Peer Reviewed:  

2012

 

Ahmed W W, Li T C, Rubakhin S S, Chiba A, Sweedler J V, Saif T A. Mechanical tension modulates local and global vesicle dynamics in neurons. (Invited article). Journal of Cellular and Molecular Bioengineering. 2012; 5(2): 155-164.

Ahmed W, Williams B, Silver A, Saif T. Measuring nonequilibrium vesicle dynamics in neurons under Tension. Lab on a Chip. Submitted.

Anand S V, Saif T A. Cardiomyocyte powered 1-D biobot swimmers. PNAS. In Preparation.

Ban K, Wile B, Kim S, Byun J, Saafir T, Wagner M, Bao G, Yoon Y. Purification of cardiomyocytes from differentiating pluripotent stem cells using molecular beacons targeting cardiomyocyte-specific mRNA. Nature Medicine. Submitted.

Barry Z T, Platt M O. Cathepsin S cannibalism of cathepsin K as a mechanism to reduce type I collagen degradation.  Journal of Biological Chemistry. 2012; 287(33): 27723-27730.

Bhaduri B, Wickland D, Wang R, Chan V, Bashir R, Popescu G. Cardiomyocyte imaging using real time spatial light interference microscopy imaging (SLIM). PLoS One. Submitted.

Bratt-Leal  A M, Kepple Ki L, Carpenedo  R L, Cooke M T, McDevitt T C. Magnetic manipulation and spatial patterning of multi-cellular stem cell aggregates. Integrative Biology. 2011; 3(12): 1224-32.

Cha C, Antoniadou E, Saif T, Kong H. Integration of a cell-laden hydrogel with silicone substrate. Biomaterials. In Preparation.

Cha C, Jeong J, Tang X, Zill A, Zimmerman S, Prakash Y S, Saif T, Kong H. Top-down synthesis of versatile polyaspartamide linkers for single-step protein conjugation to materials. Bioconjugate Chemistry. 2012: 22, 2377-2383.

Chan  V, Collens  M B, Jeong  J H, Park  K, Kong  H, Bashir  R. Directed cell growth and alignment on protein-patterned 3D hydrogels with stereolithography.  Virtual and Physical Prototyping.   2012; 7(3): 219-228.

Chan V J , Jae H, Bajaj P, Collens M, Saif T, Kong H, Bashir R.Multi-material bio-fabrication of hydrogel cantilevers and actuators with stereolithography. Lab on a Chip. 2012; 12(1): 88-98.

Chan V, Park K, Collens M B, Kong H, Saif T A, Bashir R. Development of miniaturized walking biological machines. Scientific Reports. Submitted.

De Souza  E J, Ahmed W, Chan V, Bashir R, Saif T A. Cardiac myocytes' dynamic contractile behavior differs depending on heart segment. Biotechnology and Bioengineering. In Press.

Dennis A M, Rhee W J, Sotto D, Dublin S N, Bao G. Quantum Dot-Fluorescent Protein FRET Probes for Sensing Intracellular pH. ACS Nano. 2012: 6(4) 2917-2924.

DeVolder R, Zill A, Jeong J, Kong  H. Microfabrication of proangiogenic cell-laden alginate-g-pyrrole hydrogels.Biomaterials.2012; 33(): 7718-7726.

Farahat  W A, Wood L B, Zervantonakis I K, Schor A, Ong S, Neal D, Kamm  R D, Asada H. Ensemble Analysis of Angiogenic Growth in Three-Dimensional Microfluidic Cell Cultures.PLoS One. 2012; 7(5).

Geng Y, Wang F. High-Throughput Chemical Screening Revealed New Conditions and Regulatory Mechanisms for Fate Decisions of Human Pluripotent Stem Cells. Nature Chemical Biology. In Preparation. 2013.

Glaser D E, Burns A B, Hatano R, Medrzycki M, Fan Y, McCloskey K E. Mouse Embryonic Stem Cells for Studying Vascular Development. Stem Cells and Development. Submitted.

Han  J, Yoon Y. Epigenetic landscape of Pluripotent Stem cells. Antiox Redox Signal. 2012; 17(2): 205-23.

