Publications

Theses/Dissertations

1. 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).
2. Baculis, Brian. “Activity-Dependent Regulation of Girk and Kv7 Channels in Homeostatic Plasticity And Epilepsy.” Dissertation, Neuroscience Program, University of Illinois at Urbana-Champaign. (2022).
3. Gapinske, Lauren. “Cryopreservation of tissue engineered skeletal muscle.” Master’s Thesis, Department of Bioengineering, University of Illinois at Urbana-Champaign (2018).
4. Gapinske, Lauren. “Enhancing the Functionality and Applicability of Engineered Skeletal Muscle Tissue.” Dissertation, Department of Bioengineering, University of Illinois at Urbana-Champaign. (2022).
5. 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 (2020).
6. Kaufman, Collin. “Emergence of Functional Neuromuscular Junctions in an Engineered, Multicellular Spinal Cord-Muscle Bioactuator.” Dissertation, Neuroscience Program, University of Illinois at Urbana-Champaign (2021).
7. Murphy, Shannon. “Analysis of small molecule neurotransmitters using capillary-electrophoresis mass spectrometry: applications for studying development and disease.” Thesis, Department of Chemistry, University of Illinois at Urbana-Champaign. (2022).
8. 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 (2020).
9. 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).
10. Sinclair, Whitney. “Lung-on-a-Chip Device with In Situ Imaging Capabilities.” Dissertation, Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign. (2021).
11. 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 (2021).
12. Walters, Jennifer. “The Investigation Of The Genetic And Pharmacological Inhibition Of Striatal-Enriched Protein Tyrosine Phosphatase (Step) And Its Role In Hippocampal Excitability And Seizure Propensity.” Dissertation, Neuroscience Program, University of Illinois at Urbana-Champaign (2022).

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.

