001812
• Guan*, B.X., Bhanu, B., Talbot, P. and Lin, S. (2014, June). Bio-driven cell region detection in human embryonic stem cell assay. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(3), pp. 604-611.
• Harrison*, R., Gorham, R., and Morikis, D. (2015). Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex. Protein Science. doi: 10.1002/pro.2650
• Khachatoorian*, C., Ramirez, R., Hernandez, F., Serna, R., and Kwok, E. (2015). Overexpressed Arabidopsis Annexin4 Accumulates in Inclusion Body-like Structures. Acta Histochemica 117 (3), 279–287. doi:10.1016/j.acthis.2015.03.005.
• Larsen*, J., Espinoza, E., and Vullev, V.(2015). Bioinspired molecular electrets: bottom-up approach to energy materials and applications. Journal of Photonics for Energy, 5(1), 055598-055598.
• Rodriguez*, C., Szu, J., Eberle*, M., Wany, Y., Hsu, M., Binder, D., Park. B. (2014) Decreased light attenuation in cerebral cortex during cerebral edema detected using optical coherence tomography. Neurophotonics 1(2).
• A. Bianchi*, B. Bhanu, V. Donovan, and A. Obenaus. "Visual and Contextual Modeling for the Detection of Repeated Mild Traumatic Brain Injury." IEEE Transactions on Medical Imaging, vol. 33, no. 1, pp. 11-22, 2014. doi:10.1109/TMI.2013.2269317
• A. Cruz*, B. Bhanu, and N. Thakoor. "Vision and Attention Theory Based Sampling for Continuous Facial Emotion Recognition." IEEE Transactions on Affective Computing, 2014. doi:10.1109/TAFFC.2014.2316151
• V. Donovan*, C. Kim, A. K. Anugerah, J. S. Coats, U. Oyoyo, A. C. Pardo, and A. Obenaus. "Repeated mild traumatic brain injury results in long-term white-matter disruption." Journal of Cerebral Blood Flow & Metabolism, 2014. doi:10.1038/jcbfm.2014.6
• E. G. Freeman*, Z. Wisotsky, and A. Dahanukar. "Detection of sweet tastants by a conserved group of insect gustatory receptors." Proceedings of the National Academy of Sciences, vol. 111, no. 4, pp. 1598-1603, 2014. doi:10.1073/pnas.1311724111
• D. W. McBride*, and V. G. J. Rodgers. "A generalized free-solvent model for the osmotic pressure of multi-component solutions containing protein-protein interactions." Mathematical Biosciences, vol. 253, pp. 72-87, 2014. doi:10.1016/j.mbs.2014.04.002
• N. Ghosh, Y. Sun, B. Bhanu, S. Ashwal, and A. Obenaus. "Automated Detection of Brain Abnormalities in Neonatal Hypoxia Ischemic Injury from MR Images." Medical Image Analysis (2014). doi:10.1016/j.media.2014.05.002
• Y. Damestani, C. L. Reynolds*, J. Szu, M. S. Hsu, Y. Kodera, D. K. Binder, B. H. Park, J. E. Garay, M. P. Rao, and G. Aguilar. "Transparent nanocrystalline yttria-stabilized-zirconia calvarium prosthesis." Nanomedicine: Nanotechnology, Biology and Medicine, vol. 9, no. 8, pp. 1135-1138, 2013. doi: 10.1016/j.nano.2013.08.002
• V. Nunez, S. Upadhyayula, B. Millare, J. M. Larsen*, A. Hadian, S. Shin, P. Vandrangi, S. Gupta, H. Xu, A. P. Lin, G. Y. Georgiev and V. I. Vullev "Microfluidic Space-Domain Time-Resolved Emission Spectroscopy of Terbium (III) and Europium (III) Chelates with Pyridine-2, 6-Dicarboxylate." Analytical Chemistry, vol. 85, no. 9, pp. 4567-4577, 2013. doi:10.1021/ac400200x
• M. M. Eberle*, C. L. Reynolds*, J. I. Szu, Y. Wang, A. M. Hansen, M. S. Hsu, M. S. Islam, D. K. Binder, and B. H. Park. "In vivo detection of cortical optical changes associated with seizure activity with optical coherence tomography." Biomedical Optics Express, vol. 3, no. 11, pp. 2700-2706, 2012. doi:10.1364/BOE.3.002700
• J. I. Szu, M. M. Eberle*, C. L. Reynolds*, M. S. Hsu, Y. Wang, C. M. Oh, M. S. Islam, B. H. Park, and D. K. Binder. "Thinned-skull cortical window technique for in vivo optical coherence tomography imaging." Journal of Visualized Experiments: JoVE, vol. 69, pp. e50053-e50053, 2011. doi: 10.3791/50053Z. Wisotsky, A. Medina, E. G. Freeman*, and A. Dahanukar. "Evolutionary differences in food preference rely on Gr64e, a receptor for glycerol." Nature Neuroscience, vol. 14, no. 12, pp. 1534-1541, 2011. doi:10.1038/nn.2944

Poster Presentation + Full paper in the proceedings

• Harrison*, R. Gorham, R., Morikis, D., (2016). Synergy of putative binding modes in the factor H (CCP 1920) and C3d complex. Poster Presentation at the Biophysical Society 60th Annual Meeting. Feb 2016, Los Angeles, CA
