Bioengineering Publications

Journal Publications:

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Year 2015

  1. Kim, M.-C., Whisler, J., Silberberg Y.R., Kamm, R.D., and Asada, H.H. “Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network,” PLoS Computational Biology, Vol. 11, Issue 10, e1004535, October 2015.
  2. Neal, D., Sakar, S., Chan, V., Bashir, R., Asada, H.H., “Mechanical Characterization and Shape Optimization of Fascicle-Like 3D Skeletal Muscle Tissues Contracted with Electrical and Optical Stimuli,” Tissue Engineering Part A, Vol. 21, Issue 11-12, pp. 1848-1858, May 2015.
  3. Chan, V., Neal, D., Uzel, S. G. M., Kim, H., Bashir, R., and Asada, H. H. “Fabrication and characterization of optogenetic, multi-strip cardiac muscles,” Lab on a Chip, April 2015.
  4. Wang, M., Ong, L.L.S., Dauwels, J., Asada, H.H., “Automatic Detection of Endothelial Cells in 3D Angiogenic Sprouts from Experimental Phase Contrast Images,” SPIE Medical Imaging, Vol. 9413, pp. 1-7, March 20, 2015.

Year 2014

  1. Yan, J., Kang, Y., Xu, S., Ong, L.L.S., Zhuo, S., Bunte, R.M., Chen, N., Asada H.H., So, P.T.C., Wanless, I.R., Yu, H., “In vivo label-free quantification of liver microcirculation using dual-modality microscopy,” Journal of Biomedical Optics, Vol.19(11), pp. 116006-1-116006-6, November 2014.
  2.  Cvetkovic, C., Raman, R., Chan, V., Williams, B. J., Tolish, M., Bajaj, P., Bashir, R., Asada, H., “Three-dimensionally printed biological machines powered by skeletal muscle,” Proceedings of the National Academy of Science, Vol. 111, pp. 10125-10130, July 2014.
  3. Neal, D., Sakar, M.S., Ong, L-L. S., Asada, H.H., “Formation of Elongated Fascicle-Inspired 3D Tissues Consisting of High-Density, Aligned Cells Using Sacrificial Outer Molding”, Lab on a Chip, pp. 448-460, March 2014.
  4. Sharghi-Namini, S., Tan, E., Ong, L-L.S., Ge, R., and Asada, H. “Dll4-containing exosomes induce capillary sprout retraction in a 3D microenvironment, ” Nature, Scientific Reports, Vol. 4, p. 1-8, February 2014.
  5. Herath, S., Du, Y., Wang, D., Liao, K., Wang, Q., Chen, P.C.Y., Asada, H., “Characterization of uniaxial stiffness of extracellular matrix embedded with magnetic beads via bio-conjugation and under the influence of an external magnetic field,” Journal of the Mechanical Behavior of Biomedical Materials, Vol. 30, pp. 253-265, February 2014.
  6. Ong, L. L., Dauwels, J., Ang Jr, M. H., & Asada, H. H., “A Bayesian filtering approach to incorporate 2D/3D time-lapse confocal images for tracking angiogenic sprouting cells interacting with the gel matrix,” Medical image analysis, 18(1), 211-227, January 2014.
  7. Herath, S., Yue, D., Hui, S., Kim, M.C., Wang, D., Wang, Q., Van Vliet K.J., Asada, H.H., Chen, P., “Quantification of Magnetically Induced Changes in ECM Local Apparent Stiffness”, Biophysical Journal, Vol.106, Issue 1, pp.332-341, January 2014.

