Publications

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Lanctot, K., M. Li, and E.H. Yang, "Estimating DNA sequence entropy", Proc. 11th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'2000), pp. 409--418, 2000.
Lanctot, K., M. Li, B. Ma, S. Wang, and L. Zhang, "Distinguishing String Search Problems", The 10th Annual ACM-SIAM Symposium on Discrete Algorithms. 633-642, 1999.
Lanctot, J. K., M. Li, B. Ma, S. Wang, and L. Zhang, "Distinguishing String Search Problems", Information and Computation 185: 41-55, 2003.
Li, M., and P. Vitanyi, An introduction to Kolmogorov complexity and its applications, Springer-Verlag, 1st Edition 1993 (xx+546 pp). 2nd Edition 1997 (xx+637 pp). 3rd Edition 2008 (xx+792 pp). 4th Edition, 2008.
Li, M., T. Jiang, Y. Xu, and M.Q. Zhang, "Compressing DNA sequences", Chapter 7 in Current Topics in Computational Molecular Biology, the MIT Press, 2002.
Li, W., B. Ma, and K. Zhang, " Efficient Filtration for Similarity Search with Spaced k-mer Neighbors", IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Best student paper award, 2012.
Li, W., B. Ma, and K. Zhang, " Amino Acid Classification and Hash Seeds for Homology Search", The 1st International Conference on Bioinformatics and Computational Biology. 44-51, 2009.
Li, S.C., D. Bu, J. Xu, and M. Li, "Designing succinct structural alphabet", ISMB, Toronto, 2008.
Li, S.C., D. Bu, J. Xu, and M. Li, "Finding largest well-predicted subset of protein structure models", CPM, Italy, 2008.
Li, M., B. Ma, and L. Zhang, "Superiority and complexity of the spaced seeds", The 17th Symposium on Discrete Algorithms. 444-453, 2006.
Li, M., B. Ma, D. Kisman, and J. Tromp, " PatternHunter II: Highly Sensitive and Fast Homology Search", The 14th International Conference on Genome Informatics. 164-175, 2003.
Li, M., X. Chen, X. Li, B. Ma, and P. Vitanyi, " The Similarity Metric", The 13th SIAM Symposium on Discrete Algorithms. 863-872, 2003.
Li, M., B. Ma, and L. Wang, "Near Optimal Multiple Alignment within a Band in Polynomial Time", The 32nd ACM Symposium on Theory of Computing. 425-434, 2000.
Li, M., B. Ma, and L. Wang, "Finding similar regions in many sequences", Proc. 31st ACM Symp. Theory of Computing (STOC'99), Atlanta, 1999.
Li, M., and L. Zhang, "Better approximation of diagonal-flip transformation and rotation transformation", Proc. 4th Int'l Computing and Combinatorics Conference (COCOON'98), Taipei, Taiwan, pp. 85-94, 1998.
Li, M., J. Tromp, and L. Zhang, "On the nearest neighbour interchange distance measure", Proc. 2nd International Conf. on Computing and Combinatorics, (COCOON'96), Hong Kong, 1996.
Li, M., and A. Viola, "Learning secondary structures of proteins", Proc. 6th International Conference on Computing and Information, Peterborough, Ontario, 1994.
Li, M., "Towards a DNA sequencing theory (learning a string)", Proc. 31st IEEE Symp. Found. Computer Science (FOCS'90), pp. 125-134, 1990.
Li, M., "Towards a DNA sequencing theory: learning a string", Proc. 3rd ACM Workshop on Computational Learning Theory (COLT'90), Rochester, NY, page 394, 1990.
Li, W., B. Ma, and K. Zhang, "Optimizing Spaced k-mer Neighbors for Efficient Filtration in Protein Similarity Search", IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11(2): 398-406, 2014.
Li, J., B.J. McConkey, Z. Cheng, S. Guo, and B.R. Glick, "PathogenIdentification of plant growth-promoting bacteria-responsive proteins in cucumber roots under hypoxic stress using a proteomic approach", Journal of proteomics,84:119-131, 2013.
Li, S.C., D. Bu, J. Xu, and M. Li, " Finding nearly optimal GDT scores", J. Comput. Biol., 18:5, 693-704, 2011.
Li, S.C., D. Bu, and M. Li, " Residues with similar hexagon neighborhoods share similar side-chain conformations", ACM/IEEE Trans. Comput. Biology Bioinfo. 9:1, 240-248, 2011.
Li, M., " Can we determine a protein structure quickly?", J. Comput. Sci. Tech. 25:1 95-106, 2010.
Li, S.C., D. Bu, J. Xu, and M. Li, " Fragment-HMM: a new approach to protein structure prediction", Protein Science, 17 1925-1934, 2008.
Li, S.C., D. Bu, J. Xu, and M. Li, "Designing succinct structural alphabet", Bioinformatics, ISMB Special Issue, 2008.
