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
Assistant Research Professor, Department of Biomedical Informatics, The Ohio State University, Columbus, OH

Key Publications

  1. T. S. Johnson, C. Y. Yu, Z. Huang, S. Xu, T. Wang, C. Dong, W. Shao, M. A. Zaid, Y. Wang, C. Bartlett, Y. Zhang, Y. Liu K. Huang, and J. Zhang, “Diagnostic Evidence GAuge of Single cells (DEGAS): A transfer learning framework to infer impressions of cellular and patient phenotypes between patients and single cells”, Genome Medicine, 14:11 (2022) |doi.org/10.1186/s13073-022-01012

2. Wang, W. Shao, Z. Huang, H. Tang, J. Zhang, Z. Ding, K. Huang, “MOGONET Integrates Multi-omics Data Using Graph Convolutional Networks Allowing Patient Classification and Biomarker Identification”, Nature Communications, 12, 3445 (2021) |doi:10.1038/s41467-021-23774.w

3. T. S. Johnson, S. Xiang, T. Dong, M. Cheng, T. Wang, K. Yang, D. Ni, K. Huang, J. Zhang, “Combined Differential Expression and Differential Co-expression Analysis on Gene Networks Reveals Changes in Cell Population Largely Explain Core Microglia Genes’ Up-expression in Alzheimer’s Disease Brains”, Scientific Reports, 2021 Jan. 11;11:353 |doi: 0.1038/s41598-020-79740-x.

4.  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.

5.  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).

6. 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

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, 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.


Titles & Appointments

  • Assistant Professor of Medical & Molecular Genetics
  • Adjunct Assistant Professor of Biostatistics & Health Data Science
  • 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, neurodegenerative diseases such as Alzheimer's Disease, and other types of diseases.

  • Clinical Interests
    Cancer prognosis and diagnosis with computational pathology analysis;
    Bioinformatic analysis to identify disease pathways in cancer, Alzheimer's diseases and other types of diseases.
  • Awards
    Org: NIH
    Desc: R21
    Scope: National
    Date: 2023-09-01
    Org: NIH
    Desc: R01
    Scope: National
    Date: 2022-07-01
    Org: NIH
    Desc: R21
    Scope: National
    Date: 2022-07-01

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