University of California, Riverside

Department of Bioengineering

Publications by Core Bioengineering Faculty

2017| 2016| 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004


  • Gray V, Xia P, Huang Z, Moses E, Fast E, Fishman DA, Vullev VI, Abrahamsson M, Moth-Poulsena K, Tang ML CdS/ZnS Core–Shell Nanocrystal Photosensitizers for Visible to UV Upconversion. Chemical Science (2017); 8; 5488–5496. DOI: 10.1039/c7sc01610g .
  • Guerrero Y, Singh SP, Mai T, Murali RK, Tanikella L, Zahedi A, Kundra V, Anvari B. Optical characteristics and tumor imaging capabilities of near infrared dyes in free and nano-encapsulated formulations comprised of viral capsid. ACS Applied Materials & Interfaces (2017); 9: 19601-19611. DOI: 10.1021/acsami.7b03373 .
  • A. Gao, W. Xu, Y. Ponce de León, Y. Bai, M. Gong, K. Xie, B. H. Park, Y. Yin, Controllable Fabrication of Au Nanocups by Confined-Space Thermal Dewetting for OCT Imaging, Adv. Mater. 2017, 29, 1701070. DOI: 10.1002/adma.201701070 .
  • Harrison RES, Mohan RR, Gorham RD Jr, Kieslich CA, Morikis D. AESOP: A Python Library for Investigating Electrostatics in Protein Interactions. Biophysical Journal (2017);112:1761-1766. DOI: 10.1016/j.bpj.2017.04.005 .
  • Gaieb Z, Morikis D. Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding. Journal of Molecular Graphics and Modelling (2017); 74:352-358.Pubmed Link. DOI: 10.1016/j.jmgm.2017.04.012 .
  • Larsen-Clinton JM, Espinoza EM, Mayther M, Clark J, Tao C, Bao D, Larino CM, Wurch M, Lara S, Vullev VI. Fluorinated Aminoanthranilamides: Non-native Amino Acids for Bringing Proteomic Approaches to Charge-Transfer Systems. Physical Chemistry Chemical Physics (2017); 19; 7871-7876.Pubmed Link. DOI: 10.1039/C7CP00432J .
  • López-Perrote A, Harrison RES, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O. Ionic tethering contributes to the conformational stability and function of complement C3b. Molecular Immunology (2017); 85:137-147. Pubmed Link. DOI:10.1016/j.molimm.2016.12.015.
  • Burns J. M., Saager R., Majaron B., Jia W., Anvari B. Optical properties of biomimetic probes engineered from erythrocytes. Nanotechnology (2017); 035101 (12 pp). Pubmed Link. DOI:10.1088/1361-6528/28/3/035101.
  • Erudaitius D, Huang A, Kazmi S, Buettner GR, Rodgers VGJ. Peroxiporin Expression Is an Important Factor for Cancer Cell Susceptibility to Therapeutic H2O2: Implications for Pharmacological Ascorbate Therapy. PLoS ONE (2017); 12(1): e0170442. Pubmed Link. DOI:10.1371/journal.pone.0170442.
  • Gaieb Z, Morikis D. Detection of side chain rearrangements mediating the motions of transmembrane helices in molecular dynamics simulations of G protein-coupled receptors. Computational and Structural Biotechnology Journal (2017); 15:131-137. PMC Link. DOI:10.1016/j.csbj.2017.01.001.
  • Tong M.Q, Hasan M.M., Lee S.S., Md. Rezuanul Haque, Kim D.H., Islam M.S., Adams M.E., and Park B.H. OCT intensity and phase fluctuations correlated with activity-dependent neuronal calcium dynamics in the Drosophila CNS [Invited]. Biomed. Opt. Express (2017); 8, 726-735. DOI: 10.1364/BOE.8.000726.
  • Xia P., Huang Z., Li X., Romero J. J., Vullev V. I., Pau G. S. H., Tang M. L. On the Efficacy of Anthracene Isomers for Triplet Transmission from CdSe Nanocrystals. ChemComm (2017); 53, 1241–1244. RSC Link. DOI: 10.1039/C6CC08229G.
  • Low, K.*, Wong, L.*, Maldonado, M., Manjunath, C., Horner, C., Perez, M., Myung, V.N., Nam, J. (2017) Physicoelectrochemical characterization of pluripotent stem cells during self‐renewal or differentiation by a multi‐modal monitoring system. Stem Cell Reports 8: 1-11. DOI: 10.1016/j.stemcr.2017.03.021.
  • He N, Langley J, Huddleston DE, Ling H, Xu H, Liu C, Yan F, Hu XP: Improved Neuroimaging Atlas of the Dentate Nucleus. The Cerebellum 2017. DOI: 10.1007/s12311-017-0872-7.


  • A. Tambo and B. Bhanu. Segmentation of pollen tube growth videos using dynamic bi-modal fusion and seam carving.” IEEE Transactions on Image Processing (2016); 25(5):1993-2004. Pubmed Link. DOI: 10.1109/TIP.2016.2538468.
  • 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); 11(2):e0148642. Pubmed Link. DOI: 10.1371/journal.pone.0148642.
  • Adapala, R.K., Thoppil, R.J., Ghosh, K., Cappelli, H.C., Dudley, A.C., Paruchuri, S., Keshamouni, V., Klagsbrun, M., Meszaros, J.G., Chilian, W.M. and Ingber, D.E. Activation of mechanosensitive ion channel TRPV4 normalizes tumor vasculature and improves cancer therapy. Oncogene (2016); 35(3):314-22. Pubmed Link. DOI: 10.1038/onc.2015.83
  • B. Bhanu and P. Talbot (Eds.). From Live Imaging to Knowledge. Video Bioinformatics (2016); ISBN: 978-3-319-23723-7. Springer Link DOI: 10.1007/978-3-319-23724-4.