Year 2013

  1. Chan V., Asada H. H., and Bashir, R., “Utilization and control of bioactuators across multiple length scales,” Lab Chip, 2014 (Advanced Article), Front Cover Article, Lab on a Chip HOT article, Issue 4, pp. 653-670, November 2013.
  2. Ang, X. M., Lee, M. H., Blocki, A., Chen, C., Ong, L. L., Asada, H. H., … & Raghunath, M., “Macromolecular crowding amplifies adipogenesis of human bone marrow-derived mesenchymal stem cells by enhancing the pro-adipogenic microenvironment,” Tissue engineering Part A, 20(5-6), 966-981, March 2014.
  3. Kim, M.-C., Lam, R.H.W., Thorsen, T., and Asada, H., “Mathematical Analysis of Oxygen Transfer through Polydimethylsiloxane Membrane between Double Layers of Cell Culture Channel and Gas Chamber in Microfluidic Oxygenator”, Microfluidics and Nanofluidics, Vol. 15, Issue 3, pp. 285-296, February 2013.
  4. Kim, M.-C., Neal, D., Kamm, R., and Asada, H., “Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries,” PLoS Computational Biology 9(2): e1002926, February, 2013.

Year 2012

  1. Kim, M.-C.,  Kim, C.,  Wood, L., Neal, D., Kamm, R., and Asada, H., “Integrating Focal Adhesion Dynamics, Cytoskeleton Remodeling, and Actin Motor Activity for Predicting Cell Migration on 3D Curved Surfaces of Extracellular Matrix,” Integrative Biology, Vol. 4(11), pp. 1386-1397, September 2012.
  2. Kim, Choong, Chung, Seok, Liu, Yuchun, Kim, Min-Cheol, Chan, Jerry K. Y., Asada, H., and Kamm, D., “In Vitro Angiogenesis Assay for the Study of Cell-Encapsulation Therapy”, in Lab on a Chip, Vol. 12, Issue 16, pp.2942-2950, May 2012.
  3. Ge, R., Tan, E., Sharghi-Namini, Soheila, Asada, H., “Exosomes in Cancer Microenvironment and Beyond: Have We Overlooked These Extracellular Messengers?”, Cancer Microenvironment, Vol. 5, Issue 3, pp.323-332, May 2012.
  4. Wood, L., Ge, R., Kamm, R., and Asada, H., “Nascent vessel elongation rate is inversely related to diameter in in vitro angiogenesis“, Integrative Biology, Vol. 4, Issue 9, pp.1081-1089, July 2012.
  5. Sakar, M.S., Neal, D., Boudou, T., Borochin, M., Lic, Y., Weiss, R. Kamm, R.D., Chen, C. and Asada, H., “Formation and optogenetic control of engineered 3D skeletal muscle bioactuators,” Lab on a Chip 12, no. 23 (2012): 4976-4985, October 2012.
  6. Mayalu, M.N.; Asada, H.H.;, “A Time-Based Approach to Stochastic Modeling of Intracellular Signaling Events,” Proc. Of the Dynamic Systems and Control Conference (DSCC), October 2012.
  7. Neal, D., Sakar, M. S., Asada, H. H., “Bioengineered Fascicle-Like Skeletal Muscle Tissue Constructs,” Proc. Of the 2012 ASME Summer Bioengineering Conference, June 2012.
  8. Farahat, W., Wood, L., Zervantonakis, I., Schor, A., Ong, S., Neal, D., Kamm, R., and Asada, H., “Ensemble Analysis of Angiogenic Growth in Three-Dimensional Microfluidic Cell Cultures”, PLoS ONE, Vol. 7, Issue 5, April 2012.
  9. Hahn, J.-O., Reisner, A., Jaffer, F.A., and Asada, H., “Subject-Specific Estimation of Central Aortic Blood Pressure Using an individualized Transfer Function: a Preliminary feasibility Study”, IEEE Transactions on Information Technology in Biomedicine, Issue 99, PMID: 22147332, Vol. 16, No. 2, pp. 212 – 220, March 2012.

Year 2011

  1. Wood, L., and Asada, H., “Cellular Stochastic Control of the Collective Output of a Class of Distributed Hysteretic Systems”, ASME J. of Dynamic Systems, Measurement, and Control, Vol. 133, Issue 6, pp. 61011- 61022, November 2011.
  2. Wood, L., Kamm, R., and Asada, H., “Stochastic Modeling and Identification of Emergent Behaviors of an Endothelial Cell Population in Angiogenic Pattern Formation”, The Int. Journal of Robotics Research, vol. 30, no.6, pp. 659-677, May 2011.

