38859-Zhang, Jie

Jie Zhang, PhD

Associate Professor of Medical & Molecular Genetics

Adjunct Assistant Professor, School of Informatics & Computing

Associate professor in Center for Computational Biology and Bioinformatics

Email
jizhan@iu.edu
Address
HITS 5015
410 W. 10th, Ave,
Indianapolis, IN 46202
PubMed:
CV:
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Bio

B.S. in Biological Sciences and Biotechnology, Tshinghua University, China 1991-1996
Ph.D. in Biochemistry, University of Illinois, Urbana-Champaign, IL, USA 1997-2002
Postdoc in Bioinformatics, The Ohio State University, Columbus, OH, USA 2009-2014
Assistant Research Professor, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA 2015-2017
Assistant Professor, Department of Medical & Molecular Genetics, Indiana University, School of Medicine, IN, USA 2017-2024

 

Key Publications

  1. X. Huang, A. Jannu, Z. Song, N. Jury-Garfe, C. Lasagna-Reeves, T. Johnson, K. Huang, J. Zhang,“Predicting Alzheimer’s Disease Subtypes and Understanding Their Molecular Characteristics in Living Patients with Transcriptomic Trajectory Profiling”, Alzheimer's & Dementia, 2025 Jan 15;21(1):e14241| doi: 10.1002/alz.14241.

  2. 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

  3. 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

  4.  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.

  5. 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.

  6. 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).

  7. 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

  8. 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)

  9. 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.

  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.

 

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