• Zahedi*, A., On*, V., Lin, S., Bays*, B., Omaiye, E., Bhanu, B., Talbot, P. (2016). Quantitative evaluation of pluripotent stem cell processes, quality, and biomarkers using StemCellQC, a Video Bioinformatics Software Toolkit. Poster Presentation at the International Society for Stem Cell Research, June 2016, San Francisco, CA
• Tambo*, A.L., Bhanu, B., (2015). Dynamic Bimodal fusion of images for segmentation of pollen tubes in video. Poster Presentation at IEEE International Conference on Image Processing, September 2015, Quebec City, Canada
• Zahedi*, A., Phandthong, R., On*, V., Talbot, P. (2015). Mitochondrial redox state, morphology and mitophagy in stressed neural stem cells. Poster Presentation at the Annual Meetings of the American Society of Cell Biology, December 2015, San Diego, CA
• Zahedi*, A., On*, V., Lin, S., Bays*, B., Omaiye, E., Bhanu, B., Talbot, P. (2015). StemCellQC: A toolkit for evaluating the effects of tobacco products including electronic cigarettes on prenatal development. Poster Presentation at the Tobacco Control, Research, and Education: Joining Forces to Address New Challenges (sponsored by TRDRP), October 2015, Sacramento, CA
• Cruz*, A.C., Bhanu, B. and Thakoor, N.S. (2014, October). One shot emotion scores for facial emotion recognition. IEEE International Conference on Image Processing.
• Guan*, B.X., Bhanu, B., P. Talbot, P., Lin S., and Weng*, N. (2014, October). Comparison of texture features for human embryonic stem cells with bio-inspired multi-class support vector machine. IEEE International Conference on Image Processing.
• Hill*, D., Anderson, L., Hill, C., and Grover, W. (2014, August). MECs: Building blocks for custom microfluidic diagnostics in the developing world. In Engineering in Medicine and Biology Society (EMBC). 36th Annual International Conference of the IEEE (pp. 786-788).
• Lin, S., Phandthong, R., Weng*, N., Montes, B. and P. Talbot (June 2014). Toxicology-in-dish: using in vitro stem cells models to predict health effects due to cigarette smoke exposure. Pacific Division of the American Association for the Advancement of Science volume 33 part 1 page 181. This presentation received the Third Place Award in the Cell and Molecular Subsection.
• Lin, S., Phandthong, R., Weng*, N., Montes, B. and P. Talbot (October 2014). Toxicology-in-dish: using in vitro stem cells models to predict health effects due to cigarette smoke exposure. Advances in Aerosol Dosimetry Research, Irvine, CA.
• Tambo*, A., Bhanu, B., Luo, N., Harlow*, G., and Yang, Z. (2014, August). IntegratedModel for Understanding Pollen Tube Growth in Video. In Pattern Recognition (ICPR). 22nd International Conference on (pp. 2727-2732).
• Zahedi* A., On*, V., Lin S., Bays*, B., Bhanu, B., and Talbot, P. (2015, March).StemCellQC™: A Smart Detection Multiplexing Toolkit for Toxicological Evaluation of Stem Cell Processes and Health. 54th Annual Society of Toxicology Meeting, San Diego, California.
• A. Bianchi*, B. Bhanu, V. Donovan* and A. Obenaus. "Detecting mild traumatic brain injury using dynamic low level context." In IEEE ICIP 2013. doi:10.1109/ICIP.2013.6738241
• A. C. Cruz*, B. Bhanu, and N. S. Thakoor. "Facial emotion recognition with anisotropic inhibited Gabor energy histograms." In IEEE ICIP 2013.
• B. X. Guan*, B. Bhanu, N. S. Thakoor, P. Talbot, and S. Lin. "Automatic cell region detection by k-means with weighted entropy." In IEEE International Symposium on Biomedical, 2013. doi:10.1109/ISBI.2013.6556501
• G. Harlow*, A. C. Cruz*, S. Li, N. S. Thakoor, A. C. Bianchi*, J. Chen, B. Bhanu, and Z. Yang. "Automated spatial analysis of ARK2: Putative link between microtubules and cell polarity." In IEEE International Symposium on Biomedical, 2013. doi:10.1109/ISBI.2013.6556623
• A. Bianchi*, B. Bhanu, V. Donovan*, and A. Obenaus. "Contextual and visual modeling for detection of mild traumatic brain injury in MRI." In IEEE ICIP, 2012. doi:10.1109/TMI.2013.2269317
• A. C. Cruz*, B. Bhanu. "A biologically inspired approach for fusing facial expression and appearance for emotion recognition." In IEEE ICIP 2012. doi:10.1109/ICIP.2012.6467437
• A. C. Cruz*, B. Bhanu and N. S. Thakoor. "Facial emotion recognition with expression energy," In ACM International Conference on Multimodal Interaction Workshops, 2012. doi:10.1145/2388676.2388777
• A. C. Cruz*, B. Bhanu and N. S. Thakoor. "Facial emotion recognition in continuous video," In International Conference on Pattern Recognition, 2012.
