Publications

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Zhang, J., X. Gao, J. Xu, and M. Li, "Rapid and accurate side chain prediction with local backbone information", RECOMB'08, 2008.
Zhang, J., X. Chen, and M. Li, "Calculating exact p-value for structured motif", CPM, 2007.
Zhang, Z., H. Lin, and M. Li, "MANGO: a new approach to multiple sequence alignment", CSB'2007. Best paper award. San Diego, CA, 2007.
Zhang, L., B. Ma, and L. Wang, "Efficient Methods for Inferring Tandem Duplication History", The 2nd Workshop on Algorithms in Bioinformatics. 97-111, 2002.
Zhang, K., L. Wang, and B. Ma, " Computing Similarity between RNA Structures", The 10th Symposium on Combinatorial Pattern Matching. 281-293, 1999.
Zhang, W.J., X. Chen, L. Xin, P. Shan, Z.G. Luo, M. Li, and ChimST, "ChimST: An efficient spectral library search tool for peptide identification for chimeric spectra in data-dependent acquisition", ACM/IEEE Trans. on Comput. Biol. and Bioinform, 2019.
Zhang, J., L. Xin, B. Shan, W. Chen, M. Xie, D. Yuen, W. Zhang, Z. Zhang, G. Lajoie, and B. Ma, "PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification", Molecular & Cellular Proteomics 11. DOI, 10.1074/mcp.M111.010587, 2012.
Zhang, L., and B. Ma, "Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Ancestral State Reconstruction", Journal of Combinatorial Optimization 21(4): 409-422, 2011.
Zhang, Z., H. Lin, and B. Ma, "ZOOM Lite: Next-generation Sequencing Data Mapping and Visualization Software", Nucleic Acids Research. 38 (suppl 2): W743-W748, 2010.
Zhang, Z., H. Lin, and M. Li, "MANGO: multiple alignment with n gapped oligos", Journal of Bioinformatics and Computational Biology, 6:3, 521-541, 2008.
Zhang, J., B. Jiang, M. Li, J. Tromp, X. Zhang, and M.Q. Zhang, "Computing exact p-values for DNA motifs", Bioinformaics, 23, 531 - 537, 2007.
Zhang, L., B. Ma, L. Wang, and Y. Xu, "Greedy Method for Inferring Tandem Duplication History", Bioinformatics. 19(12): 1497-1504, 2003.
Zhao, Y., B. Alipanahi, S.C. Li, and M. Li, " Protein secondary structure prediction using NMR chemical shift data", JBCB 8:5, 2010.
Zohora, F., N.H. Tran, X. Zhang, L. Xin, B. Shan, and M. Li, "Deeplso: a deep learning model for peptide feature detection", Nature, Scientific Report, 2019.

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