Bioinformatics Research Center

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Publications:

  • Jiang Y, Wang Yadong*, Brudno M. PRISM: Pair read informed split read mapping for base-pair level detection of insertion, deletion and structural variants.Bioinformatics. 2012 (SCI IF:5.468)
  • Li G, Wang Yadong, Su X. Improvements on a privacy-protection algorithm for DNA sequences with generalization lattices.Comput Methods Programs Biomed. 2012,108(1):1-9
  • Teng M, Wang Yadong*, Kim S, Li L, Shen C, Wang G, Liu Y, Huang TH, Nephew KP, Balch C. Empirical Bayes model comparisons for differential methylation analysis.Comparative and Functional Genomics. 2012,2012:376706 (SCI IF:1.282)
  • Teng M, Ichikawa S, Padgett LR, Wang Yadong, Mort M, Cooper DN, Koller D, Forond T, Edenberg H, Econs M, Liu Y. regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions.Bioinformatics. 2012,28(14):1879-86 (SCI IF:5.468)
  • Teng M, Balch C, Liu Y, Li M, Huang T, Wang Yadong*, Nephew KP, Li L. The Influence of cis-Regulatory Elements on DNA Methylation Fidelity.PLoS ONE. 2012,7(3):e32928 (SCI IF:4.537)
  • Jin SL, Xu L, Jiang QH. Joint Spectrum and Joint Distribution.Complex analysis and operator theory. 2012 (SCI IF:0.6)
  • Jin SL, Xu L, Jiang QH*, Duan GR. A Joint Spectral Characterization of C* Independence. Infinite Dimensional Analysis Quantum Probability and Related Topics. Vol. 15, No. 2 (2012) 1250013:1-5 (SCI IF:0.573)
  • Jin SL, Jiang QH*, Wang YD, Duan GR. On joint spectrum of infinite direct sums.Operators and Matrices. Vol. 6, No. 3 (2012), 529-533(SCI IF:0.542)
  • Teng M, Wang Yadong*, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y. Prioritizing single-nucleotide variations that potentially regulate alternative splicing.BMC Proceedings. 2011,5(Suup 9):S40.
  • Zhu S, Jiang Q, Wang G, Liu B, Teng M, Wang Yadong*. Chromatin structure characteristics of pre-miRNA genomic sequences. BMC Genomics. 2011,12(1):S2. (SCI IF:4.07)
  • Hu Y, Liu Y, Jung J, Dunker K, Wang Yadong*. Changes in predicted protein disorder tendency may contribute to disease risk.BMC Genomics. 2011,12(Suppl 5):S2. (SCI IF:4.07)
  • Shen C, Huang Y, Liu Y, Wang G, Zhao Y, Wang Z, Teng M, Wang Yadong, Flockhart DA, Skaar TC, Yan P, Nephew KP, Huang TH, Li L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor alpha regulatory networks in breast cancer.BMC Systems Biology. 2011,5:67 (SCI IF:3.15)
  • Jiang Q, Wang G,Li Y, Jin S, Wang Yadong*. Predicting Human microRNA-disease Associations Based on Support Vector Machine. International Journal of Data Mining and Bioinformatics. 2011
  • Wang G, Wang Y, Shen­­ C, Huang Y, Kuang K, Huang T, Nephew K, Li L, Liu Y. RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene  regulation. PLoS One. (SCI IF: 4.351)
  • Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ – stimulated HeLa cells. PLoS One. 2010; 5(7):e11794. (SCI IF: 4.351)