1. Baculis, Brian; Jiaren Zhang, and Hee Jung Chung. “The Role of Kv7 Channels in Neural Plasticity and Behavior.” Frontiers in Physiology. 11:568667. Mini-review article. September 18, 2020. https://doi.org/10.3389/fphys.2020.568667
2. Bell, S. E.; Park, I.; Rubakhin, S. S.; Bashir, R.; Vlasov, Y.; Sweedler, J. V. “Droplet Microfluidics with MALDI-MS Detection: The Effects of Oil Phases in GABA Analysis.” ACS Measurement Science Au. 0, 0, pp DOI: 10.1021/acsmeasuresciau.1c00017 https://pubs.acs.org/doi/full/10.1021/acsmeasuresciau.1c00017
3. Chen, Xi, Mikhail E. Kandel, Chenfei Hu, Young Jae Lee, and Gabriel Popescu. “Wolf phase tomography (WPT) of transparent structures using partially coherent illumination.” Light Sci Appl 9, 142 (2020). https://doi.org/10.1038/s41377-020-00379-4
4. Chen, X., Kandel, and G. Popescu, Spatial light interference microscopy: principle and applications to biomedicine , Advances in Optics and Photonics, 13, 353-425, 2021. https://doi.org/10.1364/AOP.417837
5. De La Toba, E. A.; Bell, S. E.; Romanova, E. V.; Sweedler, J. V. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. Annu. Rev. Anal. Chem. March 24, 2022. https://doi.org/10.1146/annurev-anchem-061020-022048
6. 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
7. 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
8. Fanous, M., C. Megan, Y. Lee, L. Rund, M. Kandel, R. Johnson, C. Best-Popescu, M. Kuchan, G. Popescu, Quantifying myelin content in brain tissue using color Spatial Light Interference Microscopy (cSLIM), November 19, 2020 PlosOne. https://doi.org/10.1371/journal.pone.0241084
9. 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
10. 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
11. Jiao, Y., Y. R. He, E. Kandel, X. Jun, W. Lu, and G. Popescu, Computational interference microscopy enabled by deep learning , APL Photonics, 6, 2021. https://doi.org/10.1063/5.0041901
12. Jiao, Y., M, Kandel, X. Liu, W. Lu, and G. Popescu, Real-time Jones phase microscopy for studying transparent and birefringent specimens, Optics Express, 28, 34190-34200 (2020). https://doi.org/10.1364/OE.397062
13. 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
14. 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 
15. 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
16. 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
17. Kandel, Mikhail, Eunjae Kim, Young Jae Lee, Gregory Tracy, Hee Jung Chung, and Gabriel Popescu. Multiscale Assay of Unlabeled Neurite Dynamics Using Phase Imaging with Computational Specificity. ACS Sensors 2021 6 (5), 1864-1874. DOI: 10.1021/acssensors.1c00100
18. Kandel, Mikhail, Yuchen R. He, Young Jae Lee, Taylor Hsuan-Yu Chen, Kathryn Michele Sullivan, Onur Aydin, M. Taher A. Saif, Hyunjoon Kong, Nahil Sobh & Gabriel Popescu. Phase imaging with computational specificity (PICS) for measuring dry mass changes in sub-cellular compartments. Nat Commun 11, 6256 (2020). https://doi.org/10.1038/s41467-020-20062-x
19. 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.
20. 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
21. Kim, B. S., Kim, M. K., Cho, Y., Hamed, E. E., Gillette, M. U., Cha, H., Miljkovic, N., Aakalu, V. K., Kang, K., Son, K.-N., Schachtschneider, K. M., Schook, L. B., Hu, C., Popescu, G., Park, Y., Ballance, W. C., Yu, S., Im, S. G., Lee, J., … Kong, H. (2020). Electrothermal soft manipulator enabling safe transport and handling of thin cell/tissue sheets and bioelectronic devices. Science Advances, 6(42), eabc5630. https://doi.org/10.1126/sciadv.abc5630
22. Ko, E., Aydin, O., Li, Z., Gapinske, L., Huang, K-Y, Saif, T., Bashir, R., Kong, H.J. Empowering engineered muscle in biohybrid pump by extending connexin 43 duration with reduced graphene oxides. Biomaterials 287, 121643. June 24, 2022. https://doi: 10.1016/j.biomaterials.2022.121643.
23. 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
24. Miller, R., Kim, Y., Park, C.G., Han, H., Kim, Y.J., Kong, H.J. Extending the bioavailability of hydrophilic antioxidants for metal ion detoxification via recrystallization with polysaccharide dopamine. ACS Applied Materials and Interface. [Under Review, 7/17/2022]
25. Murphy, Shannon E. and Jonathan V. Sweedler, Metabolomics-based mass spectrometry methods to analyze the chemical content of 3D organoid models, The Analyst. May 30, 2022. Advance Article, https://doi.org/10.1039/D2AN00599A
26. 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
27. 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
28. Pagán-Diaz, Gelson J., Karla P. Ramos-Cruz, Richard Sam, Mikhail E. Kandel, Onur Aydin, M. Taher A. Saif, Gabriel Popescu, and Rashid Bashir. “Engineering geometrical 3-dimensional untethered in vitro neural tissue mimic.” PNAS December 17, 2019 116 (51) 25932-25940; first published December 3, 2019 https://doi.org/10.1073/pnas.1916138116
29. Pagan-Diaz, G.J., Drnevich, J., Ramos-Cruz, K.P.; Richard Sam, Parijat Sengupta & Rashid Bashir.   Modulating electrophysiology 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
30. Polonschii, Cristina, Mihaela Gheorghiu, Sorin David, Szilveszter Gáspár, Sorin Melinte, Hassaan Majeed, Mikhail E. Kandel, Gabriel Popescu & Eugen Gheorghiu. High-resolution impedance mapping using electrically activated quantitative phase imaging. Light Sci Appl 10, 20 (2021). https://doi.org/10.1038/s41377-020-00461-x
31. 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
32. 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
33. 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
34. 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.
35. Son, K-N, Lee, H., Shah, D., Kalmodia, S., Miller, R.C., Ali, M., Balasubramaniam, A., Cologna, S.M., Kong, H.J., Shukla, D., Aakalu, V.K. Histatin-1 is an endogenous ligand of the sigma-2 receptor. FEBS journal 288, 23, 6815-6827. 2021. https://doi.org/10.1111/febs.16108
36. Sullivan, Kathryn, Chang Gyun Park, John D. Ito, Mikhail Kandel, Gabriel Popescu, Young Jun Kim, and Hyunjoon Kong. Matrix softness-mediated 3D zebrafish hepatocyte modulates response to endocrine disrupting chemicals. Environmental Science & Technology 2020 54 (21), 13797-13806. DOI: 10.1021/acs.est.0c01988
37. Sullivan, K.M., Ko, E., Kim, E.M., Balance, W.C., Ito, J.D., Chalifoux, M., Kim Y.J., Bashir, R., Kong, H.J. Extracellular microenvironmental control for organoid assembly. Tissue Engineering B. Rev. June 21, 2022. doi: 10.1089/ten.TEB.2021.0186.
38. Walters, J.M., Kim, E.C., Zhang, J., Jeong, H.G., Bajaj, A., Baculis, B., Tracy, G., Ibrahim, B., Christian-Hinman, C.A., Llano, D.A., Huesmann, G.R., Chung, H.J. (2022) Pharmacological inhibition of STriatal-Enriched protein tyrosine Phosphatase by TC-2153 reduces hippocampal excitability and seizure propensity. Epilepsia, 2022 Feb 21. doi: 10.1111/epi.17192
39. 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
40. 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
41. Yin, C., X. Xiao, V. Balaban, Kandel, Y. Lee, G. Popescu, and P. Bogdan, Network science characteristics of brain-derived neuronal cultures deciphered from quantitative phase imaging data, Scientific Reports, Sept. 15, 2020. https://doi.org/10.1038/s41598-020-72013-7