Yu Chih Chen

Yu-Chih Chen received his dual bachelor degrees in Electrical Engineering and Law from the National Taiwan University, Taipei in 2008, his Ph.D. degree in Electrical & Computer Engineering at the University of Michigan, Ann Arbor in 2014, where he continued to work as a research faculty in both Electrical & Computer Engineering Department and Forbes Institute for Cancer Discovery. He is currently an assistant professor in the Department of Computational and Systems Biology and UPMC Hillman Cancer Center at the ​University of Pittsburgh School of Medicine. He is also affiliated with Joint CMU-Pitt Ph.D. Program in Computational Biology. He is the recipient of Taiwan Semiconductor Manufacturing Company (TSMC) Outstanding Student Research Award (2008), Orenstein Ph.D. Fellowship (2009), Best Post-Doctoral Speaker Award in Microfluidics in Biomedical Sciences Training Program, UMich (2015), and Emerging Forbes Scholar selected by Forbes Institute for Cancer Discovery (2017). His current research focuses on high-throughput single-cell analysis, next generation sequencing (NGS), and machine learning for cancer precision medicine.

  • Bachelor, Electrical Engineering, National Taiwan University, 2003 - 2008
  • Bachelor, Law, National Taiwan University, 2003 - 2008
  • Master, Electrical Engineering and Computer Science, University of Michigan–Ann Arbor, 2009 - 2012
  • PhD, Electrical Engineering and Computer Science, University of Michigan–Ann Arbor, 2009 - 2014

  • Augimeri, G., Gonzalez, M.E., Paolì, A., Eido, A., Choi, Y., Burman, B., Djomehri, S., Karthikeyan, S.K., Varambally, S., Buschhaus, J.M., Chen, Y.C., Mauro, L., Bonofiglio, D., Nesvizhskii, A.I., Luker, G.D., Andò, S., Yoon, E., & Kleer, C.G. (2023). A hybrid breast cancer/mesenchymal stem cell population enhances chemoresistance and metastasis. JCI Insight, 8(18).American Society for Clinical Investigation. doi: 10.1172/jci.insight.164216.
  • Sarma, P., Carino, C.M.C., Seetharama, D., Pandey, S., Dwivedi-Agnihotri, H., Rui, X., Cao, Y., Kawakami, K., Kumari, P., Chen, Y.C., Luker, K.E., Yadav, P.N., Luker, G.D., Laporte, S.A., Chen, X., Inoue, A., & Shukla, A.K. (2023). Molecular insights into intrinsic transducer-coupling bias in the CXCR4-CXCR7 system. Nat Commun, 14(1), 4808.Springer Nature. doi: 10.1038/s41467-023-40482-9.
  • Zhou, M., Ma, Y., Chiang, C.C., Rock, E.C., Luker, K.E., Luker, G.D., & Chen, Y.C. (2023). High-Throughput Cellular Heterogeneity Analysis in Cell Migration at the Single-Cell Level. Small, 19(6), e2206754.Wiley. doi: 10.1002/smll.202206754.
  • Gonzalez, M.E., Naimo, G.D., Anwar, T., Paolì, A., Tekula, S.R., Kim, S., Medhora, N., Leflein, S.A., Itkin, J., Trievel, R., Kidwell, K.M., Chen, Y.C., Mauro, L., Yoon, E., Andò, S., & Kleer, C.G. (2022). EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression. iScience, 25(8), 104827.Elsevier. doi: 10.1016/j.isci.2022.104827.
  • Hartnett, E.B., Zhou, M., Gong, Y.N., & Chen, Y.C. (2022). LANCE: a Label-Free Live Apoptotic and Necrotic Cell Explorer Using Convolutional Neural Network Image Analysis. Anal Chem, 94(43), 14827-14834.American Chemical Society (ACS). doi: 10.1021/acs.analchem.2c00878.
  • Chen, Y.C., Zhang, Z., & Yoon, E. (2020). Early Prediction of Single-Cell Derived Sphere Formation Rate Using Convolutional Neural Network Image Analysis. Anal Chem, 92(11), 7717-7724.American Chemical Society (ACS). doi: 10.1021/acs.analchem.0c00710.