Year 2010

  1. Hahn, J.-O., Reisner, A., and Asada, H., “Estimation of Pulse Transit Time Using Two Diametric Blood Pressure Waveform Measurements”, Medical Engineering & Physics, Vol. 32, Issue 7, pages 753-759, September 2010.
  2. Das, A., Lauffenburger, D., Asada, H., and Kamm, R., “A Hybrid Continuum–Discrete Modeling Approach to Predict and Control Angiogenesis: Analysis of Combinatorial Growth Factor and Matrix Effects on Vessel-Sprouting Morphology”, Philosophical Transactions of the Royal Society A: Mathematical, Physical, and Engineering Sciences, vol. 368, no. 1921, pp. 2937-2960, June 2010.
  3. Hahn, J.-O., McCombie, D., Hojman, H., Reisner, A., and Asada, H., “Identification of Multi-Channel Cardiovascular Dynamics Using Dual Laguerre Basis Functions for Noninvasive Cardiovascular Monitoring“, IEEE Transactions on Control Systems Technology, Vol. 18, Issue 1, pp. 170-176,  January 2010.

Year 2009

  1. Hahn, J.-O., Reisner, A., and Asada, H., “Blind Identification of Two-Channel IIR Systems with Application to Central Cardiovascular Monitoring”, ASME Journal of Dynamic Systems, Measurement, and Control, Vol. 131, No 5, 2009. Hahn, J.-O., Reisner, A., and Asada, H., “Modeling and 2-Sensor Blind Identification of  Human Cardiovascular System”, Control Engineering Practice, Vol. 17, Issue 11, pp. 1318-1328, November 2009.
  2. Wood, L., Das, A., Kamm, R. and Asada, H., “A Stochastic Broadcast Feedback Approach to Regulating Cell Population Morphology for Microfluidic Angiogenesis Platforms”, IEEE Transactions on Biomedical Engineering, Vol.56, Issue 9, Part 2, pp.2299-2303, September, 2009.

Conference Proceedings:


Year 2016

  1. Kim, M.-C., Mayalu, M., and Asada, H.H., “Dynamic Modeling of Collective Cell Migration on an Elastic Substrate of Extracellular Matrix fiber network,” Proceedings of the 2016 American Control Conference, Boston, MA, July 6-8, 2016.
  2. Mayalu, M., Kim, M.-C., and Asada, H.H., “A Reduced Order Systems Approach to Prediction of Emergent Behaviors of Cellular Systems,” Proceedings of the 2016 American Control Conference, Boston, MA, July 6-8, 2016.

Year 2015

  1. Kim, M.-C., Whisler, J., Silberberg Y.R., Kamm, R.D., and Asada, H.H., “Computational Modeling of Cell Invasion Dynamics into a 3D ECM Fiber Network,”Proceedings of the 2015 Biomedical Engineering Society Annual Meeting (BMES), Tampa, October 7-11, 2015.
  2. Kim, H., Chan, V., Neal, D., and Asada, H.H., “Optimization of mechanical and electrical stimuli to make stronger 3D engineered skeletal muscles,”Proceedings of the 2015 Biomedical Engineering Society Annual Meeting (BMES), Tampa, October 7-11, 2015.
  3. Mayalu, M.N., and Asada, H.H., “Multi-Model Selection of Integrated Mechanistic-Empirical Models Describing T-Cell Response,” Proceedings of the 2015 American Control Conference, Chicago, IL, July 1-3, 2015.
  4. Kim, M.-C., Whisler, J., Silberberg Y.R., Kamm, R.D., and Asada, H.H., “Computational modeling of cell invasion dynamics into an extracellular matrix fiber network,” Invited seminar in a Special topic on “Modeling of cell dynamics: cytoskeleton and membrane,” 15th International Congress of Biorheology, Seoul, Korea, May 24–28, 2015.