  • Blazek, A.M., Nam, J., Gupta, R., Pradhan, M., Perera, P., Weisleder, N.L., Hewett, T.E., Chaudhari, A.M., Lee, B., Leblebicioglu, B., Butterfield, T.A., Agarwal, S. (2016) Exercise-Driven Metabolic Pathways in Healthy Cartilage. Osteoarthritis & Cartilage 24.7 (2016): 1210-1222.DOI: 10.1016/j.joca.2016.02.004
  • Cabrera A.P., Bhaskaran A, Xu J, Yang X, Scott H.A., Mohideen U, Ghosh K. Senescence increases choroidal endothelial stiffness and susceptibility to complement injury: Implications for choriocapillaris loss in AMD. Investigative Ophthalmology & Visual Science (2016); 57(14):5910-5918. Pubmed Link DOI: 10.1167/iovs.16-19727
  • Cipriano AF, Sallee A, Tayoba M, Cortez Alcaraz MC, Lin A, Guan RG, Zhao ZY, Tayoba M, Sanchez J, and Liu H. Cytocompatibility and Early Inflammatory Response of Human Endothelial Cells in Direct Culture with Mg-Zn-Sr Alloys. Acta Biomaterialia (2016). 16: 30547-5. Epub ahead of print 10/13/2016. DOI: 10.1016/j.actbio.2016.10.020. (PMID: 27746360)
  • Croker DE, Monk PN, Halai R, Kaeslin G, Schofield Z, Wu MCL, Clark RJ, Blaskovich MAT, Morikis D, Floudas CA, Cooper MA, Woodruff TM (2016) Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signaling, Immunology & Cell Biology, 94:787–795 ;Pubmed Link DOI: 10.1038/icb.2016.43. Featured Article. News and Commentary: Kember C (2016) Targeting the Dark Horse of complement: the first generation of functionally selective C5aR2 ligands, Immunology & Cell Biology, 94:717–718 Pubmed Link. DOI: 10.1038/icb.2016.62
  • Espinoza, E. M.; Larsen, J. M.; Vullev, V. I. "What Makes Oxidized N-Acylanthranilamides Stable?" J. Phys. Chem. Lett. 2016, 7, 758–764.DOI: 10.1021/acs.jpclett.5b02881
  • Espinoza, E. M.; Xia, B.; Darabedian, N.; Larsen, J. M.; Nuñez, V.; Bao, D.; Mac, J. T.; Botero, F.; Wurch, M.; Zhou, F.; Vullev, V. I. "Nitropyrene Photoprobes: Making Them, and What Are They Good for?" Eur. J. Org. Chem. 2016, 343–356. DOI: 10.1002/ejoc.201501339
  • Ferguson TB., Hu XH., Chen C. Methods, systems and computer program products for non-invasive determination of blood flow distribution using speckle imaging techniques and hemodynamic modeling (2016). Google Scholars Link.
  • Gaieb Z, Lo DD, Morikis D (2016) Molecular mechanism of biased ligand conformational changes in CC chemokine receptor 7, Journal of Chemical Information and Modeling, 56:1808–1822. Pubmed Link. DOI: 10.1021/acs.jcim.6b00367. Paper is featured in journal cover.
  • Hill DA, Anderson LE, Hill CJ, Mostaghim A, Rodgers VGJ, Grover WH (2016) MECs: Building Blocks" for Creating Biological and Chemical Instruments, PLoS ONE, DOI: 10.1371/journal.pone.0158706
  • Horner, C., Ico, G., Johnson, J., Zhao, Y., Nam, J. (2016) Microstructure-dependent mechanical properties of electrospun core-shell scaffolds at multi-scale levels. Journal of the Mechanical Behavior of Biomedical Materials 59: 207-219. DOI: 10.1016/j.jmbbm.2015.12.034
  • Horner, C., Hirota, K., Liu, J., Maldonado, M., Park, B.H., Nam, J. (2016) Magnitude-Dependent and Inversely-Related Osteogenic/Chondrogenic Differentiation of Human Mesenchymal Stem Cells by Dynamic Compressive Strain. Journal of Tissue Engineering and Regenerative Medicine. DOI: 10.1002/term.2332
  • Hu XQ., Sun Y., Lau E., Zhao M., Su SB. Advances in Synergistic Combinations of Chinese Herbal Medicine for the Treatment of Cancer. Current Cancer Drug Targets (2016); 16(4): 346-356. Ingenta Link. Pubmed Link. DOI: 10.2174/1568009616666151207105851.
  • Ico, G., Showalter, A., Bosze, W., Gott, S.C., Kim, B.S., Rao, M.P., Myung, N.V., Nam, J. (2016) Size-dependent piezoelectric and mechanical properties of electrospun P(VDF-TrFE) nanofibers. Journal of Materials Chemistry A 4, 2293-2304. DOI: 10.1039/C5TA10423H.
  • Johnson I, Wang SM, Silken C, Liu H. A systemic study on key parameters affecting nanocomposite coatings on magnesium substrates. Acta Biomaterialia. 2016 Mar 19. pii: S1742-7061(16)30120-9. DOI: 10.1016/j.actbio.2016.03.026. [PMID: 27006335]
  • Krzeszewski, M.; Kodama, T.; Espinoza, E. M.; Vullev, V. I.; Kubo, T.; Gryko, D. T. "Non-Planar Butterfly-Shaped π-Expanded Pyrrolopyrroles" Chem. Eur. J. 2016, accepted. DOI: 10.1002/chem.201603282
  • L. Feng and B. Bhanu, “Semantic Concept Co-occurrence Patterns for Image Annotation and Retrieval,” IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 38, No. 4, April 2016. DOI: 10.1109/TPAMI.2015.2469281.
  • L. Feng, B. Bhanu, and J. Hearty, ”A software system for automated identification and retrieval of moth images based on wing attributes,” Pattern Recognition, Vol 51, March 2016. DOI: 10.1016/j.patcog.2015.09.012.