• B. X. Guan*, B. Bhanu, P. Talbot, and S. Lin. "Detection of non-dynamic blebbing single unattached human embryonic stem cells." In IEEE ICIP, 2012. doi:10.1109/ICIP.2012.6467354
• A. C. Cruz*, B. Bhanu and S. Yang "A psychologically-inspired match-score fusion model for video-based facial expression recognition." In Affective Computing and Intelligent Interaction, 2011. doi:10.1007/978-3-642-24571-8_45
• B. X. Guan*, B. Bhanu, N. S. Thakoor, P. Talbot, and S. Lin. "Human embryonic stem cell detection by spatial information and mixture of Gaussians," In IEEE International Conf. On Health Informatics, Imaging and System Biology, 2011. doi:10.1109/HISB.2011.30
• K. Mkrtchyan, D. Singh, M. Liu, V. Reddy, A. Roy-Chowdhury, and M. Gopi. "Efficient cell segmentation and tracking of developing plant meristem." In IEEE ICIP, 2011. doi:10.1109/ICIP.2011.6116040
• Chakraborty, A., Liu, M., Mkrtchyan*, K., Reddy, G.V., Roy-Chowdhury, A., (2010), "Cell volume estimation from a sparse collection of noisy confocal image slices," Indian Conference on Computer Vision, Graphics and Image Processing.

Poster presentation + Abstract only in proceedings

• J. Weng*, H. Yip, S. Lin, S., Talbot, P. (2015). The P2X7 receptor is an upstream regulator of dynamic blebbing in human embryonic stem cells, Poster Presentation at the Annual Meetings of the American Society of Cell Biology, December 2015, San Diego, CA
• Olivares, S., Zahedi*, A. Phandthong R., Talbot, P. (2015). Developing a method to identify damaged mitochondria and to visualize mitophagy in stem cells. Poster Presentation at the Annual Meeting of the California Institute for Regenerative Medicine (CIRM) Bridges Interns, June 2016, San Francisco, CA
• Brett C. Bays, Kristina M. Visscher, Christophe C. Le Dantec, Aaron R. Seitz, (2014), "Alpha-band EEG activity as a signature of automaticity in perceptual learning", Poster Presented at the Vision Sciences Society 2014
• Brett C. Bays, Craig M. Bula, Christophe C. Le Dantec, Aaron R. Seitz, (2013), "Is the BDNF val66met polymorphism associated with differential statistical learning?", Poster Presented at the Society for Neuroscience 2013
• Baumgartner, L., Sparks, N.R.L., Martinez*, I.K.C., Pulyanina, P.Y., zur Nieden, N.I., (2011), "Stem Cells and their use in predictive toxicology," 2nd International EuroEpiStem: European Epigenomics and Stem Cells 2011 Meeting on Epigenomic Programming and Stem Cells for Drug Discovery, University of Paris Diderot, France.
• Bays*, B.C., Turk-Browne, N.B., Seitz, A.R., (2013, May), "Statistical learning, a singular process? Dissociating behavioral outcomes of visuo-temporal statistical learning," Poster presented at the Vision Sciences Society 2013.
• Bianchi*, A., Bhanu, B., Donovan*, V., and Obenaus, A., (2012), "Mild traumatic brain injury detection through visual and contextual modeling," Poster presented at the Traumatic Brain Injury Conference 2012, Washington DC, United States.
• Cabrera*, I.E., and Borkovich, K.A., (2011, March), "Analysis of regulator of G protein signaling (RGS) proteins in Neurospora crassa," The 26th Fungal Genetics Conference at Asilomar, Pacific Grove, CA.
• Cabrera*, I.E., Eaton, C., Servin, J., and Borkovich, K.A., (2013, March), "Localization of Ga proteins during germination in the filamentous fungus, Neurospora crassa," The 27th Fungal Genetics Conference at Asilomar, Pacific Grove, CA.
• Cabrera*, I.E., and Borkovich, K.A., (2011, March), "Analysis of for of G protein signaling (RGS) proteins in Neurospora crassa," The 26th Fungal Genetics Conference at Asilomar, Pacific Grove, CA.
• Cabrera*, I.E., Eaton, C., Servin, J., and Borkovich, K.A., (2013, March), "Localization of Ga proteins during germination in the filamentous fungus, Neurospora crassa," The 27th Fungal Genetics Conference at Asilomar, Pacific Grove, CA.
• Davis, L.A., Baumgartner, L., Keller, K.C., Trettner, S., Seeliger, A., Martinez*, I.K.C., Kuske, B., zur Nieden, N.I., (2010, October), "Applying the embryonic stem cell test to study developmental toxicity of tobacco in vitro," TRDRP Symposium, Riverside, CA, USA.