Year 2014

  1. Mayalu, M. N., Kim, M.C., Chan, V., Neal, D., Kim, H.Y., Asada, H.H., “A New Approach to Predicting Emergent Behaviors of Cell-ECM Interactions Using Stochastic Rules Generated from Mechanistic Computational Models,” Proceedings of the 7th World Congress of Biomechanics, Boston, MA, July 6-11, 2014.
  2. Silberberg, Y., Kim, M.-C., Asada, H.H., “3D Traction Force Microscopy Combined with Computer Simulation Models for the Analysis of Filopodia Dynamics”, Proceedings of 7th World Congress of Biomechanics, Boston, MA, July 6-11, 2014.
  3. Kim, M.C., Kamm, R., Asada, H.H., “Filopodia Dynamics, ECM Interaction, and 3D Cell Migration Modeling”, Proceedings of the 7th World Congress of Biomechanics, Boston, MA, July 6-11, 2014.
  4. Mayalu, M. N., and Asada, H.H. “An information-theoretic approach to integrated mechanistic-empirical modeling of cellular response based on intracellular signaling dynamics,” Proceedings of 2014 American Control Conference (ACC), pp. 1755-1760, Portland, OR, June 2014.
  5. Ong, L.-L.S., Wang, M., Dauwels, J. and Asada, H., “Segmentation of Densely Populated Cell Nuclei from Confocal Image Stacks Using 3D Non-Parametric Shape Priors,” the 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 5526-5529, Chicago, IL, August 2014.
  6. Kim, M.C., Mayalu, M. N., Asada, H.H., “Stochastic Modeling of Dynamic Cell Migration and Spreading on Dot-Patterned Microstructures,” Dynamic Systems and Control Conference, San Antonio, Texas, October 22-24, 2014,

Year 2013

  1. Kim, M-C., Chen, P., Kamm, R., Asada, H.H., “Dynamic Modeling of Tip Cell migration Incorporating Filopodia Dynamics in Degradable 3-Dimensional Extracellular Matrix,” Proceedings of the 15th International Conference on Biomedical Engineering (ICBME), Singapore, Dec. 4-7, 2013.
  2. Mayalu, M.N., Asada, H.H., “Integrated Mechanistic-Empirical Modeling of Cellular Response Based on Intracellular Signaling,” Proceedings of the 2013 ASME Dynamic Systems and Control Conference, (DSCC), Stanford, CA, October 2013.
  3. Kim, H., Neal, D., Asada, H.H., “Towards the Development of Optogenetically-Controlled Skeletal Muscle Actuators”, Proceedings of the 2013 ASME Dynamic Systems and Controls Conference, Stanford, CA, October 2013.
  4. Kim, M-C., Tan, C.W., Chan, J., Griffith, L.G., Kamm, R.D., Asada, H.H., “Integrated Cell Migration Model Incorporating Spatiotemporal Kinetics of Focal Adhesion Assembly and Disassembly”, Proceedings of the 2013 Biomedical Engineering Society Annual Meeting (BMES), Seattle, September 25-28, 2013.
  5. Kim, M-C., Kim, Y-H., Neal, D., Kamm, R.D, Asada, H.H., “Directional Mobility of Cell Migration on Tubular Conduits: Experiment and Simulation,” Proceedings of the 2013 Biomedical Engineering Society Annual Meeting (BMES), Seattle, September 25-28, 2013.
  6. Kim, M-C., Chen, P., Kamm, R.D., Asada, H.H., “Incorporating Filopodia Dynamics, Focal Adhesion Dynamics, Cytoskeleton Remodeling, and Degradation of Extracellular matrix for Predicting Tip Cell Migration in Angiogenesis,” Proceedings of the 2013 Biomedical Engineering Society Annual Meeting (BMES), Seattle, September 25-28, 2013.
  7. Neal, D., Asada, H.H., “Engineered Muscle Systems Having Individually Addressable Distributed Muscle Actuators Controlled by Optical Stimuli,” Proceedings of the IEEE Engineering in Medicine and Biology Society Conference (EMBS), July 3-7, 2013.
  8. Neal, D., Sakar, M.S., Asada, H., “Distributed Live Muscle Actuators Controlled by Optical Stimuli,” Proceedings of the ASME Summer Bioengineering Conference (SBS), Sunriver, Oregon, June 2013.
  9. Neal, D., Sakar, M.S., Asada, H.H., “Optogenetic Control of Live Skeletal Muscles: Non-Invasive, Wireless, and Precise Activation of Muscle Tissues,” Proceedings of the ASME American Control Conference (ACC), June 2013.
  10. Wang, M., Ong, L-L, Dauwels, J., Asada, H.H., “2D data-driven stalk cell prediction model based on tip-stalk cell interaction in angiogenesis,” Proceedings of 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pages 4537-4540, July 2013.

