Publications

Theses/Dissertations

Aw, Natalie. “Cerebrospinal fluid flow quantification in the brain using magnetic resonance imaging.” Master’s thesis, Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign (2019).

Grant, Lauren (Gapinske). “Cryopreservation of tissue engineered skeletal muscle.” Master’s Thesis, Department of Bioengineering, University of Illinois at Urbana-Champaign (2018).

Kandel, Mikhail E. “Gradient Light Interference Microscopy For Imaging Strongly Scattering Samples.” Dissertation, Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign (July 2020).

Pagán-Diaz, Gelson J. “Biofabrication Of Muscular and Neuronal In-Vitro Tissue For Multi-Cellular Engineered Living Systems.” Dissertation, Department of Bioengineering, University of Illinois at Urbana-Champaign (May 2020).

Ramos-Cruz, Karla. “Engineering Novel Neuronal Circuits Using Hi-Pscs Derived Neurons and Microglia.” Master’s Thesis, Department of Bioengineering, University of Illinois at Urbana-Champaign (2020).

Sullivan, Kathryn. “Developing Disease-State Liver Models to Determine the Effects on Brain Function in vitro.” Dissertation, Department of Bioengineering, University of Illinois at Urbana-Champaign (March 2021).

Journal Articles

Our trainees continue to publish their research in peer-reviewed scientific journals. This is a short list of articles published by our trainees. MBM-affiliated authors are in bold.

Chen, Xi, Mikhail E. Kandel, Chenfei Hu, Young Jae Lee, and Gabriel Popescu. “Wolf phase tomography (WPT) of transparent structures using partially coherent illumination.” arXiv preprint arXiv:2004.05302 (2020). https://arxiv.org/abs/2004.05302

Fanous, M. J., Li, Y., Kandel, M. E., Abdeen, A. A., Kilian, K. A., & Popescu, G. (2019). Effects of substrate patterning on cellular spheroid growth and dynamics measured by gradient light interference microscopy (GLIM). Journal of Biophotonics. 2019 Dec;12(12):e201900178. DOI: 10.1002/jbio.201900178. https://doi.org/10.1002/jbio.201900178

Fanous, Michael J. and Li, Yanfen, Kandel, Mikhail E., and Kilian, Kristopher A. (2019). “Patterned substrates modulate growth and dynamics of 3D cellular system.” Cold Spring Harbor perspectives in biology. 632034. https://doi.org/10.1101/632034

Fanous, Michael, Megan P. Caputo, Young Jae Lee, Laurie A. Rund, Catherine Best-Popescu, Mikhail E. Kandel, Rodney W. Johnson, Tapas Das, Matthew J. Kuchan, and Gabriel Popescu. “Quantifying myelin in brain tissue using color spatial light interference microscopy (cSLIM).” arXiv preprint arXiv:2003.01053 (2020). DOI: https://doi.org/10.1101/2020.03.27.012229

Ganguli, A.; Mostafa, A.; Saavedra, C.; Kim, Y.; Le, P.; Faramarzi, V.; Feathers, R.W.; Berger, J.; Ramos-Cruz, K.P.; Adeniba, O.; Pagan Diaz, G.J.; Drnevich, J.; Wright, C.L.; Hernandez, A.G.; Lin, W.; Smith, A.M.; Kosari, F.; Vasmatzis, G.; Anastasiadis, P.Z.; Bashir, R.. “Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging.” Science Advances. 23 Apr 2021 : EABC1323. DOI: 10.1126/sciadv.abc1323.  https://advances.sciencemag.org/content/7/17/eabc1323

Grant, Lauren (Gapinske) and Raman, Ritu and Cvetkovic, Caroline and Ferrall-Fairbanks, Meghan C. and Pagán-Diaz, Gelson J. and Hadley, Pierce and Ko, Eunkyung and Platt, Manu O. and Bashir, Rashid. (2019). “Long-Term Cryopreservation and Revival of Tissue-Engineered Skeletal Muscle.” Tissue engineering. Part A. 25 (13-14). https://doi.org/10.1089/ten.tea.2018.0202

Kandel, M.E., Hu, C., Kouzehgarani, G.H., Min, E., Sullivan, K.M., Kong, H., Li, J.M., Robson, D.N., Gillette, M.U., Best-Popescu, C., Popescu, G. “Epi-illumination gradient light interference microscopy for imaging opaque structures.” Nature Communications 10,4691 (2019). https://doi.org/10.1038/s41467-019-12634-3

Kandel, M.E. and Lu, W. and Liang, J. and Aydin, O. and Saif, T.A. and Popescu, G. (2019). “Cell-to-cell influence on growth in large populations.” Biomedical optics express. 10 (9) 4664-4675.  https://doi.org/10.1364/BOE.10.004664 

Kandel, Mikhail E., Yuchen R. He, Young Jae Lee, Taylor Hsuan-Yu Chen, Kathryn Michele Sullivan, Onur Aydin, M. Taher A. Saif, Hyunjoon Kong, Nahil Sobh, and Gabriel Popescu. “PICS: Phase Imaging with Computational Specificity.” arXiv preprint arXiv:2002.08361 (2020). https://arxiv.org/abs/2002.08361

Kandel, Mikhail E., Marcello Rubessa, Yuchen R. He, Sierra Schreiber, Sasha Meyers, Luciana Matter Naves, Molly K. Sermersheim, G. Scott Sell, Michael J. Szewczyk, Nahil Sobh, Matthew B. Wheeler, Gabriel Popescu. Reproductive outcomes predicted by phase imaging with computational specificity of spermatozoon ultrastructure. Proceedings of the National Academy of Sciences Jul 2020, 202001754; DOI: 10.1073/pnas.2001754117 https://doi.org/10.1073/pnas.2001754117

Kaufman, C.D., Liu, S.C., C. Cvetkovic, G. Naseri Kouzehgarani, R. Bashir, M.U. Gillette. 2019. “Emergence of Functional Neuromuscular Junctions in an Engineered, Multicellular Spinal Cord-Muscle Bioactuator.”  APL Bioengineering. 4, 026104 (2020); https://doi.org/10.1063/1.5121440.