• Donovan*, V., Bianchi*, A., Hartman, R., Bhanu, B., Carson, M., and Obenaus, A., (2012, July), "Semi-automated analysis of abnormal tissue development following repetitive mild traumatic brain injury," Poster presented at the National Neurotrauma Society, Pheonix, Arizona.
• Donovan*, V., Bianchi*, A., Coats, J., Bhanu, B., and Obenaus, A., (2012, January), "Semi-automated analysis of abnormal tissue development following repetitive mild traumatic brain injury," Poster presented at the Center for Glial Neuronal Interactions, UC Riverside.
• Donovan*, V., Coats, J., Badaut, J., Wilson, S., Huang, L., Obenaus, A., (2011, July), "Long-term white matter changes in a bilateral model of repetitive mild traumatic brain injury," Poster presented at the National Neurotrauma Society, Hollywood, Florida.
• Donovan*, V., Coats, J., Badaut, J., Wilson, S., Obenaus, A., Huang, L., (2011, January), "A model of recurrent mild traumatic brain injury in the adult rat," Poster presented at the Center for Glial Neuronal Interactions, UC Riverside.
• Donovan*, V., Coats, J., Mohd-Yusof, A., Wilson, S., Badaut, J., Obenaus, A., Huang, L., (2010, November), "A rat model of recurrent mild traumatic brain injury in opposite hemispheres," Poster presented at the Society for Neuroscience, San Diego, California.
• Eberle*, M.M., Rodriguez*, C.L., Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K, & Park, B.H. (2013, November). "The localization of changes in optical backscattering during seizure progression in vivo with optical coherence tomography." Poster session presented at the annual meeting of the Society for Neuroscience, Neuroscience 2014, San Diego, CA.
• Eberle*, M.M., Rodriguez*, C.L., Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K, & Park, B.H. (2013, February). "In vivo detection of cortical optical changes associated with seizure activity with optical coherence tomography." Poster session presented at the annual meeting of the Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XVII, SPIE Photonics West BiOS, San Francisco, CA.
• Eberle*, M.M., Reynolds*, C.L., Szu, J.I., et al., (2012, February), "In vivo detection of cortical optical changes associated with seizure activity with optical coherence tomography," Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XVII, SPIE Photonics West BiOS, San Francisco, CA.
• Harlow*, G., Cruz*, A., Bhanu*, B., Yang, Z., (2012, November), "Demonstration: Analysis of pavement cells using automated software," Poster presented at the 2012 NSF Video Bioinformatics Retreat, Lake Arrowhead, CA.
• Harlow*, G., Luo, N., Yang,Z., (2011, October), "Understanding pollen tube growth oscillation," Poster presented at the 2011 NSF Video Bioinformatics Retreat, Lake Arrowhead, CA.
• Lin, S., Weng*, J-H., Alfi, M., Yip, H., and Talbot P., (2013), "Evaluating cell health through video bioinformatics analysis of dynamic cellular behavior," Poster presented at the CIRM meeting. San Francisco.
• Martinez*, I.K.C., Sparks, N.R.L., Soto, C.H., Affeldt, H. III, Liew, C.G., zur Nieden, N.I., (2012, May), "You're not my twin: a comparison in differentiation between hESC- and hiPSC-derived osteogenic cultures using time-lapse image analysis," 12th Annual CMDB Research Symposium, Riverside, CA.
• Martinez*, I.K.C., Sparks, N.R.L., Soto, C.H., Liew, C.G., zur Nieden, N.I., (2012, April), "You're not my twin: A comparison in differentiation between hESC- and hiPSC-derived Osteogenic cultures using time lapse image analysis," Inland Empire Stem Cell Consortium 1st Annual Meeting.
• Martinez*, I.K.C., Sparks, N.R.L., Soto, C.H., Kuske, B., Bhanu, B., zur Nieden, N.I., (2012, April), "Videobioinformatics tracking of calcification in osteogenic cultures derived from human pluripotent stem cells for use in teratogenicity screening of tobacco products," Linking Tobacco Control Research and Practice for a Healthier California.
• Martinez*, I.K.C., Soto, C.H., Kuske, B., Bhanu, B., zur Nieden, N.I., (2011, June), Videobioinformatics Tracking of Calcification in Osteogenic Cultures derived from Human Pluripotent Stem Cells. June 2011. 12th Annual UC Systemwide Bioengineering Symposium, Santa Barbara, CA.
• Martinez*, I.K.C., Kuske, B., zur Nieden, N.I., (2011, February), "Its all in the mix: human embryonic stem cell differentiation into mature calcified osteoblasts using a combination of osteogenesis inducing factors," CMDB Research Symposium, Riverside, CA.
• Martinez*, I.K.C., Kuske, B., zur Nieden, N.I., (2010, December), "Analysis of static and moving images to quantify calcification of osteoblasts in culture," IGERT Videobioinformatics Colloquium, Riverside, CA, USA.
