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2019

Journal

Alvarez MM, Aizenberg J, Analoui M, Andrews AM, Bisker G, Boyden ES, Kamm RD, Karp JM, Mooney DJ, Oklu R, Peer D, Stolzoff M, Strano MS, Trujillo-de Santiago G, Webster TJ, Weiss PS, Khademhosseini A. Emerging Trends in Micro- and Nanoscale Technologies in Medicine: From Basic Discoveries to Translation. ACS Nano. 2017 Jun 27;11(6):5195-5214.

Anderson D, Jones R, Arkin A, Weiss R. Principles of Synthetic Biology: A MOOC for an Emerging Field. Synthetic Biology. 2019 May;DIO:10.1093/synbio/ysz010

Asada HH, Sotiropoulos FE. Dual Faceted Linearization of Nonlinear Dynamical Systems Based on Physical Modeling Theory. ASME Journal of Dynamic Systems, Measurement, and Control. 2019;141(2):021002.

Aydin O, Zhang X, Nuethong S, Pagan-Diaz GJ, Bashir R, Gazzola M, Saif MTA. Neuromuscular actuation of biohybrid motile bots. Proceedings of the National Academy of Sciences. 2019; 201907051.

Ballance WC, Qin EC, Chung HJ, Gillette MU, Kong H. Reactive oxygen species-responsive drug delivery systems for the treatment of neurodegenerative diseases. Biomaterials. 2019;217:119292. 

Ben-Yair R, Butty VL, Busby M, Qiu Y, Levine SS, Goren A, Boyer LA, Burns CG, Burns CE. H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. Development. 2019 Oct 9;146(19). pii:dev178632.

Boyce AS, Avent C, Adetogun A, Servance L, DeStefano L, Nerem R, Platt MO. 
Implementation and evaluation of a biotechnology research experience for African-American high school students. Eval Program Plann. 2019 Feb;72:162-169.

Brown AT, He H, Trumper E, Valdez J, Hammond P, Griffith LG. “Engineering PEG-based hydrogels to foster efficient endothelial network formation in free-swelling and confined microenvironments. 2019.

Cangellaris OV, Corbin EO, Froeter P, Michaels JA, Li X, Gillette MU. Aligning synthetic hippocampal neural circuits via self-rolled-up silicon nitride microtube arrays. ACS Appl Mater Interfaces. 2018;42:35705-35714. 

Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno-Serrano M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell. 2019 Aug 22;178(5):1115-1131.e15.

Chen Y, Ju LA, Zhou F, Liao J, Xue L, Su QP, Jin D, Yuan Y, Lu H, Jackson SP, Zhu C. An integrin αIIbβ3 intermediate affinity state mediates biomechanical platelet aggregation. Nature Materials. 2019;18,760–769

Churchill CDM, Winter P, Tuszynski JA, Levin M. EDEn – Electroceutical Design Environment: Ion Channel Tissue Expression Database with Small Molecule Modulators, iScience, 2019;11:42-56.

Daniel AP, Giblin J, Zhao Y, Lu H. Reverse-Correlation Analysis of Mechanosensation Circuit in C. elegans Reveals Temporal and Spatial Encoding, Scientific Reports, 2019;9.1:5182. 

Douglas SA, Lamothe SE, Singleton TS, Averett RD, Platt MO. Human cathepsins K, L, and S: Related proteases, but unique fibrinolytic activity. Biochim Biophys Acta Gen Subj. 2018 Sep;1862(9):1925-1932.  Epub 2018 Jun 23.

Elhebeary M, Emon MAB, Aydin O, Saif MTA. A novel technique for in situ uniaxial tests of self-assembled soft biomaterials. Lab on a Chip. 2019;19(7):1153-1161.

Eunkyung K, Yu SJ, Pagán-Díaz GJ, Mahmassani Z, Boppart MD, Im SG, Bashir R, Kong H. Reciprocity between Nanogrooved Substrate-Mediated  Muscle  Maturity  and  Neurons toward Neuromuscular Junction Formation,  Advanced Science. 2019.

Fanous M, Li Y, Kandel M, Abdeen A, Kilian K, Popescu G. Effects of substrate patterning on cellular spheroid growth and dynamics measured by gradient light interference microscopy (GLIM). Journal of Biophotonics 2019; doi:10.1002/jbio.201900178.

Glen CM, Kemp ML, Voit EO. “Agent-based modeling of morphogenetic systems: Advantages and challenges”. PLoS Comput Biol. 2019;15(3):e1006577.

Glen CM, McDevitt TC, Kemp ML. “Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment”. Nature Communications. 2018;9(1):4111.

Sun G, Lu H. “Recent Advances in Microfluidic Techniques for Systems Biology”, Analytical Chemistry. 2019;91(1):315-329.

Grant L, Raman R, Cvetkovic C, Ferrall-Fairbanks MC, Pagan-Diaz GJ, Hadley P, Ko E, Platt MO, Bashir R. Long-Term Cryopreservation and Revival of Tissue-Engineered Skeletal Muscle. Tissue Eng Part A. 2019 Jul;25(13-14):1023-1036.Epub 2019 Jan 9.