  • Jiang, Q., Hao, Y., Wang, G., Juan, L., Zhang, T., Teng, M., and Liu, Y., Wang, Y. (2010)Prioritization of disease microRNAs through a human phenome-microRNAome network.  BMC Systems Biology.2010.5( SCI IF: 4.064)
  • Guang Li, Yadong Wang, Xiaohong Su. A privacy preserving neural network learning algorithm for horizontally partitioned databases, (2010). Information technology journal.1, 1-10. (EI)
  • Jiang Q., Wang G., Zhang T., Wang Y. Predicting Human microRNA-disease Associations Based on Support Vector Machine. IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010). (EI)
  • Jiang Q., Hao Y., Wang G., Zhang T., Wang Y. Weighted network-based inference of human microRNA-disease associations. The 5th International Conference on Frontier of Computer Science and Technology - Workshop on Bioinformatics and System Biology. FCST2010. (EI)
  • Jiang Q., Wang G., Wang Y. An approach for prioritizing disease-related microRNAs based on genomic data integration. The 3rd International Conference on BioMedical Engineering and Informatics (BMEI'10). (EI&ISTP)
  • 李光,王亚东,苏小红. 隐私保持的决策树分类挖掘。 电子学报, 2010. 1, 204-211(EI)
  • Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G. and Liu, Y. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res, 37, D98-104. (SCI IF: 6.878)
  • Wang, Y.D., Wang, G.H., Yang, B., Tao, H.J., Yang, J.Y., Deng, Y.P. and Liu, Y.L. (2009) Reconstruct gene regulatory network using slice pattern model. BMC Genomics, 10, -. (SCI IF: 3.926)
  • Liu Y, Balaraman Y, Wang G, Nephew KP, Zhou FC. Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation. Epigenetics. 2009; 4(7):500-511. (SCI IF: 4.584)
  • Bhat-Nakshatri P, Wang G, Collins NR, Thomson MJ, Geistlinger TR, Carroll JS, Brown M, Hammond S, Srour EF, Liu Y, Nakshatri H. Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res. 2009; 37(14):4850-4861 (SCI IF: 6.878)
  • Jiang, W., Zhang, L.J., Na, B., Wang, L.H., Xu, J.K., Li, X., Wang, Y.D. and Rao, S.Q. (2009) Mapping and characterization of two relevance networks from SNP and gene levels. Prog Nat Sci, 19, 653-657. (SCI IF: 0.535)
  • Wang X, Teng M, Wang G, Zhao Y, Han X, Feng W, Li L, Sanford J, Liu Y, xIP-seq platform: an integrative framework for high-throughput sequencing data analysis. the Ohio Collaborative Conference on Bioinformatics (OCCBIO), Cleveland, OH, 2009, June 15.
  • Liu, Yong-Zhuang, Qiu, Shuang, Tao, Hai-Jun, Zang, Tian-Yi, Wang, Ya-Dong. A case-based reasoning approach to support web service composition.(2009). 2009 International Conference on Machine Learning and Cybernetics, pp 1471-1476.(EI)
  • Quan GR, Du Y, Huang JH, Wang YD. (2009) Prediction of Human Disease Genes Based on Associations between Phenome and Proteins. Proceedings of the 2009 2nd International Conference on Biomedical Engineering and Informatics (BMEI), Vols 1-4, 1779-1782. (EI)
  • Krivosheev I, Du L, Wang H, Zhang S, Wang Y, Li X. Global Similarity and Local Variance in Human Gene Coexpression Networks. Lecture Notes in Computer Science, (2009) 5855. 159-166.
  • 任世军,王亚东. 极大墒聚类算法的收敛性定理证明. 中国科学. 2009. 39(1—3), pp 1-7, 3.