• McBride*, D.W., Hsu, M.S., Rodgers, V.G.J., and Binder, D.K., (2012, June), "Improving survival following cerebral edema and preventing cerebral edema using a hollow fiber-hydrogel device," Poster presented at the 13th Annual UC Systemwide Bioengineering Symposium at UC Berkeley.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2012, January), "Improving survival following cerebral edema using a hollow fiber-hydrogel device," Poster presented at the 5th Annual CGNI Regional Symposium on Glial-Neuronal Interactions in Health and Disease.
• McBride*, D.W., Hsu, M.S., Park, B.H., Binder, D.K., and Rodgers, V.G.J., (2011, June), "Device for the direct reversal and treatment of cerebral edema: Enhancing the survivability of water intoxicated murine," Poster presented at the 12th Annual UC Systemwide Bioengineering Symposium at UC Santa Barbara.
• McBride*, D.W. and Rodgers, V.G.J., (2011, April), "The free-solvent model predicts the solvent accessible surface area for globular proteins," Poster presented at the Proceedings of the 2011 3rd IEEE Electron Devices Society Mini-Colloquium on MicroElectronics & 3rd IEEE Student Research Symposium at UCR (ISRS-UCR).
• McBride*, D.W., Hsu, M.S., Park, B.H., Binder, D.K., and Rodgers, V.G.J., (2011, January), "Cerebral edema: Thermodynamics of astrocytic cell swelling," Poster presented at the 4th Annual CGNI Regional Symposium on Glial-Neuronal Interactions in Health and Disease.
• McBride*, D.W., and Rodgers, V.G.J., (2012, October), "Development of the free-solvent model for the osmotic pressure of crowded protein solutions," Poster presented at the BMES Annual Meeting.
• McBride*, D.W., Hsu, M.S., Rodgers, V.G.J, and Binder, D.K., (2012, July), "Improving Survival following cerebral edema and preventing cerebral edema using a hollow fiber-hydrogel device," Poster presented at the National Neurotrauma.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2011, November), "Novel hollow fiber-hydrogel device improves survival following cerebral edema," Poster presented at the SFN Neuroscience 2011.
• McBride*, D.W. and Rodgers, V.G.J., (2011, October)"The free-solvent model predicts the solvent accessible surface area for globular proteins," Poster presented at the AIChE Annual Meeting.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K, (2011, October), "Novel hollow fiber-hydrogel device improves survival following cerebral edema," Poster presented at the BMES Annual Meeting.
• McDevitt, E.A., Bays*, B.C., Rokem, A., Silver, M.A., Mednick, S.C., (2012), "Men need a nap to show perceptual learning of motion direction discrimination, but women do not," Poster presented at the Vision Sciences Society.
• Oliveira* M.C., Wang Y., Oh C.M., Islam Md., Ortega A. and Park B.H. (2012), "Parallelized algorithms for high speed multi-functional spectral domain optical coherence tomography." 13th Annual University of California Systemwide Bioengineering Symposium Berkeley, CA
• Oliveira*, M.C., Islam, Md., Henry, F.P., Randolph, M.A., Park, B.H., and de Boer, J.F., (2012), "Extracting structural features of rat sciatic nerve using multi-functional spectral-domain optical coherence tomography," Poster presented at the SPIE Photonics West 2012, San Francisco, CA.
• Oliveira*, M.C., Oh, C.M., Wang, Y., Ortega, A. and Park, B.H., (2010), "Endoscopic optical coherence tomography and structural examination of peripheral nerves," Poster presented at the 2010 Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) National Conference, Anaheim, CA.
• Price, F.D., Geransar, R.M., Ding, H., Kaniowska, D., Dienelt, A., Trettner, S., Martinez*, I.K.C., Martin, C., zur Nieden, N.I., (2010, September), "Engineering osteogenic progenitors from embryonic stem cells, Biospine 3," 3rd International Congress Biotechnologies for Spinal Surgery, Amsterdam, Netherlands.
• Rodriguez*, C.L., Eberle*, M.M, Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K., & Park, B.H. (2013, November). "Detection of cerebral edema using optical coherence tomography." Poster session presented at the annual meeting of the Society for Neuroscience, Neuroscience 2014, San Diego, CA.
• Rodriguez*, C.L., Eberle*, M.M, Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K., & Park, B.H. (2013, February). "Identification of in vivo brain structures using optical coherence tomography." Poster session presented at the annual meeting of the Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XVII, SPIE Photonics West BiOS, San Francisco, CA.
• Rucker, T., Singhal, A., Davis, L.A., Ding, H., Kuske, B., Trettner, S., Martinez* I.K.C., zur Nieden, N.I., (2010, October), "Cell surface marker expression in embryonic stem cells overexpressing a stable form of beta-catenin," German Society for Cytometry, Leipzig, Germany.
• Seeliger, A., Gschwandtner, K., Price, F.D., Geransar, R.M., Ding, H., Kaniowska, D., Dienelt, A., Trettner, S., Martinez*, I.K.C., zur Nieden, N.I., (2010, August), "Directing osteogenic ESC fate - Wnt proteins, miRNAs and metabolites," Beckman Research Institute, City of Hope, Los Angeles, CA, USA.