  • Humphries, B.A., Cutter, A.C., Buschhaus, J.M., Chen, Y.C., Qyli, T., Palagama, D.S.W., Eckley, S., Robison, T.H., Bevoor, A., Chiang, B., Haley, H.R., Sahoo, S., Spinosa, P.C., Neale, D.B., Boppisetti, J., Sahoo, D., Ghosh, P., Lahann, J., Ross, B.D., Yoon, E., Luker, K.E., & Luker, G.D. (2020). Enhanced mitochondrial fission suppresses signaling and metastasis in triple-negative breast cancer. Breast Cancer Res, 22(1), 60.Springer Nature. doi: 10.1186/s13058-020-01301-x.
  • Park, S.R., Namkoong, S., Friesen, L., Cho, C.S., Zhang, Z.Z., Chen, Y.C., Yoon, E., Kim, C.H., Kwak, H., Kang, H.M., & Lee, J.H. (2020). Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage. Cell Rep, 32(8), 108077.Elsevier. doi: 10.1016/j.celrep.2020.108077.
  • Chen, Y.C., Gonzalez, M.E., Burman, B., Zhao, X., Anwar, T., Tran, M., Medhora, N., Hiziroglu, A.B., Lee, W., Cheng, Y.H., Choi, Y., Yoon, E., & Kleer, C.G. (2019). Mesenchymal Stem/Stromal Cell Engulfment Reveals Metastatic Advantage in Breast Cancer. Cell Rep, 27(13), 3916-3926.e5.Elsevier. doi: 10.1016/j.celrep.2019.05.084.
  • Chen, Y.C., Jung, S., Zhang, Z., Wicha, M.S., & Yoon, E. (2019). Co-culture of functionally enriched cancer stem-like cells and cancer-associated fibroblasts for single-cell whole transcriptome analysis. Integr Biol (Camb), 11(9), 353-361.Oxford University Press (OUP). doi: 10.1093/intbio/zyz029.
  • Cheng, Y.H., Chen, Y.C., Lin, E., Brien, R., Jung, S., Chen, Y.T., Lee, W., Hao, Z., Sahoo, S., Min Kang, H., Cong, J., Burness, M., Nagrath, S., S Wicha, M., & Yoon, E. (2019). Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells. Nat Commun, 10(1), 2163.Springer Nature. doi: 10.1038/s41467-019-10122-2.
  • Humphries, B.A., Buschhaus, J.M., Chen, Y.C., Haley, H.R., Qyli, T., Chiang, B., Shen, N., Rajendran, S., Cutter, A., Cheng, Y.H., Chen, Y.T., Cong, J., Spinosa, P.C., Yoon, E., Luker, K.E., & Luker, G.D. (2019). Plasminogen Activator Inhibitor 1 (PAI1) Promotes Actin Cytoskeleton Reorganization and Glycolytic Metabolism in Triple-Negative Breast Cancer. Mol Cancer Res, 17(5), 1142-1154.American Association for Cancer Research (AACR). doi: 10.1158/1541-7786.MCR-18-0836.
  • Zhang, Z., Chen, L., Wang, Y., Zhang, T., Chen, Y.C., & Yoon, E. (2019). Label-Free Estimation of Therapeutic Efficacy on 3D Cancer Spheres Using Convolutional Neural Network Image Analysis. Anal Chem, 91(21), 14093-14100.American Chemical Society (ACS). doi: 10.1021/acs.analchem.9b03896.
  • Anwar, T., Arellano-Garcia, C., Ropa, J., Chen, Y.C., Kim, H.S., Yoon, E., Grigsby, S., Basrur, V., Nesvizhskii, A.I., Muntean, A., Gonzalez, M.E., Kidwell, K.M., Nikolovska-Coleska, Z., & Kleer, C.G. (2018). p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis. Nat Commun, 9(1), 2801.Springer Nature. doi: 10.1038/s41467-018-05078-8.
  • Chen, Y.C., Humphries, B., Brien, R., Gibbons, A.E., Chen, Y.T., Qyli, T., Haley, H.R., Pirone, M.E., Chiang, B., Xiao, A., Cheng, Y.H., Luan, Y., Zhang, Z., Cong, J., Luker, K.E., Luker, G.D., & Yoon, E. (2018). Functional Isolation of Tumor-Initiating Cells using Microfluidic-Based Migration Identifies Phosphatidylserine Decarboxylase as a Key Regulator. Sci Rep, 8(1), 244.Springer Nature. doi: 10.1038/s41598-017-18610-5.