Hu C, Popescu G. Quantitative Phase Imaging (QPI) in Neuroscience. IEEE Journal of Selected Topics in Quantum Electronics 25:1–9, 2019.

Hu C, Sam R, Shan M, Nastasa V, Wang M, Kim T, Gillette MU, Sengupta P, Popescu G. Optical excitation and detection of neuronal activity. J. Biophotonics. 2018;12(3):9pp. 

Hu C, Santi M, Adelaja O, Kajdacsy-Balla A, Popescu G, Kobak W. Imaging Collagen Properties in the Uterosacral Ligaments of Women With Pelvic Organ Prolapse Using Spatial Light Interference Microscopy (SLIM). Frontiers in Physics 7. 2019.

Jayaram DT, Kumar A, Kippner LE, Ho PY, Kemp ML, Fan Y, Payne CK. TiO 2 nanoparticles generate superoxide and alter gene expression in human lung cells. RSC Advances. 2019;9(43):25039-47.

Kamm RD, Bashir R, Arora N, Dar RD, Gillette MU, Griffith LG, Kemp ML, Kinlaw K, Levin M, Martin AC, McDevitt TC, Nerem RM, Powers MJ, Saif TA, Sharpe J, Takayama S, Takeuchi S, Weiss R, Ye K, Yevick HG, Zaman MH. “Perspective: The promise of multi-cellular engineered living systems”. APL Bioengineering. 2019;2(4):040901.

Kandel ME, Lu W, Liang J, Aydin O, Saif TA, Popescu G. Cell-to-cell influence on growth in large populations. Biomedical Optics Express. 2019;10(9),4664-4675.

Kandel ME, Hu C, Naseri Kouzehgarani G et al. Epi-illumination gradient light interference microscopy for imaging opaque structures. Nat Commun. 2019;10, 4691 doi:10.1038/s41467-019-12634-3.

Bates K, Jiang S, Bates R, Chaudhary S, Jackson-Holmes E, Jue M, McCaskey E, Goldman D, Lu H. “Fast, versatile, and quantitative annotation of complex images”. BioTechniques. 2019;66.6:269-275. 

Khodaverdian V, Tapadar S, MacDonald IA, Xu Y, Ho PY, Bridges A, Rajpurohit P, Sanghani BA, Fan Y, Thangaraju M, Hathaway NA, Oyelere AK. Deferiprone: Pan-selective Histone Lysine Demethylase Inhibition Activity and Structure Activity Relationship Study. Sci Rep. 2019;9(1):4802.

Kim H, Kim MC, Asada HH. Extracellular matrix remodelling induced by alternating electrical and mechanical stimulations increases the contraction of engineered skeletal muscle tissues. Scientific reports. 2019;9(1),2732.

Ko E, Yu SJ, Pagan‐Diaz GJ, Mahmassani Z, Boppart MD, Im, SG, Kong H. Matrix topography regulates synaptic transmission at the neuromuscular junction. Advanced Science. 2019;6(6),1801521.

Levin M, Martyniuk CJ. The bioelectric code: An ancient computational medium for dynamic control of growth and form. BioSystems. 2018;164:76-93.

Li Y, Fanous MJ, Kilian KA, Popescu G. Quantitative phase imaging reveals matrix stiffness-dependent growth and migration of cancer cells. Scientific Reports. 2019;9.

Li Z, Seo Y, Aydin O, Elhebeary M, Kamm R, Kong H, Saif M. Biohybrid valveless pump-bot powered by engineered skeletal muscle. Proceedings of the National Academy of Sciences. 2019;116(5),pp.1543-1548.

Mapar F, Weiss R. Switching Delay Analysis for Two Neuronal Toggle Switch Designs: Direct and Staged Mutual Inhibition. 9th International IEEE/EMBS Conference on Neural Engineering (NER). 2019 May;DIO:10.1109/NER.2019.8717123

Mathews J, Levin M. The Body Electric 2.0: Recent Advances in Developmental Bioelectricity for Regenerative and Synthetic Bioengineering. Current Opinion in Biotechnology. 2018;52:134-144.

Mayalu M, Kim M, Asada H. Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space. PLOS Computational Biology. 2019;15(9), p.e1006798.

Mehdipour N, Briers D, Haghighi I, Glen C, Kemp ML, Belta C. Spatial-Temporal Pattern Synthesis in a Network of Locally Interacting Cells. 57th IEEE Conference on Decision and Control. 2018.

Mehdipour N, Briers D, Haghighi, I, Glen C, Kemp M, Belta C. Spatial-Temporal pattern Synthesis in a Network of Locally Interacting Cells. 2018;3516-3521. 10.1109/CDC.2018.8618702.

Naseri Kouzehgarani G, Bothwell MY, Gillette MU. Circadian Rhythm of Redox State in Hippocampal CA1 Regulates Neuronal Excitability. European Journal of Neuroscience. 2019;00: 1-13.

Offeddu GS, Haase K, Gillrie MR, Li R, Morozova O, Hickman D, Knutson CG, Kamm RD. An on-chip model of protein paracellular and transcellular permeability in the microcirculation. Biomaterials. 2019;212,115.