  • Laurie SS., Hu X., Lee SMC., Martin DS., Phillips TR., Ploutz-Snyder R., Smith SM., Stenger MB., Taibbi G., Zwart SR., Vizzeri G. Effect of 1% inspired CO2 during head-down tilt on ocular structures, cerebral blood flow, and visual acuity in healthy human subjects (2016). NTRS Link.
  • Li C., Yoshimi N., Hu X., Li S., Gao Y. Liposome and personal care composition comprising thereof (2016). Google Scholars Link.
  • Liu Y., Lü X., Wu C., Hu X., Duan Z, Deng G., Wang H., Zhu X., Zeng H., Wang P., Wang W., Lu Q. The migration of Tarim plume magma toward the northeast in Early Permian and its significance for the exploration of PGE-Cu–Ni magmatic sulfide deposits in Xinjiang, NW China: As suggested by Sr–Nd–Hf isotopes, sedimentology and geophysical data. Ore Geology Reviews (2016); 72: 538–545. DOI: 10.1016/j.oregeorev.2015.07.020.
  • Ma D., Li S., Xu L., Hu X., Zhang G., Jia C., Yuan X. Fabrication of anodic alumina oxide templates in a mixture solution of 1, 3-propanediol and H3PO4. Anti-Corrosion Methods and Materials (2016); 63 (3): 210-213. Emerald Insight Link. DOI: 10.1108/ACMM-11-2015-1612.
  • Mac, J. T.; Nuñez, V.; Burns, J. M.; Guerrero, Y. A.; Vullev, V. I.; Anvari, B. "Erythrocyte-Derived Nano-Probes Functionalized with Antibodies for Targeted Near Infrared Fluorescence Imaging of Cancer Cells" Biomedical Optics Express 2016, 7, 1311–1322. DOI: 10.1364/BOE.7.001311
  • Mohan RR, Huber GA, Morikis D (2016) Electrostatic steering accelerates C3d:CR2 association, Journal of Physical Chemistry B 120:8416-8423. DOI: 10.1021/acs.jpcb.6b02095. Special issue for Professor J. Andrew McCammon Festschrift.
  • Maldonado, M., Luu, R.J., Ramos, M., Nam, J. (2016) ROCK Inhibitor Primes Human Induced Pluripotent Stem Cells to Selectively Differentiate Towards Mesendodermal Lineage via Epithelial-Mesenchymal Transition-like Modulation, Stem Cell Research 17.2 (2016): 222-227. DOI: 10.1016/j.scr.2016.07.009.
  • Maldonado, M., Ico, G., Low, K., Luu, R.J., Nam, J. (2016) Enhanced Lineage-Specific Differentiation Efficiency of Human Induced Pluripotent Stem Cells by Engineering Colony Dimensionality Using Electrospun Scaffolds, Advanced Healthcare Materials 5(12): 1408-12. featured on the journal cover. DOI: 10.1002/adhm.201600141.
  • Mohan RR, Cabrera AP, Harrison RES, Gorham RD Jr, Johnson LV, Ghosh K, Morikis D (2016) Peptide Redesign for Inhibition of the complement system: Targeting age-related macular degeneration, Molecular Vision 22:1280-1290. DOI:
  • Monickaraj, F., McGuire, P.G., Nitta, C.F., Ghosh, K. and Das, A. Cathepsin D: an Mϕ-derived factor mediating increased endothelial cell permeability with implications for alteration of the blood-retinal barrier in diabetic retinopathy. The FASEB Journal 30.4 (2016): 1670-82. Pubmed Link DOI: 10.1096/fj.15-279802
  • M. K. Ravoori, S. Singh, R. Bhavane, A. K. Sood, B. Anvari, J. Bankson, A. Annapragada, and V. Kundra, “Multimodal magnetic resonance and near infrared fluorescence imaging of intraperitoneal ovarian cancer using a dual-mode-dual gadolinium liposomal contrast agent,” Scientific Reports, 22, 38991, DOI: 10.1038/srep38991, 2016.
  • Nalbandian, M.J., Zhang, M., Sanchez, J., Nam, J., Cwiertny, D.M., Myung, N.V. Mesoporous θ-Alumina/Hematite (θ-Al2O3/Fe2O3) Composite Nanofibers for Heavy Metal Removal. Science of Advanced Materials. DOI: 10.1166/sam.2017.3013
  • Nuñez, V.; Vullev, V. I. "Chemical Aspects of Biocompatible Interfaces," Encyclopedia of Surface and Colloid Science, Third Edition 2016, pp. 1-22. DOI: 10.1081/E-ESCS3-120051159
  • Purc, A.; Espinoza, E. M.; Nazir, R.; Romero, J. J.; Skonieczny, K.; Jeżewski, A.; Larsen, J. M.; Gryko, D. T.; Vullev, V. I. "Gating that Suppresses Charge Recombination – the Role of Mono-N-Arylated Diketopyrrolopyrrole" J. Am. Chem. Soc. 2016, in press. DOI: 10.1021/jacs.6b04974.
  • Scott, H.A., Quach, B., Yang, X., Ardekani, S., Cabrera, A.P., Wilson, R., Messaoudi-Powers, I. and Ghosh, K. Matrix Stiffness Exerts Biphasic Control Over Monocyte-Endothelial Adhesion via Rho-mediated ICAM-1 Clustering. Integrative Biology (2016); 8(8):869-78 Pubmed Link DOI: 10.1039/c6ib00084c
  • Sarshar, M., Liu, T., Anvari, B. (2016) Combined optical micromanipulation and interferometric topography (COMMIT), Biomedical Optics Express 7, 1365-1374 DOI: 10.1364/BOE.7.001365
  • Skonieczny, K.; Jaeduk Yoo, J.; Larsen, J. M.; Espinoza, E. M.; Barbasiewicz, M.; Vullev, V. I.; Lee, C.-H.; Gryko, D. T. "How To Reach Intense Luminescence for Compounds Capable of Excited-State Intramolecular Proton Transfer?" Chem. Eur. J. 2016, 22, 7485–7496. DOI: 10.1002/chem.2015049 44
  • Song P., Ye Z., Huang A., Chen H., Hu X., Ding R., He L. Theoretical investigation on input properties of DI and CTIA readout integrated circuit. Optical and Quantum Electronics (2016) 48 (3): 1-7. DOI: 10.1007/s11082-016-0376-6
  • Su N, Guan R, Wang X, Wang Y, Jiang W, Liu H. Grain Refinement in an Al-Er Alloy during Accumulative Continuous Extrusion Forming. Journal of Alloys and Compounds (2016). 680: 283-290. DOI: 10.1016/j.jallcom.2016.04.137
  • Tian Q, Deo M, Rivera-Castaneda L, Liu H. "Cytocompatibility of Magnesium Alloys with Human Urothelial Cells: A Comparison of Three Culture Methodologies." ACS Biomaterials Science and Engineering (2016). DOI: 10.1021/acsbiomaterials.6b00325.