Li, M., B. Ma, D. Kisman, and J. Tromp, "PatternHunter II: Highly Sensitive and Fast Homology Search", Journal of Bioinformatics and Computational Biology. 2(3): 417-440, 2004.
Li, M., X. Chen, X. Li, B. Ma, and P. Vitanyi, "The Similarity Metric", IEEE Transaction Information Theory 50: 3250-3264, 2004.
Li, M., B. Ma, and L. Wang, " On the Closest String and Substring Problems", Journal of the ACM 49(2): 157-171, 2002.
Li, M., B. Ma, and L. Wang, "Finding similar regions in many sequences", Journal of Computer and System Sciences (Special Issue for STOC'99). 65, 73-96, 2002.
Li, M., J. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, "An information-based sequence distance and its application to whole mitochondrial genome phylogeny", Bioinformatics, 17:2, 149-154, 2001.
Li, M., and L. Zhang, "Twist-rotation transformations of binary trees and arithmetic expressions", Journal of Algorithms, 32, 155-166, 1999.
Li, M., J. Tromp, and L. Zhang, "On the nearest neighbour interchange distance between evolutionary trees", Journal of Theoretical Biology, 182, 463-467, 1996.
Liang, C., J. Smith, C. Hendrie, K.W.M. Siu, and M. Li, "A comparative study of mass spec de novo sequencing software", 51st ASMS Conference, Poster, Montreal, Canada, 2003.
Lin, G., B. Ma, and K. Zhang, " Edit Distance between Two RNA Structures", The 5th Conference on Computational Molecular Biology. 211-220, 2001.
Lin, H., L. He, and B. Ma, "A Combinatorial Approach to the Peptide Feature Matching Problem for Label-Free Quantification", Bioinformatics. 29 (14): 1768-1775, 2013.
Lin, H., Z. Zhang, M.Q. Zhang, B. Ma, and M. Li, "ZOOM! Zillions of oligos mapped", Bioinformatics. 24:21, 2431-2437, 2008.
Lin, H., Z.F. Zhang, Q.F. Zhang, D.B. Bu, and M. Li, "A note on the single genotype resolution problem", Journal of Computer Science and Technology, 19:2, 254-257, 2004.
Liu, Y., B. Ma, K. Zhang, and G. Lajoie, " An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra", International Symposium on Bioinformatics Research 126-137, 2014.
Liu, X., B. Ma, and L. Wang, "The 7th Annual International Conference on Computational Systems Bioinformatics. 37-47", The 7th Annual International Conference on Computational Systems Bioinformatics. 37-47, 2008.
Liu, J., B. Ma, and M. Li, " PRIMA: Peptide Robust Identification from MS/MS Spectra", The 3rd Asia-Pacific Bioinformatics Conference. 181-191, 2005.
Liu, J., B. Ma, and K. Zhang, "Algorithms for searching RNA motifs in genomic sequences", The 6th Atlantic Symposium on Computational Biology and Genome Informatics, 2005.
Liu, Y., B. Ma, K. Zhang, and G. Lajoie, "An approach for peptide identification by de novo sequencing of mixture spectra", IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:326-336, 2017.
Liu, Y., W. Sun, J. John, G. Lajoie, B. Ma, and K. Zhang, "De Novo Sequencing Assisted Approach for Characterizing Mixture MS/MS Spectra", IEEE transactions on nanobioscience 15 (2), 166-176, 2016.
Liu, Y., W. Sun, G. Lajoie, B. Ma, and K. Zhang, " An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database", International Symposium on Bioinformatics Research and Applications 223-234. Norfolk, Virginia, 2015.
Liu, X., L. Xin, B. Shan, and B. Ma, "Better Score Function for Peptide Identification with ETD MS/MS Spectra", BMC Bioinformatics. 11 (Suppl 1): S4, 2010.
Liu, X., Y. Han, D. Yuen, and B. Ma, " Automated Protein (Re)sequencing with MS/MS and a Homologous Database Yields Almost Full Coverage and Accuracy", Bioinformatics 25(17): 2174-2180, 2009.
Liu, J., B. Ma, and K. Zhang, " An Algorithm for Searching RNA Motifs in Genomic Sequences", Biomolecular Engineering 24: 343-350, 2007.
Liu, J., B. Ma, and M. Li, " PRIMA: Peptide Robust Identification from MS/MS Spectra", Journal of Bioinformatics and Computational Biology 4(1): 125-138, 2006.
Liu, J., and M. Li, "Finding cancer biomarkers from mass spectrometry data by decision lists", Journal of Computational Biology. 12:7, 969-977, 2005.
Lobb, B., and A.C. Doxey, "Novel function discovery through sequence and structural data mining", Current Opinion in Structural Biology. 38:53-61, 2016.
Lobb, B., D. Kurtz, G. Moreno-Hagelsieb, and A.C. Doxey, "Remote homology and the functions of metagenomic dark matter", Frontiers in Genetics. 6:234, 2015.

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