• Sparks, N.R.L., Martinez*, I.K.C., zur Nieden, N.I., (2012, April), "Snus tobacco extract inhibits osteogenic differentiation of human embryonic stem cells via reactive oxygen species," Inland Empire Stem Cell Consortium 1st Annual Meeting.
• Sparks, N.R., Evans, S., Martinez*, I.K.C., zur Nieden, N.I., (2012, April), "Osteogenic toxicity of chewing tobacco correlates with changes in ROS production and altered levels of beta-catenin," Poster presented at the Linking Tobacco Control Research and Practice for a Healthier California.
• Sparks, N.R., Soto, C., Martinez*, I.K.C., Kuske, B., Liew, C.G., zur Nieden, N.I., (2012, January), "You're not my twin: A comparison in differentiation kinetics and yield between hESC and hiPSC-derived osteogenic cultures," Poster presented at the CSUPERB: CSU Biotechnology Symposium.
• Sparks, N.R., Martinez*, I.K.C., Kuske, B., zur Nieden, N.I., (2011, July), "Sidestream tobacco smoke inhibits osteogenic differentiation of hESCs through modulation of ROS," Poster presented at the CIRM grantee meeting, San Francisco, CA.
• Sparks, N.R.L., Evans, S., Martinez*, I.K.C., zur Nieden, N.I., (2012, April), "Osteogenic toxicity of chewing tobacco correlates with changes in ROS production and altered levels of Beta-catenin," Linking Tobacco Control Research and Practice for a Healthier California.
• Sparks, N.R.L., Martinez*, I.K.C., Kuske, B., zur Nieden, N.I., (2011, July), "Sidestream tobacco smoke inhibits osteogenic differentiation of hESCs through modulation of ROS," CIRM grantee meeting, San Francisco, CA.
• Ung*, N., (2011), "Quantitative analysis of endomembrane dynamics in tobacco pollen tubes," Poster presented at the Plant Biology 2011, American Society of Plant Biologists (ASPB) , Minneapolis, MN.
• Weng*, J-H., Yip, H, Lin, S. and Talbot, P., (2011), "Timeline and mechanism of apoptotic blebbing in human embryonic stem cells," Poster presented at the World Stem Cell Summit. Los Angeles.
• Weng*, J-H. and Talbot, P., (2013), "The role of P2X7 receptor in cell blebbing in human embryonic stem cells," Presented at Inland Empire Stem Cell Consortium Symposium, Loma Linda University.
• Wisotsky, Z., Medina, A., Freeman*, E., Dahanukar, A., (2012, April), "Logic of glycerol input to behavioral output in Drosophila," Poster presented at the Achems, Huntington Beach, CA.

Poster only presentations

• Antrim, L., Lin, S. On*, V., Zahedi*, A., and Talbot, P. (2014, November). StemCellQC: A New Software Platform for Evaluating Stem Cell Health. Poster Presented at Annual Inland Empire Stem Cell Symposium. San Bernardino, CA.
• Antrim, L., Lin, S. On*, V., Zahedi*, A., and Talbot, P. (2014). StemCellQC: A New Software Platform for Evaluating Stem Cell Health. Poster Presented at Annual CIRM Bridges Trainee Meeting. San Francisco, CA.
• Bays*, B., and Seitz, A. (2014, October). Classifying EEG Patterns of Visual Learning Processes. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Cabrera*, I., Tambo*, A., Cruz*, A., Guan*, B., Bhanu, B., and Borkovich, K. (2014, October). Quantitative Analyses During Growth and Development in the Filamentous Fungus, Neurospora crassa. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Coffman*, S., Broitman-Maduro, G., Maduro, M., Ding, S. (2014, October). Identification of Genes Required for RNAi-Mediated Antiviral Immunity by a Forward Genetic Screen in C. Elegans. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Eberle*, M., Hsu, M., Rodriguez*, C., Szu, J., Oliveira*, M., Binder, D., Park, B. (2014, October). Localization of Attenuation Changes During Seizure Activity in vivo with Optical Coherence Tomography. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Freeman*, E., Tong, M., Dahanukar, A. (2014, October). Tracking the Feeding Behaviors in Drosophila Melanogaster. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Khachatoorian*, C. (2014). Investigation of electronic cigarette exhaled residue. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Larsen*, J., and Vullev, V. (2014, October). Dipole mediated rectification of charge transfer and optical tools for molecular mechanics. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Lin, S., Phandthong, R., Weng*, N., Montes, B., and Talbot, P. (2014). Toxicology-in-a-Dish: Using In Vitro Stem Cell Models to Predict Health Defects Due to Cigarette Smoke Exposure. Poster Presented at Inland Empire Stem Cell Consortium Annual Conference, California State University, San Bernardino, CA.
• Lin, S., Phandthong, R., Weng*, N., Montes, B., and Talbot P. (2014, June). Toxicology-in-dish: using in vitro stem cells models to predict health effects due to cigarette smoke exposure. Pacific Division of the American Association for the Advancement of Science volume 33 part 1 page 181.