Cangellaris OV, Corbin EA, Froeter P, Li X, Gillette MU. “Biocompatible Self-Rolled-Up Silicon Nitride Microtube Arrays Align Hippocampal Neuronal Circuits.” ACS Appl. Mater. Interfaces. 2018 Sep; 10(42), pp. 35705-35714.

Offeddu GS,  Possenti L,  Loessberg‐Zahl JT,  Zunino P,  Roberts J, Han X,  Hickman D,  Knutson CG,  Kamm RD. Application of Transmural Flow Across In Vitro Microvasculature Enables Direct Sampling of Interstitial Therapeutic Molecule Distribution. Small.  2019;1902393:https://doi.org/10.1002/smll.201902393.

Osaki T, Serrano J, Kamm R. Cooperative Effects of Vascular Angiogenesis and Lymphangiogenesis. Regenerative Engineering and Translational Medicine. 2018;4(3)pp:120-132.

Pagan-Diaz GJ, Zhang X, Grant L, Kim Y, Aydin O, Cvetkovic C, Ko E, Solomon E, Hollis J, Kong H, Saif T, Gazzola M, Bashir R. Simulation and Fabrication of Stronger, Larger, and Faster Walking Biohybrid Machines, Adv. Funct. Mater. 2018;28,1801145.

Parks AN, Nahata J, Edouard NE, Temenoff JS, Platt MO. Sequential, but not Concurrent, Incubation of Cathepsin K and L with Type I Collagen Results in Extended Proteolysis. Sci Rep. 2019 Apr 1;9(1):5399.

Peña JS, Robles D, Zhang S, Vazquez M. A Milled Microdevice to Advance Glia-Mediated Therapies in the Adult Nervous System. Micromachines. 2019;10,513.

Punjiya M, Nehad HR, Mathews J, Levin M, Sonkusale S. A flow through device for simultaneous dielectrophoretic cell trapping and AC electroporation. Scientific Reports. 2019;9:11988.

Qin EC, Kandel ME, Liamas E, Shah TB, Kim C. Graphene oxide substrates with N-cadherin stimulates neuronal growth and intracellular transport. Acta Biomaterialia, 2019.

Pena JS, Vazquez M. Reducing health disparities in adult vision loss via interfaces with emerging technology. Nature Eye. 2019 Apr;33(4):532-533.

Dutta S, Djabrayan NJ, Torquato S, Shvartsman SY, Krajnc M. Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo. Biophys J. 2019 Aug 20;117(4):743-750. 

Shin Y,  Choi SH,  Kim E,  Bylykbashi E,  Kim JA,  Chung S,  Kim DY,  Kamm RD,  Tanzi RE.  Blood–Brain Barrier Dysfunction in a 3D In Vitro Model of Alzheimer’s Disease. Adv. Sci.  2019;6,1900962:https://doi.org/10.1002/advs.201900962

Singh T, Vazquez M. Time-Dependent Addition of Neuronal and Schwann Cells Increase Myotube Viability and Length in an In Vitro Tri-culture Model of the Neuromuscular Junction. Regenerative Engineering and Translational Medicine. 2019;1-12.

Takabayashi M, Majeed H, Kajdacsy-Balla A, Popescu G. Tissue spatial correlation as cancer marker. Journal of Biomedical Optics. 2019;24:1.

Takayama S. “Embracing Heterogeneity and Disorder” Israel J Chem 2019, 59, 95-99. 

Whited J, Levin M. Bioelectrical controls of morphogenesis: from ancient mechanisms of cell coordination to biomedical opportunities, Current Opinion in Genetics & Development. 2019;57: 61-69.

Wong L, Kumar A, Gabela-Zuniga B, Chua J, Singh G, Happe CL, Engler AJ, Fan Y, McCloskey KE. Substrate stiffness directs diverging vascular fates. Acta Biomater. 2019;96:321-329. 

Wu M, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios S, Humphrey M, Zhang Z, Novoa E, Kellis M, Weiss R, Rabkin S, Tabach Y, Lu T. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Nature Communications. 2019 Jul;DIO:10.1007/s12213-019-00119-x.

Yamanishi C, Oliver CR, Kojima T, Takayama S. Stigmatic Microscopy Enables Low-Cost, 3D, Microscale Particle Imaging Velocimetry in Rehydrating Aqueous Two-Phase Systems. Frontiers in chemistry. 2019;7,311:doi:10.3389/fchem.2019.00311

Yamanishi C, Robinson S, Takyama S. Biofabrication of phenotypic pulmonary fibrosis assays. Biofabrication. 2019;11,3:doi:10.1088/1758-5090/ab2286

Mapar F, Weiss R. Design and Analysis of Staged Mutual Inhibition to Implement Bi-Stable Neuronal Toggle Switch. Proceedings of the 2018 IEEE Biomedical Circuits and Systems Conference (BioCAS). 2018 Oct;DOI: 10.1109/BIOCAS.2018.8584816. Published Conference Proceeding.

Books

Hu C, Popescu G. Quantitative Phase Imaging: Principles and Applications. Label-Free Super-Resolution Microscopy. 2019 Sep;Springer,Cham.