Kim Y, Pagán-Diaz G, Gapinske L, Kim Y, Suh J, Solomon E, Foster Harris J, Nam S, Bashir R. “Integration of Graphene Electrodes with 3D Skeletal Muscle Tissue Models”, Advanced Healthcare Materials, (January 2020). Doi: https://doi.org/10.1002/adhm.201901137

Le, P. and Lim, S. and Baculis, B. and Chung, H. and Kilian, K. and Smith, A. (2019). “Counting growth factors in single cells with infrared quantum dots to measure discrete stimulation distributions.” Nature communications. https://doi.org/10.1038/s41467-019-08754-5

Pagán-Diaz, Gelson J. and Zhang, Xiaotian and Grant, Lauren and Kim, Yongdeok and Aydin, Onur and Cvetkovic, Caroline and Ko, Eunkyung and Solomon, Emilia and Hollis, Jennifer and Kong, Hyunjoon and Saif, Taher and Gazzola, Mattia and Bashir, Rashid. (2018). “Simulation and Fabrication of Stronger, Larger, and Faster Walking Biohybrid Machines.” Advanced Functional Materials. 28 (23) 1801145. doi:10.1002/adfm.201801145

Pagán-Diaz, Gelson J., Jenny Drnevich, Karla P. Ramos-Cruz, Richard Sam, Parijat Sengupta, Rashid Bashir. “Modulating behavior of motor neural networks via optogenetic stimulation during neurogenesis and synaptogenesis.” Sci Rep 10, 12460 (2020). https://doi.org/10.1038/s41598-020-68988-y

Engineering geometrical 3-dimensional untethered in vitro neural tissue mimic.” 

Qin, E.C., Kandel, M.E., Liamas, E., Shah, T.B., Kim, C., Kaufman, C.D., Zhang, Z.J., Popescu, G., Gillette, M.U., Leckband, D.E.Kong, H.J. Graphene oxide substrates with N-cadherin stimulates neuronal growth and intracellular transport. Acta Biomaterial 90:412-423 (2019). Acta Biomaterial 90:412-423 (2019). DOI: https://doi.org/10.1016/j.actbio.2019.04.005

Rubessa, M., Kandel, M.E., Schreiber, S., Meyers, S., Beck, D. H., Popescu, G., & Wheeler, M. B. (2020). “Morphometric analysis of sperm used for IVP by three different separation methods with spatial light interference microscopy.” Systems Biology in Reproductive Medicine, 66(1), 26-36. DOI: https://doi.org/10.1080/19396368.2019.1701139

Rubessa, Marcello, Jean M. Feugang, Mikhail E. Kandel, Sierra Schreiber, Jade Hessee, Francesca Salerno, Sascha Meyers, Iwei Chu, Gabriel Popescu, and Mathew B. Wheeler. “High-throughput sperm assay using label-free microscopy: morphometric comparison between different sperm structures of boar and stallion spermatozoa.” Animal Reproduction Science (2020): 106509. DOI: https://doi.org/10.1073/pnas.1916138116

Sinclair, W.E., Chang, H., Dan, A., Kenis, P., Murphy, C., & Leckband, D.E. Gold nanoparticles disrupt actin organization and pulmonary endothelial barriers. Sci Rep 10, 13320 (2020). https://doi.org/10.1038/s41598-020-70148-1.

Wang, Yi, Mikhail E. Kandel, Michael J. Fanous, Chenfei Hu, HsuanYu Chen, Xiaoxu Lu, and Gabriel Popescu. “Harmonically decoupled gradient light interference microscopy (HD-GLIM).” Optics Letters 45, no. 6 (2020): 1487-1490. DOI: https://doi.org/10.1364/OL.379732

Xie, Y.; Castro, D. C.; Bell, S. E.; Rubakhin, S.; Sweedler, J. V. “Single-Cell Classification Using Mass Spectrometry Through Interpretable Machine Learning.” Analytical Chemistry. June 10, 2020. DOI: 1021/acs.analchem.0c01660

Accepted / Under Review

Chen, Xi, Mikhail E. Kandel, Chenfei Hu, Young Jae Lee, Gabriel Popescu. “Wolf phase tomography (WPT) of transparent structures using partially coherent illumination.” arXiv:2004.05302. April 11, 2020. https://arxiv.org/abs/2004.05302 

Neuronal outgrowths radiate from a 7 DIV rat spinal cord. Choline Acetyltransferase (motor neurons, red) and Tuj1 (neuron cytoskeleton, blue) immunohistochemistry colocalize indicating that these processes are nearly entirely cholinergic. Astrocytes (GFAP, green) are also present in great number demonstrating the multicellular complexity of the spinal cord. Collin Kaufman, Trainee
Neuronal outgrowths radiate from a 7 DIV rat spinal cord. Choline Acetyltransferase (motor neurons, red) and Tuj1 (neuron cytoskeleton, blue) immunohistochemistry colocalize indicating that these processes are nearly entirely cholinergic. Astrocytes (GFAP, green) are also present in great number demonstrating the multicellular complexity of the spinal cord.
Collin Kaufman, Trainee