• Lin, S., Phandthong, R., Weng*, N., Montes, B., and Talbot, P. (2014, October). Toxicology-in-dish: using in vitro stem cells models to predict health effects due to cigarette smoke exposure. Poster Presented at Advances in Aerosol Dosimetry Research, Irvine, CA.
• Mkrtchyan*, K. Chakraborty, A., Roy-Chowdhury, A. (2014, October). Optimal Landmark Selection for Registration of 4D Confocal Image Stacks. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Rodriguez*, C., Szu, J., Eberle*, M., Hsu, M., Binder, D., Park, B. (2014, October). Using Optical Coherence Tomography to Detect Cerebral Edema In Vivo. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Rodriguez*, C., Szu, J., Eberle*, M., Hsu, M., Binder, D., Park, B. (2015, February). Decreased optical attenuation detected during cerebral edema in vivo with optical coherence tomography. Poster presentation, SPIE Photonics West Conference, San Francisco, CA.
• Rodriguez*, C., Szu, J., Eberle*, M., Hsu, M., Binder, D., Park, B. (2015, September). Change in optical attenuation of the cerebral cortex during cerebral edema detected using optical coherence tomography. Poster presentation, Brain Edema Conference, Huntington Beach CA.
• Tambo*, A., Bhanu, B., (2014, October). Image Segmentation Using Seam Carving. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Ung*, N., Tambo*, A., Bhanu, B., Raikhel, N. (2014, October). EndoQuant: An Image Analysis Package for Quantitative Automated Cellular Phenotyping. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Weng*, N., Phandthong, G., Yip, H., and Talbot P., (2014, October). Rapid evaluation of human embryonic stem cell health through video bioinformatics analysis of blebbing behavior. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Zahedi*, A., On*, V., Lin, S., Bays*, B., Bhanu, B., and Talbot, P., (2015, March). StemCellQC™: A Smart Detection Multiplexing Toolkit for Toxicological Evaluation of Stem Cell Processes and Health. Poster session presented at the 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Zahedi*, A., On*, V., Lin, S., Bays*, B., Bhanu, B., and Talbot, P., (2015, March). StemCellQC™: A Smart Detection Multiplexing Toolkit for Toxicological Evaluation of Stem Cell Processes and Health. Poster session presented at the 54th Annual Society of Toxicology Meeting, San Diego, California.
• Zahedi*, A., On*, V., Lin, S., Bays*, B., Bhanu, B., and Talbot, P., (2014, November). Using Video Bioinformatics to Evaluate Health of Stem Cell Populations for Disease Prevention. Poster session presented at the 3rd Annual Inland Empire Stem Cell Symposium, Cal State University San Bernardino, San Bernardino, California.
• Zahedi*, A., On*, V. (2015, February). StemCellQC: A Smart-Detection Multiplexing Toolkit for Evaluation of Cellular Processes and Health. Poster Presented at the UCR Stem Cell Seminar series.
• Brett C. Bays, Christophe C. Le Dantec, Aaron R. Seitz, (2013), "What is the relation of alpha band activity in human EEG to perceptual and contextual learning?", Poster Presented at the UCR NSF IGERT for Video Bioinformatics 2013 Conference and Retreat.
• Bays*, B.C., Dantec, C.L., and Seitz, A.R., (2012), "Dissociable neural processes underlying statistical learning," Poster presented at the UCR NSF IGERT for Video Bioinformatics 2012 Conference and Retreat.
• Hill*,D., (2011, June), "Stem cell toxicity testing with a modularized microfluidic high throughput chemical screening (MMHTCS) system," Poster presented at the Bioengineering Symposium Santa Barbra.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2011, October), "Detection of cerebral edema using optical coherence tomography," Poster presented at the IGERT Video Bioinformatics Retreat.
• McBride*, D.W., Hsu, M.S., Park, B.H., Binder, D.K., and Rodgers, V.G.J., (2011, April), "Device for treatment of brain edema," Poster presented at the Department of Bioengineering Graduate Student Recruitment Day at UC Riverside.
• Oliveira*, M. C., Islam, M.S., Haque, M.R., Oh, C.M., Wang, Y., & Park, B.H. (2014, February). "Depth resolved optical detection of nerve activity in Limulus nerve and murine brain slice using common-path OCT." Poster session presented at the SPIE Photonics West 2014, San Francisco, CA.

Oral Presentation (with full paper)

• Cruz*, A., Bhanu, B., and Yang, S., (2011), "A psychologically-inspired match-score fusion model for video-based facial expression recognition," Affective Computing and Intelligent Interaction, Lecture Notes in Computer Science.
• Cruz*, A.C., Bhanu, B., and Thakoor, N., (2012), "Facial emotion recognition with expression energy," Int. Conf. on Multimodal Interfaces (ICMI), Santa Monica, CA, USA, 457-464.
• Guan*, B.X., Bhanu, B., Talbot, P., & Lin, S., (2012), "Automated human embryonic stem cell detection," Proc. 2nd IEEE International Conf. On Health Informatics, Imaging and System Biology, San Diego, CA. (Best Paper Award).
