headshot of Yu Chih Chen

Yu Chih Chen

Assistant Professor
YUC151@pitt.edu
Lab Website Google Scholar Bioengineering Department

overview

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.

about

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., Paoli, 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., Ando, 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 Science and Business Media LLC. 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., Paoli, 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., Ando, S., & Kleer, C.G. (2022). EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression. ISCIENCE, 25(8), 104827.Elsevier BV. 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. Analytical Chemistry, 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 Research, 22(1).Springer Science and Business Media LLC. 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 Reports, 32(8), 108077.Elsevier BV. 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 Reports, 27(13), 3916-3926.e5.Elsevier BV. 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. Integrative Biology, 11(9), 353-361.Oxford University Press (OUP). doi: 10.1093/intbio/zyz029.

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. Molecular Cancer Research, 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. Analytical Chemistry, 91(21), 14093-14100.American Chemical Society (ACS). doi: 10.1021/acs.analchem.9b03896.

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).The Company of Biologists. doi: 10.1242/dev.164038.

Zhang, Z., Chen, Y., 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).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 BV. 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, LLC. doi: 10.18632/oncotarget.22225.

Bai, S., Ingram, P., Chen, Y.C., Deng, N., Pearson, A., Niknafs, Y., 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 RESEARCH, 76(21), 6396-6409.American Association for Cancer Research (AACR). doi: 10.1158/0008-5472.CAN-16-0225.

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. MOLECULAR CANCER THERAPEUTICS, 14(7), 1717-1727.American Association for Cancer Research (AACR). doi: 10.1158/1535-7163.MCT-14-0607.

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.

Yoon, H.K., Lou, X., Chen, Y.C., Koo Lee, Y.E., Yoon, E., & Kopelman, R. (2014). Nanophotosensitizers Engineered to Generate a Tunable Mix of Reactive Oxygen Species, for Optimizing Photodynamic Therapy, Using a Microfluidic Device. Chemistry of Materials, 26(4), 1592-1600.American Chemical Society (ACS). doi: 10.1021/cm403505s.

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. Macrophages Enhance Migration in Inflammatory Breast Cancer Cells via RhoC GTPase Signaling. Scientific Reports, 6(1).Springer Science and Business Media LLC. doi: 10.1038/srep39190.

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. p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis. Nature Communications, 9(1).Springer Science and Business Media LLC. doi: 10.1038/s41467-018-05078-8.

Baac, H.W., Ok, J.G., Maxwell, A., Lee, K.T., Chen, Y.C., Hart, A.J., Xu, Z., Yoon, E., & Guo, L.J. Carbon-Nanotube Optoacoustic Lens for Focused Ultrasound Generation and High-Precision Targeted Therapy. Scientific Reports, 2(1).Springer Science and Business Media LLC. doi: 10.1038/srep00989.

Chen, Y.C., Allen, S.G., Ingram, P.N., Buckanovich, R., Merajver, S.D., & Yoon, E. Single-cell Migration Chip for Chemotaxis-based Microfluidic Selection of Heterogeneous Cell Populations. Scientific Reports, 5(1).Springer Science and Business Media LLC. doi: 10.1038/srep09980.

Chen, Y.C., Cheng, Y.H., Ingram, P., & Yoon, E. Single Cell Proteolytic Assays to Investigate Cancer Clonal Heterogeneity and Cell Dynamics Using an Efficient Cell Loading Scheme. Scientific Reports, 6(1).Springer Science and Business Media LLC. doi: 10.1038/srep27154.

Chen, Y.C., Cheng, Y.H., Kim, H.S., Ingram, P.N., Nor, J.E., & Yoon, E. 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., 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. Functional Isolation of Tumor-Initiating Cells using Microfluidic-Based Migration Identifies Phosphatidylserine Decarboxylase as a Key Regulator. Scientific Reports, 8(1).Springer Science and Business Media LLC. doi: 10.1038/s41598-017-18610-5.

Chen, Y.C., Ingram, P., & Yoon, E. Electrolytic valving isolation of cell co-culture microenvironment with controlled cell pairing ratios. The Analyst, 139(24), 6371-6378.Royal Society of Chemistry (RSC). doi: 10.1039/c4an01282h.

Chen, Y.C., Ingram, P.N., Fouladdel, S., McDermott, S.P., Azizi, E., Wicha, M.S., & Yoon, E. High-Throughput Single-Cell Derived Sphere Formation for Cancer Stem-Like Cell Identification and Analysis. Scientific Reports, 6(1).Springer Science and Business Media LLC. doi: 10.1038/srep27301.

Chen, Y.C., Lou, X., Zhang, Z., Ingram, P., & Yoon, E. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures. Scientific Reports, 5(1).Springer Science and Business Media LLC. doi: 10.1038/srep12175.

Chen, Y.C., Zhang, Z., Fouladdel, S., Deol, Y., Ingram, P.N., McDermott, S.P., Azizi, E., Wicha, M.S., & Yoon, E. Single cell dual adherent-suspension co-culture micro-environment for studying tumor–stromal interactions with functionally selected cancer stem-like cells. Lab on a Chip, 16(15), 2935-2945.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00062b.

Cheng, Y.H., Chen, Y.C., Brien, R., & Yoon, E. Scaling and automation of a high-throughput single-cell-derived tumor sphere assay chip. Lab on a Chip, 16(19), 3708-3717.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00778c.

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. Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells. Nature Communications, 10(1).Springer Science and Business Media LLC. doi: 10.1038/s41467-019-10122-2.

Zhang, Z., Chen, L., Humphries, B., Brien, R., Wicha, M.S., Luker, K.E., Luker, G.D., Chen, Y.C., & Yoon, E. Morphology-based prediction of cancer cell migration using an artificial neural network and a random decision forest. Integrative Biology, 10(12), 758-767.Oxford University Press (OUP). doi: 10.1039/c8ib00106e.

Zhang, Z., Chen, Y.C., Cheng, Y.H., Luan, Y., & Yoon, E. Microfluidics 3D gel-island chip for single cell isolation and lineage-dependent drug responses study. Lab on a Chip, 16(13), 2504-2512.Royal Society of Chemistry (RSC). doi: 10.1039/c6lc00081a.