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Yuji  Zhang
 

Yuji Zhang Ph.D.

Academic Title: Assistant Professor
Primary Appointment: Epidemiology & Public Health
yuzhang@som.umaryland.edu
Location: Howard Hall, 109C
Phone: 410-706-8523
Fax: 410-706-8548
 

Personal History:

Dr. Yuji Zhang is an assistant professor in the Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Cancer Center, and the Department of Epidemiology and Public Health, University of Maryland School of Medicine since 2014. Her research focuses on developing translational bioinformatics and biostatistical approaches to understand the physiological states of the cell and the organism, including disease states. She has more than 10 years of bioinformatics, biostatistics, and systems biology research experience on integrative analysis of multi-source biological data to extract and analyze novel associations among different biological entities. During her appointment at Mayo Clinic College of Medicine between 2010-2014, Dr. Zhang has participated in numerous federal and government-funded projects, in which she serves as co-principle investigator/co-investigator leading the bioinformatics and statistical analyses. These projects includes Mayo Comprehensive Cancer Center grant, International Consortium grant for Prostate Cancer Genetics (ICPCG), Consortium of extracellular RNA biomarker discovery (exRNA), and Functional Significance Study of Prostate Cancer risk-SNPs. After she joined the faculty at the University of Maryland School of Medicine in July 2014, Dr. Zhang serves as a bioinformatics faculty in the University of Maryland Greenebaum Cancer Center and lead bioinformatics effort in the Biostatistics Shared Service at the School of Medicine. Her mission is to leverage the gap between the analytical needs of multi-source big data in the biological field and advanced computational approaches.

Research Interests:

Dr. Zhang's main research interests include network systems biology; systems pharmacology; personalized medicine; integrative analysis of multi-source biological data; next-generation sequencing data analysis; and long non-coding RNA analysis.


Publications:

  1. Zhang Y, Tao C, Jiang G, Nair A, Su J, Chute CG, Liu H. (2014) Network-based Analysis Reveals Distinct Association Patterns in a Semantic MEDLINE-based Drug-Disease-Gene Network. Journal of Biomedical Semantics. (in press)
  2. Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Isaksson Vogel R, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bently D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, Kingsbury Z, Peden J, Chien J, Swisher EM, Hartmann LC, Kalli KR, Goode EL, Sicotte H, Kaufmann SH, Harris RS. (2013) APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Res, 73(24):7222-31.
  3. Craig TA*, Zhang Y*, Magisc AT, Funk CC, Price ND, Ekker SC, Kumar R. (2013) Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing. Zebrafish, ahead of print. doi:10.1089/zeb.2013.0899. (* co-first authors)
  4. Zhang Y, Li D, Tao C, Shen F, Liu H. (2013) An integrative computational approach to identify disease-specific networks from PubMed literature information. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2013, 72-75.
  5. Zhang Y, Tao C, He Y, Kanjamala1 P, Liu H. (2013) Network-based Analysis of Vaccine-related Associations Reveals Consistent Knowledge with the Vaccine Ontology. Journal of Biomedical Semantics, 4:33.
  6. Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP. (2013) Calculating Sample Size Estimates for RNA Sequencing Data. J Comput Biol, 20(12): 970-978.
  7. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. (2013) Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One, 8(8):e71745.
  8. Zhang Y, Tao C, He Y, Kanjamala1 P, Liu H. (2013) Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. The Workshop of Vaccine and Drug Ontology Studies (VDOS 2013), in conjunction with the International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada.
  9. Pugazhenthi S, Zhang Y, Bouchard R, Mahaffey G. (2013) Induction of an inflammatory loop by interleukin-1 beta and tumor necrosis factor-alpha involves NF- kappa B and STAT-1 in differentiated human neuroprogenitor cells. PLoS ONE, 8(7):e69585. (Sole computational biologist)
  10. Zhang Y, Xuan J, Clarke R, Ressom HW. (2013) Module-based breast cancer classification. Int J Data Min Bioinform, 7(3):284-302.
  11. Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND, Ekker SC, Kumar R. (2012) Research resource: whole transcriptome RNA sequencing detects multiple 1alpha,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. Mol Endocrinol, 26(9):1630-42.
  12. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. (2012) SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics, 28(16):2180-1.
  13. Wang J, Zhang Y, Marian C, Ressom HW. (2012) Identification of aberrant pathways and network activities from high-throughput data. Brief Bioinform, 13(4):406-19.
  14. Tao C, Zhang Y, Jiang G, Bouamrane MM, Chute CG. (2012) Optimizing semantic MEDLINE for translational science studies using semantic web technologies. MIXHS '12 Proceedings of the 2nd international workshop on Managing interoperability and compleXity in health systems, 53-8. (Sole computational biologist)
  15. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. (2012) TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics, 28(2): 277-8.
  16. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. (2010) Module-based biomarker discovery for breast cancer. Proceedings of 2010 IEEE International Conference on Bioinformatics & Biomedicine, 352-356.
  17. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. (2010) Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One, 5(4):e10268.
  18. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. (2009) Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics, 10 Suppl 1:S15.
  19. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. (2008) Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics, 9:203. (Highly accessed)
  20. Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom HW. (2008) Network motif-based identification of breast cancer susceptibility genes. The 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2008), 5696-9.
  21. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. (2008) Reverse engineering module networks by PSO-RNN hybrid modeling. Proceedings of the 2008 international conference on bioinformatics & computational biology, 401-7.
  22. Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. (2007) Integrating Multi-Source Biological Data for Transcriptional Regulatory Module Discovery. Proceedings of IEEE/NIH Life Science Systems and Applications Workshop 2007 (LISA 2007), 184-7. (Main contributor)
  23. Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R. (2006) Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB '06), 1-8. (Main contributor)
  24. Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. (2006) Inferring network interactions using recurrent neural networks and swarm intelligence. The 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2006), 4241-4. (Main contributor)
  25. Zhang Y, Zhu J, Sun X, Lu Z. (2002) A method of oligonucleotide synthesis optimization. Biotechnology, 12:26-8.