Publications

  1. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Sep 23.
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  2. Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar R. Detection of 1alpha,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing. Zebrafish. 2014 Jun; 11(3):207-18. Epub 2014 Mar 20.
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  3. Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar R. Detection of 1 alpha,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. Zebrafish. 2014; 11(3):207-18.
  4. Zhang Y, Tao C, Jiang G, Nair AA, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J Biomed Semantics. 2014; 5:33. Epub 2014 Aug 6
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  5. Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Vogel RI, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bentley D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Res. 2013 Dec 15; 73(24):7222-31. Epub 2013 Oct 23.
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  6. Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP. Calculating sample size estimates for RNA sequencing data. J Comput Biol. 2013 Dec; 20(12):970-8. Epub 2013 Aug 20.
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  7. Zhang Y, Tao C, He Y, Kanjamala1 P, Liu H. Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. The International Conference of Biomedical Ontology 2013. Jul 2013.
  8. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics. 2013; 4(1):33. Epub 2013 Nov 11.
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  9. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One. 2013; 8(8):e71745. Epub 2013 Aug 19.
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  10. Pugazhenthi S, Zhang Y, Bouchard R, Mahaffey G. Induction of an inflammatory loop by interleukin-1beta and tumor necrosis factor-alpha involves NF-kB and STAT-1 in differentiated human neuroprogenitor cells. PLoS One. 2013; 8(7):e69585. Epub 2013 Jul 29.
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  11. Zhang Y, Xuan J, Clarke R, Ressom HW. Module-based breast cancer classification. Int J Data Min Bioinform. 2013; 7(3):284-302.
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  12. Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND, Ekker SC, Kumar R. Research resource: whole transcriptome RNA sequencing detects multiple 1alpha,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. Mol Endocrinol. 2012 Sep; 26(9):1630-42. Epub 2012 Jun 25
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  13. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Aug 15; 28(16):2180-1. Epub 2012 Jun 10.
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  14. Wang J, Zhang Y, Marian C, Ressom HW. Identification of aberrant pathways and network activities from high-throughput data. Brief Bioinform. 2012 Jul; 13(4):406-19. Epub 2012 Jan 27.
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  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. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics. 2012 Jan 15; 28(2):277-8. Epub 2011 Nov 15.
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  16. Tao C, Zhang Y, Jiang G, Bouamrane MM, Chute CG. Optimizing semantic MEDLINE for translational science studies using semantic web technologies. International Conference on Information and Knowledge Management, Proceedings. 2012:53-7.
  17. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Module-based biomarker discovery for breast cancer. Proceedings of 2010 IEEE International Conference on Bioinformatics & Biomedicine, Hongkong, China,. 2010 Dec 18-21:352-356.
  18. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One. 2010; 5(4):e10268. Epub 2010 Apr 21.
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  19. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics. 2009; 10 Suppl 1:S15. Epub 2009 Jul 07.
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  20. Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom HW. Network motif-based identification of breast cancer susceptibility genes. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:5696-9.
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  21. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics. 2008; 9:203. Epub 2008 Apr 21.
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  22. Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. Integrating Multi-Source Biological Data for Transcriptional Regulatory Module Discovery. Proceedings of Third IEEE/NIH Life Science Systems and Applications Workshop, Bethesda, MD. 2007:184-7.
  23. Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. Inferring network interactions using recurrent neural networks and swarm intelligence. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:4241-4.
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  24. Ressom HW, Zhang Y, Xuan J, Wang J, Clarke R. Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. Proceedings of the Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Toronto, ON, Canada, 2006:1-8.
  25. Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. Inferring network interactions using recurrent neural networks and particle swarm optimization. Proceedings of the First International Conference on Computational Systems Biology, Shanghai, China, 2006:387 - 92.
  26. Zhang Y, Zhu J, Sun X, Lu Z. A method of oligonucleotide synthesis optimization. Biotechnolgy. 2002; 12:26-8.