Publications

  1. Zhang Y, Xuan J, Clarke R, Ressom HW. Module-based breast cancer classification. International Journal of Data Mining and Bioinformatics. 2013; 7(3):284-302. 2207874
  2. 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 2273104
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  3. 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. 2252532
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  4. 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. 2230499
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  5. 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. 2206702
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  6. 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. 2293277
  7. 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. 2116828
  8. 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. 2109775
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  9. 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. 2109777
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  10. 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. 2109826
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  11. Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. Reverse engineering module networks by PSO-RNN hybrid modeling Proceedings of the 2008 international conference on bioinformatics & computational biology, Las Vegas, NV,. 2008:401-7. 2109827
  12. 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. 2116827
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  13. 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. 2109828
  14. 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. 2116829
  15. 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. 2109831
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  16. 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. 2109832
  17. Zhang Y, Zhu J, Sun X, Lu Z. A method of oligonucleotide synthesis optimization. Biotechnolgy. 2002; 12:26-8. 2109950