Hatano R, Luna J, Mercurio K, Glaser D E, Leppert V, McCloskey K E. Endothelial Cells Derived from Embryonic Stem Cells Respond to Cues from Topographical Surface Patterns. Journal of Biological Engineering. Submitted.

Jeong GS, Shin Y, Kwon G H, Kamm R D, Lee S H, Chung S. Sprouting angiogenesis under a chemical gradient regulated by interaction with endothelial monolayer in microfluidic platoform. Anal Chem. 2011; 83(22): 8454-9.

John S, Shkumatov A, Kong H. Matrix-mediated capillary network formation. Biomacromolecules. In Preparation.

Kim  H , Kim J, Yoon Y. Emerging Therapy for Diabetic Neuropathy: Cell Therapy Targeting Vessels and Nerves.  Endocrine, Metabolic & Immune Disorders-Drug Targets. 2012; 12(2): 168-178.

Kim M C, Kim C, Wood L, Neal D, Kamm R D, Asada H H.Integrating Focal Adhesion Dynamics, Cytoskeleton Remodeling, and Actin Motor Activity for Predicting Cell Migration on 3D Curved Surfaces of Extracellular Matrix. Integrative Biology.2012; 4: 1386-1397.

Lee S, Yoon Y. Revisiting cardiovascular regeneration with bone marrow-derived angiogenic and  vasculogenic cells. British Journal of Pharmacology. 2012.

Li W, Lee S, Kim S M, Lee R T, Hammond P T. Microbead-based ex-vivo 3D microenvironment enhances survival and function of rat pancreatic B-cells. Biomaterials. In Preparation.

Liang Y, Jeong J, DeVolder  R, Cha C, Wang F, Tong Y, Kong H.A Cell-Instructive Hydrogel to Regulate Malignancy of 3D Tumor Spheroids with Matrix Rigidity. Biomaterials.   2011; 32(35): 9308-15.

Liao X, Lu S, Zhuo Y, Winter C, Xu W, Wang Y. Visualization of Src and FAK activity during the differentiation process from HMSCs to osteoblast by FRET biosensor. PLoS ONE. In Press. 2012.

Majumder A, Banerjee S, Harrill, J, A, Machacek, D, W, Mohamad, O, Bacanamwo M, Mundy W R, Wei L, Dhara S K, Stice S L. Neurotrophic Effects of Leukemia Inhibitory Factor on Neural Cells Derived from Human Embryonic Stem Cells.Stem Cells. 2012: 30(11): 2387-99.

Majumder A, Dhara S K, Raymond S, Cao K, Medrzycki M, Fan Y, Stice S L. Rapid production of cryopreservable astrocytes from human embryonic stem cell derived neural progenitors. Stem Cell Research. In Preparation.

Mayalu  M N, Asada  H H. A Time-Based Approach to Stochastic Modeling of Intracellular Signaling Events.  Proceedings of Dynamic Systems and Control Conference. 2012.

McCloskey K E, Glaser D E, Burns A, Hatano R, Medrzycki M , Fan Y. Specialized Mouse Embryonic Stem Cells for Studying Vascular Development. Submitted - Stem Cells and Development. Submitted.

L J, Collens M B, Perry G L, Bashir R. Spatial distribution and analysis of neurons in culture. Integrative Biology. 2011; 3: 1167-1178.

 

Millet L J, Gillette M U.New perspectives on neuronal development via microfluidic environments.Trends in Neurosciences. In Press. 2012; online.

Millet L J, Gillette M U. Over a Century of Neuron Culture: From the Hanging Drop to Microfluidic Devices. Yale J. Bio. Med. In Press.

Mir M, Babacan S D, Bednarz M, Do M, Golding I, Popescu G. Visualizing Escherichia coli Sub-Cellular Structure Using Sparse Deconvolution Spatial Light Interference Tomography. PLoS ONE. 2012: 7(6) e39816.

Mir M, Wang Z, Shen S, Bednarz  M, Bashir R, Golding I, Prasanth S, Popescu G.  Optical Measurement of Cell Cycle Dependent Mass Growth.  PNAS. 2011; 108(32): 13124-13129.

Moon S, Ban K, Kim C , Kim S, Byun J, Song M , Park I , Yu S P , Yoon Y. Development of a novel two-dimensional directed differentiation system for generation of cardiomyocytes from human pluripotent stem cells. International Journal of Cardiology. In Press.

