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Han, X., L. He, L. Xin, B. Shan, and B. Ma, "PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications", RECOMB Satellite Meeting on Computational Proteomics, 2011.
Han, Y., B. Ma, and K. Zhang, " SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error", The 3rd IEEE Computer Society Bioinformatics Conference, 206-215. (Best Paper Award), 2004.
Han, Y., B. Ma, and K. Zhang, "An Automata Approach to Match Gapped Sequence Tags", The Ninth International Conference on Implementation and Application of Automata. 167-177, 2004.
Han, X., L. He, L. Xin, B. Shan, and B. Ma, "PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications", Journal of Proteomics Research 10(7): 2930-2936, 2011.
Han, Y., B. Ma, and K. Zhang, " An Automata Approach to Match Gapped Sequence Tags", International Journal of Foundations of Computer Science 16(3): 487-497, 2005.
Han, Y., B. Ma, and K. Zhang, "SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error", Journal of Bioinformatics and Computational Biology 3(3):697-716, 2005.
Hao, Y., X.Y. Zhu, M.L. Huang, and M. Li, "Discovering patterns to extract protein-protein interactions from the literature: part II", Bioinformatics, 21:15, 3294-3300, 2005.
He, L., X. Han, and B. Ma, " De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide", The 9th Asia Pacific Bioinformatics Conference, 2012.
He, L., L. Xin, B. Shan, G. Lajoie, and B. Ma, "GlycoMaster DB:Software to Assist the Automated Identification of N-Linked Glycopeptides by Tandem Mass Spectrometry", Journal of Proteome Research. 13(9):3881-95, 2014.
He, L., X. Han, and B. Ma, "De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide", Journal of Bioinformatics and Computational Biology 11(4), 2013.
He, L., and B. Ma, "ADEPTS: Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra", Journal of Bioinformatics and Computational Biology 8(6): 981-994, 2010.
Heffelfinger, G.S., "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling", OMICS, 6:4, 305-330, 2002.
Ho, R., and B.J. McConkey, "Modulating glycosylation of recombinant monoclonal antibodies for therapeutic applications", Current topics in biotechnology. 6:57-69, 2011.
Holtby, D., S.C. Li, and M. Li, "LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins", ECOMB 2012. pp. 113-126. Barcelona, Spain, April 21-24, 2012.
Holtby, D., S.C. Li, and M. Li, "LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins J", Computat. Biol., 20:3, 212-223, 2013.
Huang, M.L., X.Y. Zhu, and M. Li, "A hybrid method for relation extraction from biomedical literature", International Journal of Medical Informatics Special issue: Natural language processing on biomedicine and its applications. 75:6, 443-455, 2006.
Huang, M.L., X.Y. Zhu, Y. Hao, D.G. Payan, K. Qu, and M. Li, "Discovering patterns to extract protein-protein interactions from full texts", Bioinformatics. 20 3604-3612, 2004.
Hudek, A.K., and D.G. Brown, "Ancestral sequence alignment under optimal conditions", BMC Bioinformatics 6:273, 2005.
Hughes, C., B. Ma, and G. Lajoie, "De novo sequencing methods in proteomics", In Proteome Bioinformatics. Methods in Molecular Biology 604. Humana Press. Springer, 2010.

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