  • Tian Q, Rivera-Castaneda L, Liu H. Optimization of nano-hydroxyapatite/poly(lactic-co-glycolic acid) coatings on magnesium substrates using one-step electrophoretic deposition. Materials Letters (2016). Available online 19 September 2016. DOI: 10.1016/j.matlet.2016.09.072.
  • Tie D, Guan R, Liu H, Cipriano A, Liu Y, Wang Q, Huang Y, Hort N. An In Vivo Study on the Metabolism and Osteogenic Activity of Bioabsorbable Mg-1Sr Alloy. Acta Biomaterialia (2016) Jan 1;29:455-467. DOI: 10.1016/j.actbio.2015.11.014. Epub 2015 Nov 11. (PMID: 26577986)
  • Wetteland CL, Nguyen NYT, and Liu H. "Concentration-dependent behaviors of bone marrow derived mesenchymal stem cells and infectious bacteria toward magnesium oxide nanoparticles."Acta biomaterialia 35 (2016): 341-356. DOI: 10.1016/j.actbio.2016.02.032
  • Wu Q.,Tang Y., Hu X., Wang Q., Lei W., Zhou L., Huang J. Regulation of Th1/Th2 balance through OX40/OX40L signalling by glycyrrhizic acid in a murine model of asthma. Respirology (2016) Jan; 21 (1): 102-11. Pubmed Link. DOI: 10.1111/resp.12655.
  • Yang, X., Scott, H.A., Monickaraj, F., Xu, J., Ardekani, S., Nitta, C.F., Cabrera, A., McGuire, P.G., Mohideen, U., Das, A. and Ghosh, K. Basement membrane stiffening promotes retinal endothelial activation associated with diabetes. The FASEB Journal 30.2 (2016): 601-6011 Pubmed Link DOI: 10.1096/fj.15-277962
  • Yao K., Hu X., Li Q., Yin M. A Novel Control to Achieve Optimal Reduction of the E-Cap's Ripple Current for Discontinuous-Conduction Mode Boost PFC Converter. IEEE Transactions on Power Electronics (2016) Sept; 31 (6): 4331-4342. IEEE Xplore Link. DOI: 10.1109/TPEL.2015.2475358.
  • Zewde N, Gorham RD Jr, Dorado A, Morikis D (2016) Quantitative modeling of the alternative pathway of the complement system, PLOS ONE 11:e0152337 (26 pages, 43 pages supplementary information). DOI: 10.1371/journal.pone.0152337.
  • Zhang C, Brown MQ, van de Ven W, Zhang Z-M, Wu B, Young MC, Synek L, Borchardt D, Harrison R, Pan S, Luo N, Huang Y-M, Ghang Y-J, Ung N, Li R, Isley J, Morikis D, Song J, Guo W, Hooley RJ, Chang C, Yang Z, Zarsky V, Muday GK, Hicks GR, Raikhel NV (2016) Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis, Proceedings of the National Academy of Sciences (USA) 113:E41-E50. DOI: 10.1073/pnas.1521248112.
  • Zhang D., Hu X., Henning RH., Brundel BJJM. Keeping up the balance: role of HDACs in cardiac proteostasis and therapeutic implications for atrial fibrillation. Cardiovascular research (2016); 109 (4): 519-526. Pubmed Link. DOI: 10.1093/cvr/cvv265.
  • Zhang Y., Huang J., Chen D., Zhai L.-M.,Chen X., Hu X.-B., Lin Y.-H., Jin H.-B., Zhang X.-Y., Feng C.-F., Jia H.-Y., Zhou X.-X., Danzengluobu, Chen T.-L., Labaciren, Liu M.-Y., Gao Q., Zhaxiciren. Performance of new 8-inch photomultiplier tube used for the Tibet muon-detector array. Journal of Instrumentation (2016); 11(6). IOPscience Link. DOI: 10.1088/1748-0221/11/06/P06016<.
  • Zhou L., Hu X., Yin H. A randomized multicentric control study of the TCu220IUD gamma-IUD and VCu200IUD of Shenzhen district. Chinese Journal of Family Planning (2003); (9):545-548. Poplin Link.









    • Biglione, N., Rodgers, V.G.J., Peeples, T.L., "Determining Design and Scale-up Parameters for Degradation of Atrazine with Suspended Pseudomonas sp. ADP in Aqueous Bioreactors, Biotechnology Progress, 24(3) 588-592 (2008). DOI: 10.1021/bp070415p.
    • Cheng, A; C. Pasion, X. Shen, and J. Liao. A novel strategy of protein engineering in dissecting SUMO interactions within the JAK/STAT pathway (2008). UC Riverside Undergraduate Research Journal. 2, Article 11.
    • Cheung, A. S., Yang, J., Kieslich, C. A., Morikis, D. (2008) Computational Prediction of Association Free Energies for the C3d-CR2 Complex and Comparison to Experimental Data, UCR Undergraduate Research Journal 2:13-22.