Neal D S, Sakar M S, Asada H H. Bioengineered Fascicle-Like Skeletal Muscle Tissue Constructs. Proceedings of ASME Summer Bioengineering Conference. 2012.

Nishitani  W S, Saif T, Wang Y. Calcium signaling in live cells on elastic gels under mechanical vibration at subcellular levels.  PLoS ONE.   2011; 6(10): 326181.

Oelker  A M, Morey S M, Griffith L G, Hammond P T. Helix versus coil polypeptide macromers: gel networks with decoupled stiffness and permeability. Soft Matter. 2012; 8: 10887-10895.

Park C, Lee Ji Y, Yoon Y. Role of Bone Marrow-Derived Lymphatic Endothelial Progenitor Cells for Lymphatic Neovascularization.Trends in Cardiovascular Medicine. 2011; 21(5): 135-140.

Phelps E  A, Enemchukwu N O, Fiore V F, Sy J C, Murthy N, Sulchek T A, Barker T H, Garcia A J. Maleimide cross-linked bioactive PEG hydrogel exhibits improved reaction kinetics and cross-linking for cell encapsulation and in-situ delivery. Advanced Materials. 2012; 24(1): 64-70.

 

Qu Q, Wang F. High-efficiency differentiation of motor neurons from human pluripotent  stem cells depends upon tightly controlled temporal modulation of differentiation signals. Cell Stem Cell. Submitted. 2013.

Rich M, Millett L, Bashir R, Kong H. Ink-Jet Printing of Muscle Strip. Biomaterials. In Preparation.

Sakar  M S, Neal D, Boudou T B, Michael A, Li Y, Weiss R, Kamm R D, Chen C S, Asada H H. Formation and Optogenetic Control of Engineered 3D Skeletal Muscle Bioactuators. Lab on a Chip. 2012; 12.

Salimath  A S, Phelps  E A, Boopathy A V , Che P L, Brown  M E, Garcia A J, Davis M E. Dual delivery of hepatocyte and vascular endothelial growth factors via a protease-degradable hydrogel improves cardiac function.  Biomaterials &PLoS ONE. Submitted.  2012.

Schmidt, J  J, Jeong  J H, Cha  C, Chan V, Free R, Bashir R, Kong H.  Controlling the dependency between hydrogel rigidity and permeability with inflexibility of polymer cross-linker.  Macromolecules. Submitted. 2012.

Shin Y, Han S, Jeon  J S, Yamamoto K, Zervantonakis I K, Sudo R, Kamm R D, Chung  S. Microfluidic assay for simultaneous culture of multiple cell types on surfaces or within hydrogels. Nature Prot. 2012; 7(7): 1247-1259.

Shin Y, Jeon  J S, Han S, Jung G S, Shin S, Lee S H, Sudo R, Kamm R D, Chung S. In vitro 3D collective sprouting angiogenesis under orchestrated ANG-1 and VEGF gradients. Lab Chip.   2011; 11(13): 2175-2181.

Singh V R, Choi  H, Yew E Y S, Bhattacharya D, Yuan L, Sheppard C J R , Rajapaske  J C, Barbastathis G, So P T C. Improving signal-to-noise ratio of structured light microscopy based on photon reassignment. Biomedical Optics Express. 2012; 3(1): 206-214.

Slusarczyk  A L, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nature Reviews Genetics. 2012; 13(6): 406-420.

Subramanian V, Mazumder  A, Surface L E, Fields P, Alwan A, Butty V, Torrey L, Thai K K, Levine S S, Bathe M, Boyer L A. H2AZ extended acidic patch is necessary for formation specialized chromatin states. Submitted. 2012.

Tang  X , Ali M Y, Saif T A. A Novel Technique for Micro-patterning Proteins and Cells on Polyacrylamide Gels.  Soft Matter. 2012; 8: 7197-7206.

Vickerman V, Kamm R D. Mechanism of a flow-gated angiogenesis switch: early signaling events at cell-matrix and cell-cell junctions. Integr.Biol.(Camb). 2012; 4(8): 863-74.

