Chi Zhang

Assistant Professor

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Ph.D. Bioinformatics with a secondary master’s degree in statistics

Advisor: Dr. Ying Xu.

The University of Georgia, Athens, GA (2010.9-2015.11)

Thesis: Identification of the key micro-environmental alterations, genomic alterations and their associations in cancer initiation and progression

B.S. Bachelor of Science in Mathematics and Applied Mathematics

Peking University, Beijing, China (2006.9-2010.7)


2016.8-now Assistant Professor

Center for Computational Biology and Bioinformatics

Department of Medical and Molecular Genetics

Indiana University, School of Medicine

2017.09-now Adjunct Assistant Professor

Department of Electrical and Computer Engineering,

Purdue University


I joined the Department of Medical and Molecular Genetics, Indiana University School of Medicine in August of 2016 as an Assistant Professor. I currently hold primary appointment in the School of Medicine. Before joining IUSM, from 2008-2016, I was trained as a computational cancer biologist with a Ph.D. in bioinformatics and statistics, and a B.S. degree in mathematics. I view myself as a computational biologist capable of asking and addressing biological questions of cancer through omics data analysis and computational modeling, as well as a bioinformatician capable of developing machine learning algorithms and statistical tools in support of both my own research and for collaborative service. Currently, I mainly focused on (1) independent research in computational modeling of disease microenvironment, cell type specific activity and transcriptional regulation, and computational algorithm development, and (2) collaborative research in identification of biological characteristics related to disease progression and drug resistance.


  1. Computational modeling of cancer microenvironment

  2. Role of cancer microenvironment in cancer progression, and drug resistance.

  3. Cell-cell interaction in a disease microenvironment

  4. Utilizing single cell RNA-seq/FISH data to improve the understanding of a complex tissue

  5. Bi-clustering and local low rank pattern identification in high dimensional data

  6. Knowledge graph and tensor decomposition

  7. Computational model of drug resistance mechanisms



B670 (Spring 2019) Topics in public health: Statistical Learning & High Dimensional Data Analysis. Co-instructor.

G788 (Fall 2018, 2017) Next Generation Sequencing. Co-instructor.

G899 (Spring 2019, 2018) Bioinformatics, Genomics, Proteomics, and Systems Biology. Lecturer

Mentoring Experience

Till to Spring 2019

  1. Wennan Chang is a second year Ph.D. student in Electric Computer Engineering at Purdue University. Wennan joined BMDR in the fall of 2017. His primary research topic is developing a next generation deconvolution method for cell type inference, proportion and activity estimation, by using cancer bulk tissue transcriptomics data.

  2. Changlin Wan is a second year Ph.D. student in Electric Computer Engineering at Purdue University. Changlin joined BMDR in the fall of 2017. His primary research topic is developing new formulations of non-linear local low rank structure corresponding to gene co-regulation patterns in single cell RNA-seq data.

  3. Xiaoyu Lu is a second year Ph.D. student in Bioinformatics at IUPUI. Xiaoyu joined BMDR in the spring of 2018. I am co-advising Xiaoyu with Dr. Sha Cao from Biostatistics department. Xiaoyu is majorly mentored by Dr. Sha Cao. His research focus is to develop a semi-supervised deconvolution method to infer immune/hematopoietic cell proportions in the micro-environment of mouse bone marrow.

  4. Norah Alghamdi is a Ph.D. student in Bioinformatics at IUPUI. Norah is currently supported by a visiting scholar program of Saudi Arabia. Norah jointed BMDR in the November of 2018. Her first project is to study metabolic flux changes and oxidative stress in cancer.

  5. Yan Huo is a first year visiting Ph.D. student. She is funded by her college – China Medical University, one of the top ten medical schools in China. Yan jointed my lab in Oct 2018 for a one year study. Her current research project is to develop a computational method to predict most similar cancer cell line for a cancer bulk tissue sample by using RNA-seq data and genetic mutation data.

  6. Xinyu Zhou is a visiting student from Department of Computer Science, Jilin University. Xinyu is officially a visiting Ph.D. student of my Ph.D. advisor—Dr. Ying Xu from the University of Georgia. Now Xinyu works in BMDR to develop method for tensor decomposition and knowledge graph embedding.

  7. Dr. Yu Zhang is a visiting associated professor from Department of Computer Science, Jilin University. I collaborated with Dr. Zhang from 2015. Currently we have six co-authored manuscripts published or submitted. Dr. Zhang is primarily working on bioinformatics methods, computational tools, and algorithm and database development.

  8. Dr. Yan Han is a master student in Biostatistics, IUSM. Her primary research topic is the modeling of the clinical trial data of Mek Inhibitor and Cabozantinib generated in the DHART SPORE.

  9. Szuwei Du is a master student in Bioinformatics, IUPUI. He is working on development of an un-supervised method for mouse tissue data deconvolution.

  10. Siyuan Qi got his master’s degree from Dept of Electric Computer Engineering, IUPUI. He is primarily working on data processing and management to support the research in my lab.

  11. Pengcheng Wang is a master student in Computer Science, IUPUI. He is working with Dr. Yu Zhang on several tool/database development projects.

In addition, I am serving in the research/thesis committee of five Ph.D. students. My educational outreach activities include: (a) co-mentored a high school student Joshua Johnson with Dr. Yunlong Liu in the SEED program, in the summer of 2017; (b) mentored a first year college student Jordan Lyles Holly in the IU Simon Cancer Center Summer Research Program, in the summer of 2018; © mentored a fourth year undergraduate student Brooke Richardson for a summer internship, in the summer of 2018; (d) mentored high school students, Edward Dong and Jinhee Won, including introduction of programming and bioinformatics topics, from 2017 to now. Detailed graduate level mentoring experience are listed below.



czhang87 AT iu DOT edu



410 W 10 th St,

Suit 5000,

Indianapolis, IN, 46202

Campus address: HS5021