• Mkrtchyan*, K., Chakraborty, A., Roy-Chowdhury, A.K., (2013, April), "Automated registration of live imaging stacks of Arabidopsis," International Symposium on Biomedical Imaging.

Oral Presentation (with abstract)

• Zahedi*, A., On*, V., (2014, October). StemCellQC: A Smart-Detection Multiplexing Toolkit for Predicting Cell Processes and Health. 5th Annual NSF IGERT on Video Bioinformatics Retreat, UCLA Conference Center, Lake Arrowhead, California.
• Khatibzadeh, N., Zahedi*, A., and Berns, MW (2014, June). Studies of neuronal response to laser microbeam-induced site-specific axonal damage. 15th Annual UC Systemwide Bioengineering Symposium, UC Irvine, Irvine, California.
• Baumgartner, L., Sparks, N.R., Martinez*, I.K.C., Pulyanina, P., zur Nieden, N.I., (2011, November), " Stem Cells and their use in predictive toxicology," 2nd International EuroEpiStem: European Epigenomics and Stem Cells 2011 Meeting on Epigenomic Programming and Stem Cells for Drug Discovery, University of Paris Diderot, France.
• Eberle*, M.M., Rodriguez*, C.L., Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K, & Park, B.H. (2014, April). "Localization of Cortical Tissue Optical Changes during Seizure Activity in vivo with Optical Coherence Tomography." Cardiovascular and Cerebral Applications of OCT, OSA BIOMED, Miami, FL.
• Eberle*, M.M., Rodriguez*, C.L., Szu, J.I., Wang, Y., Hsu, M.S., Binder, D.K, & Park, B.H. (2014, February). "The localization of changes in optical backscattering during seizure progression in vivo with optical coherence tomography." Neurophotonics, SPIE Photonics West BiOS, San Francisco, CA.
• Freeman*, E., French, A., Wisotsky, Z., Marion-Poll, F.,Dahanukar, A." Drosophila taste receptors reveal combinatorial and cross-modality functions" (April, 2013) 2013 Annual Drosophila Research Conference
• Freeman*, E., French, A., Wisotsky, Z., Marion-Poll, F.,Dahanukar, A." Drosophila taste receptors reveal combinatorial and cross-modality functions" (July, 2012) IIGB Seminar
• McBride*, D.W. and Rodgers, V.G.J., (2012, October), "Anomalies of crowded protein thermodynamics: Deviations from ideality," Bioengineering Colloquium.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2012, September), "Improving survival following cerebral edema using a hollow fiber-hydrogel device," UC Neurotrauma.
• Oliveira*, M. C., Haque, M.R., Hsu, M.S., Binder, D.K., & Park, B.H. (2013, June). "Morphological classification of neural cell types using optical coherence phase microscopy." The 14th Annual UC Systemwide Bioengineering Symposium, San Diego, CA.
• Oliveira*, M.C., Islam, Md., Alanis, X., Henry, F., de Boer, J.F. and Park, B.H., (2011), "Quantitative Characterization of peripheral nerve structural features using optical coherence tomography," Abstract for oral presentation, 12th Annual University of California Systemwide Bioengineering Symposium, Santa Barbara, CA.
• Oliveira*, M.C., Oh, C.M., Islam, Md., Wang, Y., Ortega, A., Haque, Md. and Park, B.H., (2010), "Peripheral nerve imaging using endoscopic optical coherence tomorgraphy," Abstract for oral presentation, 11th Annual University of California Systemwide Bioengineering Symposium, Davis, CA.
• Rodriguez*, C.L., Eberle*, M.M., Szu, J.I., Hsu, M.S., Binder, D.K., & Park, B.H. (2014, February). "Detection of Cerebral Edema in vivo using optical coherence tomography." SPIE Photonics West, San Francisco, CA.

Oral Presentation (No proceeding record)

• Donovan*, V., (2010, August), "Magnetic Resonance Imaging of Repeated Mild CCI Injury in Adult Rats," UC Neurotrauma, Los Gatos, California.
• Donovan*, V., (2012, September), "Repeated mild traumatic brain injury results in increased blood deposition," UC Neurotrauma, Sonoma, California.
• Harlow*, G., (2013, April), "Pavement cell analysis reveals golden ratio in leaf cell lobes," Poster presented at the UC Riverside Botany & Plant Science Spring Seminar Series.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2012, February), "Detection of cerebral edema using optical coherence tomography," IGERT Video Bioinformatics Spring Invitational.
• McBride*, D.W. and Esfahani, E.T., (2012, January), "A fast, automatic computational method for injury detection in T2 MRI images using a symmetry-based algorithm," IGERT Colloquium.
• McBride*, D.W., Hsu, M.S., Park, B.H., Rodgers, V.G.J., and Binder, D.K., (2011, October), "Development of a novel device for detection and treatment of brain edema," IGERT Video Bioinformatics Retreat.
• McBride*, D.W. and Rodgers*, V.G.J., (2011, August), "Obtaining protein solvent accessible surface area when structural data is unavailable using osmotic pressure," Bioengineering Colloquium.

Software Developed by IGERT Fellows

• StemCellQC