    • Dimoka A., Courellis S.H., Marmarelis V.Z., Berger T.W. (2008), “Modeling the Nonlinear Dynamic Interactions of Afferent Pathways in the Dentate Gyrus of the Hippocampus” Ann Biomed Eng, May; 36(5): 852-64. DOI: 10.1007/s10439-008-9463-6.
    • Dimoka A., Gholmieh G., Courellis S.H., Marmarelis V.Z., Berger T.W., “Modeling the Nonlinear Properties of the in vitro Hippocampal Perforant Path-Dentate System using Multi-Electrode Array Technology,” IEEE Transactions on Biomedical Engineering, 55, 2, 693-702, Feb 2008. DOI: 10.1109/TBME.2007.908075.
    • Floudas, C. A., Fung, H. K., Morikis, D., Taylor, M. S., and Zhang, L. (2008) Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility, in Mathematical Modeling of Biosystems, Applied Optimization Series, p.p. 133-184, R. P. Mondaini and P. M. Pardalos (Eds.), Springer, New York. DOI: 10.1007/978-3-540-76784-8_4.
    • Fung, H. K., Floudas, C. A., Taylor, M. S., Zhang, L., and Morikis, D. (2008) Towards full-sequence de novo protein design with flexible templates for human beta-defensin-2, Biophysical Journal 94:584-599. DOI: 10.1529/biophysj.107.110627.
    • Ghosh, K., Thodeti, C.K., Dudley, A.C., Mammoto, A., Klagsbrun, M. and Ingber, D.E. Tumor-derived endothelial cells exhibit aberrant Rho-mediated mechanosensing and abnormal angiogenesis in vitro. Proceedings of the National Academy of Sciences (2008); 105(32):11305-11310. Pubmed Link DOI: 10.1073/pnas.0800835105.
    • Ghosh K. (2008). Biocompatibility of hyaluronic acid: from cell recognition to therapeutic applications. In: Reis, R., ed. Natural-based Polymers for Biomedical Applications. Cambridge, UK: Woodhead Publishing Ltd. DOI: 10.1533/9781845694814.6.716.
    • Hong, C.; Bao, D.; Thomas, M. S.; Clift, J. M. and Vullev, V. I. (2008) "Print-and- Peel Fabrication of Microelectrodes", Langmuir, 24, 8439-8442. DOI: 10.1021/la801752k.
    • Huang, X; S. Li, J.S. Schultz, Q. Wang, Q. Lin. A MEMS Affinity Glucose Sensor Using a Biocompatible Glucose-Responsive Polymer (2008). Sensors and Actuators B: Chemical, DOI: 10.1016/j.snb.2009.04.065.
    • Huynh, N., Mallik, B., Zhang, L., Martins-Green, M., and Morikis, D. (2008) Computational studies of CXCR1, the receptor of IL-8/CXCL8, using molecular dynamics and electrostatics, Biopolymers 89:52-61. Supplementary material available on-line. DOI: 10.1002/bip.20851.
    • Lyubovitsky, J.G., Xiaoman Xu, Tatiana B. Krasieva, Bogi Andersen, Bruce J. Tromberg. Characterization of dermal structural assembly in normal and pathological connective tissues by intrinsic signal multiphoton optical microscopy (2008). Proceedings of the SPIE, Volume 6859, pp. 685902-685902-9. DOI: 10.1117/12.762702.
    • Madahar, V; V. Nunez, Y. Song, and J. Liao. High-throughput Screening Assay Development for Small Molecule Inhibitor(s) of PIAS1 (2008). UC Riverside Undergraduate Research Journal. 2, Article 13.
    • Mallik, B., Zhang, L., Koide, S., and Morikis, D. (2008) pH Dependence of Stability of the 10th Human Fibronectin Type III Domain: A Computational Study, Biotechnology Progress 24:48-55. In Special Section: First International Conference on Biomolecular Engineering (ICBE). Supplementary material available on-line. DOI: 10.1021/bp0700915.
    • Millare, B.; Thomas, M.; Ferreira, A.; Xu, H.; Holesinger, M. and Vullev, V. I. (2008) "Dependence of the Quality of Adhesion between Poly(Dimethylsiloxane) and Glass Surfaces on the Conditions of Treatment with Oxygen Plasma", Langmuir, 24; 13218-13224. DOI: 10.1021/la801965s.
    • Oh, W.Y., S.H. Yun, B.J. Vakoc, G.J. Tearney, M. Shishkov, A.E. Desjardins, J.F. de Boer, B.H. Park, B.E. Bouma. High-speed polarization-sensitive optical frequency domain imaging with frequency multiplexing (2008). Optics Express 2008; 16:1096-103. DOI: 10.1364/OE.16.001096.
    • Portney, N.G., A.A. Martinez-Morales, and M. Ozkan. Nanoscale memory characterization of virus-templated semiconducting quantum dots (2008). ACS Nano, Feb; 2(2): 191-6. DOI: 10.1021/nn700240z.
    • Schumacher, K.R., A.S. Popel, B. Anvari, W.E. Brownell, and A.A. Spector. Modeling the mechanics of tethers pulled from the cochlear outer hair cell membrane (2008). Journal of Biomechanical Engineering, 130 (3):031007. DOI: 10.1115/1.2907758.
    • Su, H; M. He, H. Li, Q. Liu, J. Wang, Y. Wang, Y. Gao, L. Zhou, J. Liao, J.A. Young, and M.W. Wang. Boc5, a non-peptidic glucagon-like peptide-1 receptor agonist, invokes sustained glycemic control and weight loss in diabetic mice (2008). PLoS ONE. Aug 6; (8):e2892. DOI: 10.1371/journal.pone.0002892.
    • Wan, J.; Ferreira, A.; Xia, W.; Chow, C. H.; Takechi, K.; Kamat, P. V.; Jones, G. and Vullev V. I. (2008) “Solvent Dependence of the Charge-Transfer Properties of a Quaterthiophene-Anthraquinone Dyad”, J. Photochem. Photobiol. A, 197, 364-374. DOI: 10.1016/j.jphotochem.2008.01.016.
