Yu-Chih Chen, Ph.D.

  • Assistant Professor
  • Department of Computational and Systems Biology
  • Department of Bioengineering

Education & Training

  • Bachelor of Science in Engineering, Department of Electrical Engineering, National Taiwan University, 2008
  • Bachelor of Laws, Department of Law, Legal Science Division, National Taiwan University, 2008
  • Master of Science in Engineering, Department of Electrical Engineering and Computer Science, The University of Michigan, Ann Arbor, 2012
  • Ph.D., Department of Electrical Engineering and Computer Science, The University of Michigan, Ann Arbor, 2014

Research Interest Summary

Single-Cell Analysis and Deep Learning for Cancer Precision Medicine

Research Categories

Research Interests

Due to genomic and epigenetic instability of cancer cells, inter-patient and intra-patient heterogeneity in tumors creates formidable challenges in identifying optimal treatments. To address the challenges, I aim to establish comprehensive high-throughput multi-omics single-cell analysis including genome, epigenome, transcriptome, proteome, functional, and morphological methods. With large amounts of data collected from high-throughput single-cell multi-omics analysis, machine learning techniques can predict patient prognosis and suggest treatments for precision medicine. The integrated approach will change how we understand and treat cancer and ultimately improve outcomes for patients.

Representative Publications

Yu-Chih Chen, Zhixiong Zhang, and Euisik Yoon, “Early Prediction of Single-cell Derived Sphere Formation Using Convolutional Neural Network Image Analysis,” Analytical Chemistry, 92, 11, 7717–7724, 2020.

Yu-Chih Chen, Saswat Sahoo, Riley Brien, Seungwon Jung, Brock Humphries, Woncheol Lee, Yu-Heng Cheng, Zhixiong Zhang, Kathryn E. Luker, Max S. Wicha, Gary D. Luker, and Euisik Yoon, “Single-cell RNA-sequencing of migratory breast cancer cells: discovering drivers of cancer metastasis,” Analyst, 144, 7296 – 7309, 2019.

Zhixiong Zhang, Lili Chen, Yimin Wang, Tiantian Zhang, Yu-Chih Chen*, and Euisik Yoon*, "Label-free Estimation of Therapeutic Efficacy on 3D Cancer Spheres Using Convolutional Neural Network Image Analysis," Analytical Chemistry, 91, 21, 14093-14100, 2019.

Yu-Chih Chen*, Maria E. Gonzalez*, Boris Burman, Xintao Zhao, Talha Anwar, Mai Tran, Natasha Medhora, Ayse B. Hiziroglu, Woncheol Lee, Yu-Heng Cheng, Yehyun Choi, Euisik Yoon, and Celina G. Kleer, “Mesenchymal stem/stromal cell engulfment reveals metastatic advantage in breast cancer,” Cell Reports, 27, 3916–3926, 2019.

Yu-Heng Cheng*, Yu-Chih Chen*, Eric Lin*, Riley Brien, Yu-Ting Chen, Zhijian Hao, Woncheol Lee, Hyun Min Kang, Jason Cong, Monika Burness, Sunitha Nagrath, Max Wicha, and Euisik Yoon, “Hydro-Seq Enables Contamination-free High-throughput Single-cell RNA-sequencing for Circulating Tumor Cells,” Nature Communications, 10, 2163, 2019 (equally contributed first author).

Zhixiong Zhang, Yu-Chih Chen, Sumithra Urs, Diane Simeone, and Euisik Yoon, “Scalable Multiplexed Drug-Combination Screening Platforms Using 3D Microtumor Model for Precision Medicine,” Small, 14, 42, 2018.

Yu-Chih Chen, Brock Humphries, Riley Brien, Anne E. Gibbons, Yu-Ting Chen, Tonela Qyli, Henry R. Haley, Matthew E. Pirone, Benjamin Chiang, Annie Xiao, Yu-Heng Cheng, Yi Luan, Zhixiong Zhang, Jason Cong, Kathryn E. Luker, Gary D. Luker, and Euisik Yoon, “Functional Isolation of Tumor-Initiating Cells through Microfluidic-Based Cell Migration,” Scientific Reports, 8, 244, 2018.

Yu-Chih Chen*, Hyoung Won Baac*, Kyu-Tae Lee, Shamileh Fouladdel, Kendall Teichert, Jong G. Ok, Yu-Heng Cheng, Patrick N. Ingram, A. John Hart, Ebrahim Azizi, L. Jay Guo, Max S. Wicha, and Euisik Yoon, “Selective photo-mechanical detachment and retrieval of divided sister cells from enclosed microfluidics for downstream analyses,” ACS Nano, 11 (5), 4660–4668, 2017.

Yu-Chih Chen, Patrick N. Ingram, Shamileh Fouladdel, Sean P. McDermott, Azizi Ebrahim, Max S. Wicha, and Euisik Yoon, “High-Throughput Single-Cell Derived Sphere Formation for Cancer Stem-Like Cell Identification and Analysis,” Scientific Reports, 6, 27301, 2016.

Yu-Chih Chen*, Steven G. Allen*, Patrick N. Ingram, Ronald Buckanovich, Sofia D. Merajver, and Euisik Yoon, “Single-Cell Migration Chip for Motility-based Microfluidic Selection of Heterogeneous Cell Populations,” Scientific Reports, 5, 9980, 2015.