  • Bhat-Nakshatri P, Wang G, Appaiah H, Luktuke N, Carroll JS, Geistlinger TR, Brown M, Badve S, Liu Y, Nakshatri H. AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer. Mol Cell Biol. 2008; 28(24):7487-7503. (SCI IF: 6.057)
  • Wang, G., Wang, Y., Feng, W., Wang, X., Yang, J.Y., Zhao, Y. and Liu, Y. (2008) Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells. BMC Genomics, S22. (SCI IF: 3.926)
  • Wang, G., Wang, X., Wang, Y., Yang, J.Y., Li, L., Nephew, K.P., Edenberg, H.J., Zhou, F.C. and Liu, Y. (2007) Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome. BMC Genomics, S19. (SCI IF: 3.926)
  • Jiang, W., Li, X., Rao, S.Q., Wang, L.H., Du, L., Li, C.X., Wu, C., Wang, H.Z., Wang, Y.D. and Yang, B.F. (2008) Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Syst Biol, 2, -.( SCI IF: 3.71)
  • Dong Qiwen, Wang Xiaolong, Lin Lei, Wang Yadong. (2008) Analysis and prediction of protein local structure based on structure alphabets. Proteins-Structure Function and Bioinformatics, 72(1), pp 163-172. (SCI IF: 3.419)
  • Li, J., Tang, X., Liu, J., Huang, J. and Wang, Y. (2008) A novel approach to feature extraction from classification models based on information gene pairs. Pattern Recogn, 41, 1975-1984. (SCI IF: 3.279)
  • Xiao, Y., Li, X., Yang, Y.Y., Wang, Y.D. and Rao, S.Q. (2008) Cell cycle-dependent gene networks relevant to cancer. Prog Nat Sci, 18, 945-952. (SCI IF: 0.535)
  • Yang, Y.Y., Wang, H.Y., Li, X., Xiao, X., Fei, S., Li, C.X., Wang, H.Z., Rao, S.Q. and Wang, Y.D. (2008) A feature ensemble technology to identify molecular mechanisms for distinction between multiple subtypes of lymphoma. Prog Nat Sci, 18, 1491-1500. (SCI IF: 0.535)
  • Zhang, W., Li, L., Li, X., Jiang, W., Huo, J.M., Wang, Y.D., Lin, M.H. and Rao, S.Q. (2007) Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering. BMC Genomics, 8, -. (SCI IF: 3.926)  
  • Wang X, Wang K, Radovich M, Wang Y, Wang G, Feng W, Sanford JR, Liu Y. Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics. 2009; 10 Suppl 1:S4. (SCI IF: 3.926)  
  • Wang X, Wang G, Shen C, Li L, Wang X, Mooney SD, Edenberg HJ, Sanford JR, Liu Y. Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics. 2008; 9 Suppl 1:S17.
  • Xu, Yong-Dong, Quan, Guang-Ri, Wang, Ya-Dong, Xu, Zhi-Ming. Multiple features fusion method for identifying text topic boundaries. (2008).7th International Conference on Machine Learning and Cybernetics, ICMLC. pp 2950-2956.(EI)
  • Wang X, Wang K, Wang G, Sanford J, Liu Y: Model-based prediction of cis-acting RNA elements regulating tissue-specific alternative splicing. In: 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008, 10 (EI)
  • Guang-Ri, Quan, Yong-Dong, Xu, Ya-Dong, Wang, Zhi-Ming, Xu. A new DNA Fragment Assembly method based on long fragment filtration.(2008). BioMedical Engineering and Informatics: New Development and the Future-1st International Conference on BioMedical Engineering and Informatics, BMEI 2008, pp 39-46. (EI)
  • TaoH, WangY, GuoM, XiangL.Research on Knowledge-Based Intelligent Agent Model. The 2th International Conference on Knowledge Generation, Communication and Management: KGCM 2008.
  • Teng M, Zhang X, Wang Y, Li M, Wang G, Liu Y. Detecting Disease-related MicroRNAs Through the Analysis of Protein-Protein Interaction Networks. The International Society for Biopharmaceutical Statistics, June 30-July 2, 2008. Shanghai China.
  • Yang, B., Su, X. and Wang, Y. (2007) Distributed learning strategy based on chips for classification with large-scale dataset. Int J Pattern Recogn, 21, 899-920. (SCI IF: 1)
  • TaoH, WangY, GuoM. An Extended Contract-Net Negotiation Model Based on Task Coalition and Genetic Algorithm. International Conference on Machine Learning and Cybernetics: ICMLC2007. (EI)
  • TaoH, WangY, GuoM. A MAS Communication Model Based on Star-Ring Structure. International Conference on Machine Learning and Cybernetics: ICMLC2007. (EI)
  • Chen AB, Hamamura K, Wang G, Xing W, Mohan S, Yokota H, Liu Y. Model-based comparative prediction of transcription-factor binding motifs in anabolic responses in bone. Genomics Proteomics Bioinformatics. 2007; 5(3-4):158-165.