    • Wang, Y., and Rodgers, V.G.J., “Free-Solvent Model Shows Osmotic Pressure is the Dominant Factor in Limiting Flux During Protein Ultrafiltration”, Journal of Membrane Science, 320 (2008) 335-343. DOI: 10.1016/j.memsci.2008.04.014.
    • Yaseen, M.A., J. Yu, M.S. Wong, and B. Anvari. In-vivo fluorescence imaging of mammalian organs using charge-assembled mesocapsule constructs containing indocyanine green (2008). Optics Express, 16: 20577-20587. DOI: 10.1364/OE.16.020577.
    • Zhang, L., Mallik, B., and Morikis, D. (2008) The NMR structure of a cyclic C5aR antagonist, Biopolymers: Peptide Science 90: 803-815. DOI: 10.1002/bip.21099.



    • Buettner G.R., Ng C. F., Rodgers V.G.J., Schafer F.Q., (2006) A New Paradigm: Manganese Superoxide Dismutase Influences the Production of H2O2 in Cells and Thereby their Biological State, Free Radical Biology and Medicine, 41(8) 1338-1350 . DOI: 10.1016/j.freeradbiomed.2006.07.015.
    • Ermilov, S., Murdock, D. R., Qian, F., Brownell, W. E., and Anvari, B. (2006) Studies of plasma membrane mechanics and plasma membrane-cytoskeleton interactions using optical tweezers and fluorescence imaging, Journal of Biomechanics, doi:10.1016/j.biomech.2005.12.006. DOI: 10.1016/j.jbiomech.2005.12.006.
    • Gao, D., McBean, N., Schultz, J. S., Yan,Y., Mulchandani, A., Chen, W. (2006) Fabrication of Antibody Arrays Using Thermally Responsive Elastin Fusion Proteins J. Am. Chem. Soc., 128 (3), 676 -677. DOI: 10.1021/ja056364e.
    • Ghosh, K., Ren, X.D., Shu, X.Z., Prestwich, G.D. and Clark, R.A. Fibronectin functional domains coupled to hyaluronan stimulate adult human dermal fibroblast responses critical for wound healing. Tissue Engineering (2006); 12(3):601-613. Pubmed DOI: 10.1089/ten.2006.12.601.
    • Gliko, O., Reddy, G. D., Anvari, B., Brownell, W. E. and Saggau, P., (2006) Standing wave total internal reflection fluorescence microscopy to measure the size of nanostructures in living cells, Journal of Biomedical Optics, Journal of Biomedical Optics, 11(6), 064013. DOI: 10.1117/1.2372457.
    • Ji, Y., Ghosh, K., Shu, X.Z., Li, B., Sokolov, J.C., Prestwich, G.D., Clark, R.A. and Rafailovich, M.H. Electrospun three-dimensional hyaluronic acid nanofibrous scaffolds. Biomaterials (2006); 27(20):3782-3792. Pubmed Link DOI: 10.1016/j.biomaterials.2006.02.037.
    • Ji, Y., Ghosh, K., Li, B., Sokolov, J.C., Clark, R.A. and Rafailovich, M.H. Dual‐Syringe Reactive Electrospinning of Cross‐Linked Hyaluronic Acid Hydrogel Nanofibers for Tissue Engineering Applications. Macromolecular Bioscience (2006); 6(10):811-817. Pubmed Link DOI: 10.1002/mabi.200600132.
    • Mallik, B. and Morikis, D. (2006) Applications of molecular dynamics simulations in immunology: a useful computational method in aiding drug and vaccine design, Current Proteomics 3:259-270. DOI: 10.2174/157016406780655568.
    • Mehra, T.D., Ghosh, K., Shu, X.Z., Prestwich, G.D. and Clark, R.A. Molecular stenting with a crosslinked hyaluronan derivative inhibits collagen gel contraction. Journal of Investigative Dermatology (2006); 126(10):2202-2209. Pubmed Link DOI: 10.1038/sj.jid.5700380.
    • Morikis, D., and Zhang, L. (2006) An immunophysical study of the complement system: examples for the pH dependence of protein binding and stability, Journal of Non-Crystalline Solids 352:4445-4450. DOI: 10.1016/j.jnoncrysol.2006.01.104.
    • Morikis, D., Mallik, B., and Zhang, L. (2006) Biophysical and bioengineering methods for the study of the complement system at atomic resolution. WSEAS Transactions on Biology and Biomedicine 6:408-413.
    • Nagamine, K., Shimomura, S., Imai, K., Schultz, J.S. (2006) Probing magnetism in human blood by muon spin relaxation. Physica B, 374-375: 444-447. DOI: 10.1016/j.physb.2005.11.128.
    • Pavlou, P.A. and Dimoka, A. (2006) The Nature and Role of Feedback Text Comments in Online Marketplaces: Implications for Trust Building, Price Premiums, and Seller Differentiation, Information Systems Research, (17:4). DOI: 10.1287/isre.1060.0106.
    • Rizos, A. K., Tsikalas, I., Morikis, D., Galanakis, P., Spyroulias, G. A., and Krambovitis, E. (2006) Characterization of the interaction between peptides derived from the gp120/V3 domain of HIV-1 and the amino terminal of the chemokine receptor CCR5 by NMR spectroscopy and light scattering, Journal of Non-Crystalline Solids 352:4451-4458. DOI: 10.1016/j.jnoncrysol.2006.01.137.
    • Rodgers, V.G.J., and Wang, Y., (2006) Ultrafiltration and Nanofiltration Membranes, for the Encyclopedia of Surface and Colloid Science, Second Edition; Taylor & Francis: New York, 8, 6394 – 6415.
    • Schultz, J.S. (2006) Inside the Cell – A New Paradigm for Unit Operations and Unit Processes? Chemical Engineering Education. 40(2): 126-139.
    • Schultz, J.S. (2006) Optically-based Affinity Biosensors for Glucose. In Topics in Fluorescence Spectroscopy, Volume 11, Glucose Sensing. Editors C.D. Geddes and J.R. Lakowicz., pp 283-310. DOI: 10.1007/0-387-33015-1_11.