Year 2012

  1. Mayalu, M.N.; Asada, H.H.;, “A Time-Based Approach to Stochastic Modeling of Intracellular Signaling Events,” Proc. Of the Dynamic Systems and Control Conference (DSCC), October 2012.
  2. Neal, D., Sakar, M. S., Asada, H. H., “Bioengineered Fascicle-Like Skeletal Muscle Tissue Constructs,” Proc. Of the 2012 ASME Summer Bioengineering Conference, June 2012.
  3. Kim, M., Kamm, R.D., Asada, H.H., “Introduction of Integrated Cell migration Model: Comparisons with Cell Migration Experiments,” BMES 2012, Oct 24-27, 2012, Atlanta, GA.
  4. Kim, M., Kim, C., Wood, L., Neal, D., Kamm, R.D., Asada, H.H., “2-D Cell Migration on the 3-D Curved Surfaces: Experiment and Simulation,” BMES 2012, Oct 24-27, 2012, Atlanta, GA.

Year 2011

  1. Wood, L., and Asada, H., “An Experimentally Tuned Dynamic Model Predicting Cell Migration For Guidance Of Sprouting Endothelial Cells”, Proc. Of 2011 ASME Dynamic Systems and Control Conference, Vol. 2, pp. 595-601, Oct. 31-Nov.2, 2011.
  2. Farahat, W., Wood, L., Zervantonakis, I., Schor, A., Ong, S., Neal, D., Kamm, R. and Asada, H., “Ensemble Analysis of Angiogenic Growth in Three-Dimensional Microfluidic Cell Cultures”, in Proc. Of PLOS 2011- 6th Workshop on Programming Languages and Operating Systems, October 2011.
  3. Ong, L.L.S., Wood, L. B., Ang, M. H. and Asada H. H., “Stochastic Tracking of Migrating Live Cells Interacting with 3D Gel Environment Using Augmented-Space Particle Filters”,  Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 2011, Pages 3931—3936, San Francisco, CA, 25-30 September 2011.
  4. Asada, H.H., Wang, Y-X, and Mayalu, M, “Molecular Signaling Observer and Predictor: A Framework For Closed-loop Control Of Cell Behaviors Having Long Time Delay”, Proceedings of 2011 American Control Conference(ACC), page 2314-2319, June 29-July 1, 2011.
  5. Ramanathan, K., Ong, L.L.S., Asada, H. H., and Ang, M. H.,” Automated tracking of biological cells in an “in-vitro” environment using active contours and distance measures”, Proceedings of the IEEE 5th International Conference on Cybernetics and Intelligent Systems (CIS), 2011, Pages 241—246, Qingdao, China, 17—19 September, 2011.
  6. Asada, H.H., Wang, Y-X, and Mayalu, M, “Molecular Signaling Observer and Predictor: A Framework For Closed-loop Control Of Cell Behaviors Having Long Time Delay”, Proceedings of 2011 American Control Conference(ACC), page 2314-2319, June 29-July 1, 2011.
  7. Neal, D., and Asada, H., “Co-Fabrication of Live Skeletal Muscles as Actuators in a Millimeter Scale Mechanical System“, Proc. of 2011 IEEE Int. Conference on Robotics and Automation (ICRA), page 3251-3256,  Shanghai, China, 9-13 May 2011.
  8. Ong, L.L.S, Ang, M. H. and Asada, H.H, “Simultaneous Tracking of Cell Nuclei and Conduit Parameters from Time-Lapse Confocal Microscopy Images”, Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), 2011, Pages 1011—1014, Chicago, IL, 30 March – 2 April 2011.
  9. Kim, M-C, Klapperich, C., and Asada, H.H., “Numerical Methods for Simulating Biconcave Cells in the Microfluidic Device”, Proceeding of the 2nd conference on Advanced In Microfluidics and Nanofluiducs 2011, Jan 5- 7, 2011, Singapore.