White D E, Kinney MA, McDevitt TC, Kemp ML. Spatial Pattern Dynamics of 3D Stem Cell Differentiation via Rules-Based Computational Modeling. PLoS Computational Biology. Submitted.

Wong K H, Chan J M, Kamm R D, Tien J. Microfluidic Models of Vascular Functions. Annu Rev Biomed Eng. In Press. 2012.

Wong K H, Chan J M, Kamm R D, Tien J. Microfluidic Models of Vascular Functions. Annu Rev Biomed Eng. In Press. 2012.

Wood L B, Ge R, Kamm R D, Asada H H. Nascent vessel elongation rate is inversely related to diameter in in vitro angiogenesis. Intgrative Biology.2012; 4(9): 1081-1089.

Zhang  Y, Cooke  M, Panjwani  S, Cao K, Krauth  B, Ho P, Medrzycki  M, Berhe D T, Pan C, McDevitt T C, Fan Y. Histone H1 Depletion Impairs Embryonic Stem Cell Differentiation. Plos Genetics. 2012;8(5).

Zhou J, Li D, Wang F. Assessing the function of mTOR in human embryonic stem cells.  Methods in Molecular Biology. 2012; 821: 361-72.

Zorlutuna P, Jeong J H, Kong H, Bashir R. Stereolithography-Based Hydrogel Microenvironments to Examine Cellular Interactions.Advanced Functional Materials. 2011; 21(19): 3642-3651.

 

2011

Anand SV, Saif TA. Characterization and Control of Myotube Contraction on 1-D Polymeric Devices. Biomaterials. In Preparation.  

Anand SV, Liu C, Gillette M, Saif TA. Realization and characterization of extrinsic factors governing the formation of neuromuscular junctions. Biophysical Journal. In Preparation. 

Anderson SM, Shergill B, Barry ZT, Manousiouthakis E, Chen TT, Botvinick E, Platt MO, Iruela-Arispe ML, Segura T. VEGF internalization is not required for VEGFR-2 phosphorylation in bioengineered surfaces with covalently linked VEGF. Integrative Biology. 2011;3: 887-896.

Asada HH, Wang Y, 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. 2011: 2314-19.

 

Bajaj P, Reddy Jr. B, Millet L, Wei C, Zorlutuna P, Bao G, Bashir R. Patterning the differentiation of C2C12 skeletal myoblasts. Integrative Biology. 2011;3(9): 897-909.

Beal J, Lu T, Weiss R. Automatric compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One. 2011;6(8): e22490.

Cha C, Jeong J, Shim J, Kong H. Tuning the dependency between stiffness and permeability of cell-encapsulating hydrogel with hydrophilic pendant chains. Acta Biomaterialia. 2011;7: 3719-28.

Chan V, Jeong J, Hyun BP, Collens M, Saif T, Kong H, Bashir R. Multi-material biofabrication of hydrogel cantilevers and actuators with stereolithography. Lab on a Chip. In Press.

Glaser D, McCloskey KE. A new mouse ESC line for studying vascular cell fate. In Preparation. 

Han J, Yoon Y. Epigenetic landscape of Pluripotent Stem cells Antiox Redox Signal. In Press.

Han J, Yoon Y. Induced Pluripotent Stem Cells: Emerging Techniques for Nuclear Reprogramming. Antiox Redox Signal 2011. 2011;15(7): 1799-1820. 

He Y, Kapoor A, Cook S, Liu S, Xiang Y, Rao CV, Kenis P, Wang F. The non-receptor tyrosine kinase Lyn controls neutrophil adhesion by recruiting the CrkL/C3G complex to and activatingRap1 at the leading edge. J. Cell Science. 2011;124: 2153-64. 

Jeong J, Chan V, Cha C, Zorlutuna P, Dyck C, Hsia KJ, Bashir R, Kong H. 'Living microvascular stamp for patterning of functional neovessels; Orchestrated control of matrix property and geometry. Advanced Materials. In Press. 

Kaur J, Shkumatov A, Fields C, Kuhlenschmidt M, Hofmann MC. Endothelial differentiation of mouse spermatogonial stem cells in three-dimensional collagen gels needs the CCN3/NOV extracellular matrix protein. In preparation.

Li D, Zhou J, Chowdhury F, Cheng J, Wang N, Wang F. Role of mechanical factors in fate decisions of stem cells. Regenerative Medicine. 2011: 6: 229-240.