    • Vullev, V. I.; Wan, J.; Heinrich, V.; Landsman, P.; Bower, P. E.; Xia, B.; Millare, B. and Jones, G., II (2006) Nonlithographic Fabrication of Microfluidic Devices," J. Am. Chem. Soc. , 128, 16062-16072. DOI: 10.1021/ja061776o.
    • Wu, J. and Morikis, D. (2006) Molecular thermodynamics for charged biomacromolecules, Fluid Phase Equilibria 241:317-333. Special Festschrift issue in honor of Professor John M. Prausnitz. DOI: 10.1016/j.fluid.2005.12.044.
    • Zhao, A. and Rodgers, V.G.J., “Using TEM to Couple Transient Protein Distribution and Release for PLGA Microparticles for Potential Use as Vaccine Delivery Vehicles”, Journal of Controlled Release, 113(1) 15-22 (2006). DOI: 10.1016/j.jconrel.2006.03.018.
    • Zhang, L. and Morikis D. (2006) Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics, Biophysical Journal 90:3106-3119. Supplementary material. DOI: 10.1529/biophysj.105.068130.


    • Arya, M., Romo, G. M., Cruz, M. A., Lopez, Jose A. and Anvari, B.(2005) “Dynamic force spectroscopy glycoprotein Ib-IX and von Willebrand factor,” Biophysical Journal, 88: 4391-4401. DOI: 10.1529/biophysj.104.046318.
    • Ermilov, S., Murdock, D. R., El-Daye, D., Brownell, W. E., and Anvari, B. (2005) “Effects of salicylate on plasma membrane mechanics,” Journal of Neurophysiology, 94: 2105-2110. DOI: 10.1152/jn.00414.2005.
    • Ghosh, K., Shu, X.Z., Mou, R., Lombardi, J., Prestwich, G.D., Rafailovich, M.H. and Clark, R.A. Rheological characterization of in situ cross-linkable hyaluronan hydrogels. Biomacromolecules (2005); 6(5):2857-2865. Pubmed Link DOI: 10.1021/bm050361c.
    • Liao J, Tao J, Lin G, and Liu D. (2005). Chemistry and Biology of Sphingolipids. Tetrahedron. 61(20):4715-4733. DOI: 10.1016/j.tet.2005.02.075.
    • Mallik, B. and Morikis, D. (2005) "Development of a quasi-dynamic pharmacophore model for anti-complement peptide analogues", Journal of the American Chemical Society 127, 10967-10976. DOI: 10.1021/ja051004c.
    • Mallik, B., Katragadda, M., Spruce, L. A., Carafides, C., Tsokos, C. G, Morikis, D. , and Lambris, J. D. (2005) "Design and NMR characterization of active analogs of compstatin containing non-natural amino acids", Journal of Medicinal Chemistry 48, 274-286. DOI: 10.1021/jm0495531.
    • Mayers, B. T.; Vezenov, D. V.; Vullev, V. I.; Whitesides, G. M. "Arrays and Cascades of Fluorescent Liquid-Liquid Waveguides: Broadband Light Sources for Spectroscopy in Microchannels," Anal. Chem. 2005, 77, 1310-1316. DOI: 10.1021/ac048692n.
    • Morikis D., and Lambris, J. D. (2005) Structure, dynamics, activity, and function of compstatin and design of more potent analogs, in Structural Biology of the Complement System, p.p. 317-340, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL. DOI: 10.1201/9780849350368.ch14.
    • Morikis D., and Lambris, J. D. (2005), The building blocks of the complement system, in Structural Biology of the Complement System, p.p. 1-18, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL. DOI(Book): 10.1111/j.1440-1711.2006.01470.x.
    • Morikis D., Holland, M. C. H., and Lambris, J. D. (2005) Structure of the anaphylatoxins C3a and C5a, in Structural Biology of the Complement System, p.p. 161-177, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL.DOI(Book): 10.1111/j.1440-1711.2006.01470.x.
    • Morikis, D., and Lambris, J. D. (Eds.) (2005) Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL (ISBN 0-8247-2540-9). 370 pages. For Book Reviews see: Gordon, D. (2006) Immunology and Cell Biology 84:486; Tsokos, G. (2005) Clinical Immunology 116:306; Martinez, O. P. (2006) World Allergy Organization: DOI(Book): 10.1111/j.1440-1711.2006.01470.x.
    • 1. Morikis D, Lambris JD (Eds.) (2005) Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL (ISBN 0-8247-2540-9). 370 pages. Link.
    • Morikis, D., Floudas, C. A., and Lambris, J. D. (2005) Structure-based integrative computational and experimental approach for the optimization of drug design, in ICCS 2005, Lecture Notes in Computer Science: Computational Science, p.p. 680-688, V. S. Sunderam, G. D. van Albada, P. M. A. Sloot, and J. J. Dongarra (Eds.), Springer-Verlag, Berlin-Heidelberg. DOI: 10.1007/11428848_88.
    • Murdock, D. R., Ermilov, S., Spector, A. A., Popel, A. S., Brownell, W. E. and Anvari, B. (2005) “Effects of chlorpromazine on mechanical properties of outer hair cell plasma membrane,” Biophysical Journal, 89: 4090-4095. DOI: 10.1529/biophysj.105.069872.
    • Sfyroera, G., Katragadda, M., Morikis, D., Isaacs, S. N., and Lambris, J. D. (2005) Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins Journal of Immunology 174, 2143-2151. DOI: 10.4049/jimmunol.174.4.2143.
    • Vullev, V. I. "Modulation of Dissociation Kinetics by External Force: Examination of the Bell Model," J. Biol. Sci. 2005, 5, 744-758. DOI: 10.3923/jbs.2005.744.758.
