38859-Zhang, Jie

Jie Zhang, PhD

Assistant Professor of Medical & Molecular Genetics

HITS 5015
410 W. 10th, Ave,

Indianapolis, IN 46202
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B.S. in Biological Sciences and Biotechnology,  Tshinghua University, China

Ph.D. in Biochemistry, University of Illinois, Urbana-Champaign, IL

Postdoc in Bioinformatics, The Ohio State University, Columbus, OH

Key Publications

1. J. Cheng, Z. Han, R. Mehra, W. Shao, M. Cheng, Q. Feng, D. Ni, K. Huang, L. Cheng, and J. Zhang, “Computational analysis of pathological images enables a better diagnosis of translocation renal cell carcinoma”, Nature Communications, (2020) 11:1778, doi: 10.1038/s41467-020-15671-5.

2.  L. Sun*, J. Zhang*, W. Chen*, Y. Chen, X. Zhang, M. Yang, M. Xiao, F. Ma, Y. Yao, M.Ye, Z. Zhang, K. Chen, F. Chen, Y. Ren, S. Ni, Xi Zhang, Z. Yan, Z. Sun, H. Zhou, H. Yang, S. Xie, M E. Haque, K. Huang, Y. Yang, “Attenuation of SMARCA4 and ERK-ETS signaling suppress dopaminergic degeneration in Drosophila Parkinson’s disease models”, Aging Cell, (2020) doi:10.1111/acel.13210 (*co-first author). 

3. Z, Huang, T. Johnson, Z. Han, B.R. Helm, S. Cao, C. Zhang, P. Salama, M. Rizkalla, C. Y. Yu, J. Cheng, S. Xiang, X. Zhan, J. Zhang, K. Huang, “Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations”, BMC Medical Genomics, 13, 41 (2020), doi:10.1186/s12920-020-0686-1.

4.  T. Wang, T. S. Johnson, W. Shao, Z. Lu, B. R. Helm, J. Zhang*, and K. Huang*, “BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes”, Genome Biology, (2019) 20:165. (*co-corresponding authors).

5. T. S. Johnson, T. Wang, Z. Huang, C. Y. Yu, Y. Wu, Y. Han, Y. Zhang, K. Huang, and J. Zhang, “LAmbDA: Label Ambiguous Domain Adaptation Dataset Integration Reduces Batch Effects and Improves Subtype Detection”, Bioinformatics, Apr. 30, 2019, doi: 10.1093/bioinformatics/btz295

6. S. Xiang, Z. Huang, H. Wang, Z. Han, C. Y. Yu, D. Ni, K. Huang, and J. Zhang, “Condition-specific Gene Co-expression Network Mining Identified Key Pathways and Regulators in Alzheimer’s Disease”, BMC Medical Genomics, 2018 Dec 31;11(Suppl 6):115. doi: 10.1186/s12920-018-0431-1.

7.  J. Chen*, J. Zhang*, Y. Han, X. Wang, X. Ye, Y. Meng, A. Pawani, Z. Han, Q. Feng, and K. Huang, “Integrative analysis of histopathological images and genomic data for predicting clear cell renal cell carcinoma prognosis”, Cancer Research, 2017 Nov; 77(21): e91-e100. (*co-first authors)

8. J. Zhang, and K. Huang, “Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers”, BMC Genomics, 2017 Jan 25;18(Suppl 1):1045. doi: 10.1186/s12864-016-3259-0.

9. J. Zhang, Z. Abrams, J. D. Parvin, and K. Huang. “Integrative analysis of somatic mutations and transcriptomic data to functionally stratify breast cancer patients”. BMC Genomics. 2016 Aug 22;17 Suppl 7: 513.

10.   J. Zhang, and K. Huang, “Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers”. Cancer Inform. 2016 Jul 24;13(Suppl 3):137-46.

12.  S. Shroff*, J. Zhang*, and K. Huang, “Gene Co-Expression Analysis Predicts Genetic Variants Associated with Drug Responsiveness in Lung Cancer”, AMIA Joint Summits Transl Sci Proc. 2016 Jul 20; 2016: 32-41. (*equal contributions, Winner of the Marco Ramoni Distinguished Paper award)

12.   T. Bailey, P. Krajewski, I. Ladunga, C. Lefebvre, Q. Li, T. Liu, P. Madrigal, C. Taslim, and J. Zhang, Practical Guidelines for the Comprehensive Analysis of ChIP-seq data”, PloS Comp. Biol. Nov 14, 2013, 9(11): e1003326, DOI: 10.1371/journal.pcbi.1003326

13. Y. Xiang, J. Zhang, and K. Huang, "Mining tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction", BMC Genomics, 14(S5): S4, 2013.

14. J. Zhang, K. Lu, Y. Xiang, M. Islam, S. Kotian, Z. Kais, C. Lee, M. Arora, H. Liu, J. D. Parvin, and K. Huang, “Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability”, PLoS Comput. Biol. 8(8): e1002656. doi:10.1371 /journal.pcbi.1002656, 2012.

15. J. Zhang, J. D. Parvin, and K. Huang, “Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development”, BMC Genomics, 13 (suppl.8): S5, 2012.

Titles & Appointments

  • Assistant Professor of Medical & Molecular Genetics
  • Adjunct Assistant Professor, School of Informatics & Computing
  • Assistant Professor in Center for Computational Biology and Bioinformatics
  • Education
    2002 PhD University of Illinois
    1996 BS Tsinghua University
  • Research

    Our lab is focused on developing and applying translational bioinformatics and system biology methods to identify disease genes, pathways, and biomarkers with applications in cancers, neurological diseases, and other types of diseases.

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