  • Menon, R., Otto, E.A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y.C., Troyanskaya, O., Spence, J.R., Kretzler, M., & Cebrián, C. (2018). Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development, 145(16), dev164038.The Company of Biologists. doi: 10.1242/dev.164038.
  • Zhang, Z., Chen, L., Humphries, B., Brien, R., Wicha, M.S., Luker, K.E., Luker, G.D., Chen, Y.C., & Yoon, E. (2018). Morphology-based prediction of cancer cell migration using an artificial neural network and a random decision forest. Integr Biol (Camb), 10(12), 758-767.Oxford University Press (OUP). doi: 10.1039/c8ib00106e.
  • Zhang, Z., Chen, Y.C., Urs, S., Chen, L., Simeone, D.M., & Yoon, E. (2018). Scalable Multiplexed Drug-Combination Screening Platforms Using 3D Microtumor Model for Precision Medicine. Small, 14(42), e1703617.Wiley. doi: 10.1002/smll.201703617.
  • Chen, Y.C., Baac, H.W., Lee, K.T., Fouladdel, S., Teichert, K., Ok, J.G., Cheng, Y.H., Ingram, P.N., Hart, A.J., Azizi, E., Guo, L.J., Wicha, M.S., & Yoon, E. (2017). Selective Photomechanical Detachment and Retrieval of Divided Sister Cells from Enclosed Microfluidics for Downstream Analyses. ACS Nano, 11(5), 4660-4668.American Chemical Society (ACS). doi: 10.1021/acsnano.7b00413.
  • Gonzalez, M.E., Martin, E.E., Anwar, T., Arellano-Garcia, C., Medhora, N., Lama, A., Chen, Y.C., Tanager, K.S., Yoon, E., Kidwell, K.M., Ge, C., Franceschi, R.T., & Kleer, C.G. (2017). Mesenchymal Stem Cell-Induced DDR2 Mediates Stromal-Breast Cancer Interactions and Metastasis Growth. Cell Rep, 18(5), 1215-1228.Elsevier. doi: 10.1016/j.celrep.2016.12.079.
  • Kim, H.S., Chen, Y.C., Nör, F., Warner, K.A., Andrews, A., Wagner, V.P., Zhang, Z., Zhang, Z., Martins, M.D., Pearson, A.T., Yoon, E., & Nör, J.E. (2017). Endothelial-derived interleukin-6 induces cancer stem cell motility by generating a chemotactic gradient towards blood vessels. Oncotarget, 8(59), 100339-100352.Impact Journals. doi: 10.18632/oncotarget.22225.
  • Allen, S.G., Chen, Y.C., Madden, J.M., Fournier, C.L., Altemus, M.A., Hiziroglu, A.B., Cheng, Y.H., Wu, Z.F., Bao, L., Yates, J.A., Yoon, E., & Merajver, S.D. (2016). Macrophages Enhance Migration in Inflammatory Breast Cancer Cells via RhoC GTPase Signaling. Sci Rep, 6(1), 39190.Springer Nature. doi: 10.1038/srep39190.
  • Bai, S., Ingram, P., Chen, Y.C., Deng, N., Pearson, A., Niknafs, Y.S., O'Hayer, P., Wang, Y., Zhang, Z.Y., Boscolo, E., Bischoff, J., Yoon, E., & Buckanovich, R.J. (2016). EGFL6 Regulates the Asymmetric Division, Maintenance, and Metastasis of ALDH+ Ovarian Cancer Cells. Cancer Res, 76(21), 6396-6409.American Association for Cancer Research (AACR). doi: 10.1158/0008-5472.CAN-16-0225.
  • Chen, Y.C., Cheng, Y.H., Ingram, P., & Yoon, E. (2016). Single Cell Proteolytic Assays to Investigate Cancer Clonal Heterogeneity and Cell Dynamics Using an Efficient Cell Loading Scheme. Sci Rep, 6(1), 27154.Springer Nature. doi: 10.1038/srep27154.