    • Vullev, V. I.; Jiang, H.; and Jones II, G. "Excimer Sensing," In Advanced Concepts in Fluorescence Spectroscopy: Part B: Macromolecular Sensing (Topics in Fluorescence Spectroscopy, Vol. 10), Geddes, C. D. and Lakowicz, J. R. Eds.; Springer Science + Business Media, Inc.; 2005, P211-240
    • Vullev, V. I.; Jones, G., II "Nanosecond Laser Flash Photolysis: Dealing with Dynamic-Range and Response-Time Limitations of the Detection System," J. Appl. Sci. 2005, 5, 517. DOI: 10.3923/jas.2005.517.526.


    • Anvari, B., Torres, J. H. and McIntyre, B. W.(2004) “Regulation of pseudopodia localization in lymphocytes through application of mechanical forces by optical tweezers,” Journal of Biomedical Optics, 9: 865-872. DOI: 10.1117/1.1778178.
    • Ermilov, S., and Anvari, B. (2004) “Dynamic measurements of transverse optical trapping force in biological applications,” Annals of Biomedical Engineering, 32: 1016-1026, 2004. DOI: 10.1023/B:ABME.0000032464.79116.07.
    • F. Qian, S. Ermilov, D. Murdock, W. E. Brownell, and B. Anvari; “Combining optical tweezers and patch clamp techniques for studies of cell membrane electromechanics,” Review of Scientific Instruments, 75: 2937-2942. DOI: 10.1063/1.1781382.
    • Floudas, C. A., Klepeis, J. L., Lambris, J. D., and Morikis, D. (2004) De novo protein design: an interplay of global optimization, mixed-integer optimization and experiments, in FOCAPD 2004, Sixth International Conference on Foundations of Computer-Aided Process Design, Discovery through Product and Process Design, pp. 133-146, C. A. Floudas and R. Agrawal (Eds.), CACHE Corporation, Austin TX. Proceedings of the Conference held at Princeton University, Princeton, NJ, 7/11-16/2004.Link
    • Holland, M. C. H., Morikis, D., and Lambris, J. D. (2004) Synthetic small molecule complement inhibitors, Current Opinion in Investigational Drugs 5:1164-1173. Link.
    • Katragadda, M., Morikis, D. , and Lambris, J. D. (2004) Thermodynamics studies on the interaction of the third complement component and its inhibitor, compstatin Journal of Biological Chemistry 279, 54987-54995. DOI: 10.1074/jbc.M409963200.
    • Kim, J. H., Morikis, D. , and Ozkan, M. (2004) Adaptation of inroganic quantum dots for stable molecular beacons Sensors and Actuators B: Chemical 102 , 315-319. DOI: 10.1016/j.snb.2004.04.107.
    • Kim, J. H., Stephens, J. P., Morikis, D. , and Ozkan, M. (2004) Hybrid inorganic-organic molecular beacons Sensor Letters 2 , 85-90. DOI: 10.1166/sl.2004.042.
    • Klepeis, J. L., Floudas, C. A., Morikis, D. , Tsokos, C. G., and Lambris, J. D. (2004) Design of peptide analogues with improved activity using a novel de novo protein design approach Industrial & Engineering Chemistry Research 43 , 3817-3826. DOI: 10.1021/ie0340995.
    • Mastellos, D., Morikis, D., Strey, C., Holland, M. C., and Lambris, J. D. (2004) From atoms to systems: a cross-disciplinary approach to complement mediated functions, Molecular Immunology 41:153-164. DOI: 10.1016/j.molimm.2004.03.016.
    • Morikis, D. and Lambris J. D. (2004) Physical methods for structure, dynamics, and binding in immunological research, Trends in Immunology 25:700-707. Special anniversary issue for the 25th year birthday of Immunology Today/Trends in Immunology. DOI: 10.4049/jimmunol.172.12.7537.
    • Morikis, D. and Lambris, J. D. (2004) The electrostatic nature of C3d-complement receptor 2 association Journal of Immunology 172 , 7537-7547. Supplementary material DOI: 10.4049/jimmunol.172.12.7537.
    • Morikis, D., Soulika, A. M., Mallik, B., Klepeis, J. L., Floudas, C. A., and Lambris, J. D. (2004) Improvement of the anti-C3 activity of compstatin using rational and combinatorial approaches, Biochemical Society Transactions 32:28-32. DOI: 10.1042/bst0320028.
    • Sanna MG, Liao J, Jo E, Alfonso C, Ahn MY, Peterson MS, Webb B, Lefebvre S, Chun J, Gray N, and Rosen H. Sphingosine 1-phosphate (S1P) receptor subtypes S1P1 and S1P3, respectively, regulate lymphocyte recirculation and heart rate (2004). J Biol Chem. 279(14): 13839-48. DOI: 10.1074/jbc.M311743200.
    • Shu, X.Z., Ghosh, K., Liu, Y., Palumbo, F.S., Luo, Y., Clark, R.A. and Prestwich, G.D. Attachment and spreading of fibroblasts on an RGD peptide–modified injectable hyaluronan hydrogel. Journal of Biomedical Materials Research Part A (2004); 68(2):365-375. Pubmed Link DOI: 10.1002/jbm.a.20002.
    • Simpson, K. H., Bowden, G., Arya, M., Höök, M. and Anvari, B. (2004) “Adherence of Staphylococcus aureus fibronectin binding protein A mutants: an investigation using optical tweezers,” Biomolecular Engineering, 21: 105-111. DOI: 10.1016/j.bioeng.2004.08.001.
    • Wenzel, G. I., Pikkula, B., Choi, C. H., Anvari, B. and Oghalai, J.(2004) “Laser irradiation of the guinea pig cochlea basilar membrane,” Lasers in Surgery and Medicine, 35: 174-180. DOI: 10.1002/lsm.20091.
    • Ye, K. Jin, S., and Schultz, J.S. “Genetic engineering of a fluorescent cell marker for labeling CD34+ hematopoietic stem cells”, Biotechnol. Prog. 20 561-565 (2004). DOI: 10.1021/bp0342452.


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