 Year 2010

  1.  Farahat, W., and Asada, H., “Control of Eukaryotic Cell Migration by Modulating Extracellular Chemoattractant Gradients”, Proc. of 2010 ASME Dynamic Systems and Control Conference, MoCT2.5, September 2010.
  2. Wood, L., Kamm, R., and Asada, H., “Time-Lapse Observation Based Modeling and Identification of Cell Behaviors in Angiogenic Sprout Development”, Proc. of 2010 ASME Dynamic Systems and Control Conference, MoCT2.3, September 2010.
  3. Asada, H., “Reduced-Order Cue-Signal-Response Modeling for Angiogenic Cell Migration Control: A Principal Signal Approach”, Proc. of 2010 ASME Dynamic Systems and Control Conference, Vol. 1, pp. 445-451, MoCT2.2, September 2010.

Year 2009

  1. Farahat, W., and Asada, H., “Identification of Phenotypic State Transition Probabilities in Living Cells”, Proc. of 2009 ASME Dynamic Systems and Control Conference, Vol. 1, pp. 81-88, October 2009.

Year 2008

  1. Odhner, L., and Asada, H., “Equilibrium Point Control of Artificial Muscles Using Recruitment of Many Motor Units”, Proc. of 2nd IEEE RAS / EMBS International Conference on Biomedical Robotics and Biomechatronics (BioRob), October 19-22 2008.
  2. Wood, L.B., Das, A., Kamm, R., and Asada, H., “A Stochastic Control Framework for Regulating Collective Behaviors of an Angiogenesis Cell Population”, Proc. of 2008 IEEE Bio-Rob Conference, pp. 390-396, October 2008.
  3. Wood, L., Ueda, J., Asada, H., “Broadcast Feedback with Hysteresis Loop Control of Stochastically Behaving Cellular Units with Application to Cellular Shape Memory Alloy Actuators”, Proceedings of Dynamic Systems and Control Conference, Ann Arbor, Michigan, USA, October 20-22, 2008.
  4. Hahn, J.-O., Reisner, A., and Asada, H., “Blind Identification of 2-Channel IIR Wave Propagation Systems for Central Cardiovascular Monitoring”, Proc. of 2008 ASME Dynamic Systems and Control Conference, pp. 339-344, WeAT4.6, October 2008.
  5. McCombie, D., Reisner, A., and Asada, H., “Motion Based Adaptive Calibration of Pulse Transit Time Measurements to Arterial Blood Pressure for an Autonomous, Wearable Blood Pressure Monitor”, Proc. of 30th Annual Int. Conference of IEEE Engineering in Medicine and Biology Society, August 20-25, 2008.
  6. Hahn, J.-O., Asada, H., Reisner, A., and Jaffer, F., “A New Approach to Reconstruction of Central Aortic Blood Pressure Using Adaptive Transfer Function”, Proc. of 30th Annual Int. Conference of IEEE Engineering in Medicine and Biology Society, August 20-25 2008.
  7. Hahn, J.-O., Reisner, A., and Asada, H., “Physiologic-State-Adaptive Recovery of Aortic Blood Pressure and Flow Using Blind 2-Channel IIR Cardiovascular System Identification”, Proc. 2008 American Control Conference, pp. 838-843, June 2008.
  8. Wood, L.B., Das, A., and Asada, H., “Broadcast Feedback Control of Cell Populations Using Stochastic Lyapunov Functions with Applications to Angiogenesis Regulation”, Proc. 2008 American Control Conference, pp. 2105-2111, June 2008.

Year 2007

  1. Odhner, L., Ueda, J., and Asada, H.,” Stochastic Optimal Control Laws for Cellular Artificial Muscles”, Proc. of 2008 IEEE Int. Conference on Robotics and Automation, April 10-14 2007.