Mayalu M, Asada H. Controlling the Chronological Order of Intracellular Signaling Events Using Stochastic Time Delay Model. Proceedings of 2012 American Control Conference. Submitted.

Millet LJ, Park K, Watkins NN, Hsia KJ, Bashir R. Separating beads and cells in multichannel microfluidic devices using dielectrophoresis and laminar flow. J Vis Exp. 2011;4(48): 2545. 

Mir M, Wang Z, Shen Z, Bednarz M, Bashir R, Golding I, Prasanth SG, Popescu G. Optical measurement of cycle-dependent cell growth. Proceedings of the National Academy of Sciences. 2011;108(32): 13124-29.

Neal D, Asada HH. Co-Fabrication of Live Skeletal Muscles as Actuators in a Millimeter Scale Mechanical System. Proceedings of 2011 IEEE International Conference on Robotics and Automation. 2011;3251-58.

Schmidt J, Jeong J, Cha C, Chan V, Bashir R. Controlling the dependency between hydrogel rigidity and permeability with inflexibility of polymer cross-linker. Macromolecules. Submitted.

Sridharan S, Mir M, Popescu G. Simultaneous optical measurement of cell motility and growth. Biomedical Optics Express. 2011;2(10): 2815-20. 

Tang X, Anand SV, Saif TA. A novel cell traction force estimation technique for multiple cell-cell and cell-cluster interactions. Acta Biomaterialia. In Preparation.

Wan CR, Chung S, Kamm RD. Differentiation of embryonic stem cells into cardiomyocytes in a compliant microfluidic system. Ann Biomed Eng. 2011 Jun; 39(6): 1840-7. 

Wang R, Wang Z, Leigh J, Sobh N, Millet L, Gillette MU, Levine AJ, Popescu, G. Onedimensional deterministic transport in neurons measured by dispersion-relation phase spectroscopy. J. Phys.: Condens. Matter. 2011;23: online 374107-374115.

Wang Z, Millet L, Chan V, Ding H, Gillette MU, Bashir R, Popescu G. Label-free intracellular transport measured by Spatial Light Interference Microscopy. Journal of Biomedical Optics. 2011;16(2): 026019-026109-9. 

Wood L, Kamm RD, Asada HH. Stochastic Modeling and Identification of Emergent Behaviors of an Endothelial Cell Population in Angiogenic Pattern Formation. International Journal of Robotics Research. 2011; 30(6): 659-677.

 

2010

Asada, H., Wang, Y. X., 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, Invited Session on Dynamics and Control of Biological Systems. 

Bajaj, P., Tang, X., Saif, T., and Bashir, R., Stiffness of the substrate influences the phenotype of embryonic chicken cardiac myocytes, Journal of Biomedical Materials Research-A, Oct: 95A(4), 1261-1269, 2010.



Li, D., Zhou, J., Wang, L., Shin, M. E., Su, P., Lei, X., Kuang, H., Guo, W., Yang, H., Cheng, L., Tanaka, T. S., Reynolds, A. B., Duan, E., and Wang, F. Integrated biochemical and mechanical signals regulate multifaceted human embryonic stem cell functions, Journal of Cell Biology, Oct; 191, 631-44, 2010 (highlighted in News - In Focus, Journal of Cell Biology, 191, 2010).

Millet, L. J., Park, K., Watkins, N. N., Hsia, K.J., and Bashir, R. Separating beads and cells in multi-channel microfluidic devices using dielectrophoresis and laminar flow. Journal of Visualized Experiments (a new video journal), accepted, 2010. 

Park, K., Millet, L., Kim, N., Li, H., Jin, X., Popescu, G., Aluru, N. R., Hsia, K. J., and Bashir, R. Measurement of adherent cell mass and growth. Proceedings of the National Academy of Sciences, in press, 2010.

Seong, J., Lu, S., Wang, Y. Live cell imaging of Src/FAK signaling by FRET, Cellular and Molecular Bioengineering, in press, 2010.

 

Non-Peer Reviewed

Kamm, R.D., Nerem, R., Hsia, K.J. Cells into systems ASME Mechanical Engineering Magazine, 132 (11), 30-34, 2010.