  • Chen, Y.C., Ingram, P.N., Fouladdel, S., McDermott, S.P., Azizi, E., Wicha, M.S., & Yoon, E. (2016). High-Throughput Single-Cell Derived Sphere Formation for Cancer Stem-Like Cell Identification and Analysis. Sci Rep, 6(1), 27301.Springer Nature. doi: 10.1038/srep27301.
  • Chen, Y.C., Zhang, Z., Fouladdel, S., Deol, Y., Ingram, P.N., McDermott, S.P., Azizi, E., Wicha, M.S., & Yoon, E. (2016). Single cell dual adherent-suspension co-culture micro-environment for studying tumor-stromal interactions with functionally selected cancer stem-like cells. Lab Chip, 16(15), 2935-2945.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00062b.
  • Cheng, Y.H., Chen, Y.C., Brien, R., & Yoon, E. (2016). Scaling and automation of a high-throughput single-cell-derived tumor sphere assay chip. Lab Chip, 16(19), 3708-3717.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00778c.
  • Zhang, Z., Chen, Y.C., Cheng, Y.H., Luan, Y., & Yoon, E. (2016). Microfluidics 3D gel-island chip for single cell isolation and lineage-dependent drug responses study. Lab Chip, 16(13), 2504-2512.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00081a.
  • Burgos-Ojeda, D., Wu, R., McLean, K., Chen, Y.C., Talpaz, M., Yoon, E., Cho, K.R., & Buckanovich, R.J. (2015). CD24+ Ovarian Cancer Cells Are Enriched for Cancer-Initiating Cells and Dependent on JAK2 Signaling for Growth and Metastasis. Mol Cancer Ther, 14(7), 1717-1727.American Association for Cancer Research (AACR). doi: 10.1158/1535-7163.MCT-14-0607.
  • Chen, Y.C., Allen, S.G., Ingram, P.N., Buckanovich, R., Merajver, S.D., & Yoon, E. (2015). Single-cell Migration Chip for Chemotaxis-based Microfluidic Selection of Heterogeneous Cell Populations. Sci Rep, 5(1), 9980.Springer Nature. doi: 10.1038/srep09980.
  • Chen, Y.C., Kang, T.H., Ingram, P.N., Cheng, Y.H., & Yoon, E. (2015). Osmotically Actuated Micropumps and Control Valves for Point-of-Care Applications. Journal of Microelectromechanical Systems, 24(4), 982-989.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/jmems.2014.2364051.
  • Chen, Y.C., Lou, X., Zhang, Z., Ingram, P., & Yoon, E. (2015). High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures. Sci Rep, 5(1), 12175.Springer Nature. doi: 10.1038/srep12175.
  • Chen, Y.C., Cheng, Y.H., Kim, H.S., Ingram, P.N., Nor, J.E., & Yoon, E. (2014). Paired single cell co-culture microenvironments isolated by two-phase flow with continuous nutrient renewal. Lab Chip, 14(16), 2941-2947.Royal Society of Chemistry (RSC). doi: 10.1039/c4lc00391h.
  • Chen, Y.C., Ingram, P., & Yoon, E. (2014). Electrolytic valving isolation of cell co-culture microenvironment with controlled cell pairing ratios. Analyst, 139(24), 6371-6378.Royal Society of Chemistry (RSC). doi: 10.1039/c4an01282h.
  • Yoon, H.K., Lou, X., Chen, Y.C., Koo Lee, Y.E., Yoon, E., & Kopelman, R. (2014). Nano-photosensitizers Engineered to Generate a Tunable Mix of Reactive Oxygen Species, for Optimizing Photodynamic Therapy, Using a Microfluidic Device. Chem Mater, 26(4), 1592-1600.American Chemical Society (ACS). doi: 10.1021/cm403505s.
  • Baac, H.W., Ok, J.G., Maxwell, A., Lee, K.T., Chen, Y.C., Hart, A.J., Xu, Z., Yoon, E., & Guo, L.J. (2012). Carbon-nanotube optoacoustic lens for focused ultrasound generation and high-precision targeted therapy. Sci Rep, 2(1), 989.Springer Nature. doi: 10.1038/srep00989.
Research Interests
Biochemistry and cell biology Oncology and carcinogenesis Analytical chemistry Medicinal and biomolecular chemistry Genetics Chemical engineering
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Contact Yu Chih Chen
Assistant Professor
YUC151@pitt.edu
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