Publications

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Badger, J., P. Kearney, M. Li, J. Tsang, and T. Jiang, "Selecting the branches for an evolutionary tree: a polynomial time approximation scheme", Journal of Algorithms, 51, 1-14, 2004.
Bansal, N., M. Lewenstein, B. Ma, and K. Zhang, "On the Longest Common Rigid Subsequence Problem", Algorithmica 56(2): 270-280, 2010.
Bennett, C.H., P. Gacs, M. Li, P. Vitanyi, and W. Zurek, "Thermodynamics of computation and information distance", Proc. 25th ACM Symp. Theory of Computing (STOC'93), pp. 21-30, 1993.
Bennett, C.H., M. Li, and B. Ma, "Chain letters and evolutionary histories", Scientific American, 288:6200 (feature article), 76-81, 2003.
Bennett, C.H., P. Gacs, M. Li, P. Vitanyi, and W. Zurek, "Information Distance", IEEE Trans. Inform. Theory, 44:4, 1407-1423, 1998.
Benson, G., and R. Page, "Algorithms in Bioinformatics", Third International Workshop, Proceedings of WABI 2003, Budapest, Hungary, 2003.
Bergstrand, L., J.D. Neufeld, and A.C. Doxey, "Pygenprop: a python library for interactive programmatic exploration and comparison of organism Genome Properties", Bioinformatics, btz522, 2019.
Berry, V., T. Jiang, P. Kearney, M. Li, and T. Wareham, "Quartet cleaning: improved algorithms and simulations", ESA'99, Prague, 1999.
Blum, A., T. Jiang, M. Li, J. Tromp, and M. Yannakakis, "Linear approximation of shortest superstrings", 23rd ACM Symp. on Theory of Computing (STOC'91), pp. 328-336, 1991.
Blum, A., T. Jiang, M. Li, J. Tromp, and M. Yannakakis, "Linear approximation of shortest superstrings", Journal of the ACM, 41:4, 630-647, 1994.
Bottger, A., A.C. Doxey, M.W. Hess, K. Pfaller, W. Salvenmoser, R. Deutzmann, A. Geissner, B. Pauly, J. Altstatter, S. Munder, et al., "Horizontal gene transfer contributed to the evolution of extracellular surface structures, the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth) families", PLoS One,7:e52278, 2012.
Boucher, C., and D.G. Brown, "Detecting motifs in a large data set: applying probabilistic insights to motif finding", Proceedings of Bioinformatics and Computational Biology (BiCOB 2009), 139-150, 2009.
Boucher, C., D.G. Brown, and S. Durocher, "On the structure of small motif recognition instances", Proceedings of String Processing and Information Retrieval (SPIRE), 269-281, 2008.
Boucher, C., D.G. Brown, and P. Church, "A graph clustering approach to weak motif recognition", Proceedings of WABI, 149-160, 2007.
Boucher, C., and B. Ma, "Closest String with Outliers", The 9th Asia Pacific Bioinformatics Conference. BMC Bioinformatics 12(Suppl 1): S55, 2011.
Brejova, B., D.G. Brown, I.M. Harrower, and T. Vinar, "New bounds for motif finding in strong instances", Proceedings of CPM, 94-105, 2006.
Brejova, B., D.G. Brown, M. Li, and T. Vinar, "Clone of ExonHunter: a comprehensive approach to gene finding", ISMB'2005 Michigan, 2005.
Brejova, B., D.G. Brown, I.M. Harrower, A. Lopez-Ortiz, and T. Vinar, "Sharper upper and lower bounds for Consensus-Pattern", Proceedings of CPM,1-10, 2005.
Brejova, B., D.G. Brown, and T. Vinar, "The most probable labeling problem in HMMs and its applications to bioinformatics", Proceedings of WABI, 426-437, 2004.
Brejova, B., D.G. Brown, and T. Vinar, "Optimal DNA signal recognition models with a fixed amount of intrasignal dependency", Proceedings of WABI, 78-94, 2003.
Brejova, B., D.G. Brown, and T. Vinar, "Optimal spaced seeds for hidden Markov models, with applications to homologous coding regions", Proceedings of CPM, 42-54, 2003.
Brejova, B., D.G. Brown, and T. Vinar, "Vector seeds: an extension to spaced seeds allows substantial improvements in sensitivity and specificity", Proceedings of WABI, 39-54, 2003.
Brejova, B., T. Vinar, Y. Chen, S. Wang, G. Zhao, D.G. Brown, M. Li, and Y. Zhou, "Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence", Nucleic Acids Research 37: e52, 2009.
Brejova, B., D.G. Brown, and T. Vinar, "The most probable annotation problem in HMMs and its application to bioinformatics", Journal of Computing and System Sciences, 73 (7): 1060-1077, 2007.
Brejova, B., D.G. Brown, M. Li, and T. Vinar, "ExonHunter: a comprehensive approach to gene finding", Bioinformatics 21:S1, i57-i65, 2005.
Brejova, B., D.G. Brown, M. Li, and T. Vinar, "Pygenprop: a python library for interactive programmatic exploration and comparison of organism Genome Properties", Bioinformatics 21 (S1):i57-i65, 2005.
Brejova, B., D.G. Brown, and T. Vinar, "Vector seeds: an extension to spaced seeds", Journal of Computer and System Sciences 70: 364-380, 2005.
Brejova, B., D.G. Brown, and T. Vinar, "Optimal spaced seeds for homologous coding regions", Journal of Bioinformatics and Computational Biology 1(4): 595-610, 2004.
Broom, A., A.C. Doxey, Y.D. Lobsanov, L.G. Berthin, D.R. Rose, P.L. Howell, B.J. McConkey, and E.M. Meiering, "Modular evolution and the origins of symmetry, reconstruction of a three-fold symmetric globular protein", Structure 20:161-171, 2012.
Brown, D.G., M. Li, and B. Ma, "The Homology Search Methods", In The Practical Bioinformatician, edited by Limsoon Wong. World Scientific, 2004.
Brown, D.G., and D. Dexter, "Combinatorial approaches to half-sibling reconstruction", Proceedings of the 2012 Workshop on Algorithms in Bioinformatics (WABI), 44-56, 2012.
Brown, D.G., and J. Truszkowski, "Fast phylogeny algorithms using locality-sensitive hashing", Proceedings of WABI, 14-29, 2012.
Brown, D.G., and J. Truszkowski, "Fast error-tolerant quartet phylogeny algorithms", Proceedings of the Symposium on Combinatorial Pattern Matching (CPM), 147-161, 2011.
Brown, D.G., and J. Truszkowski, "Toward a practical O(n log n) quartet phylogeny algorithm", Proceedings of WABI, 14-25, 2011.
Brown, D.G., and T. Berger-Wolf, "Discovering kinship through small subsets", Proceedings of WABI, 111-123, 2010.
Brown, D.G., and I.M. Harrower, "Toward an algebraic understanding of haplotype inference by pure parsimony", Proceedings of the 2006 Computational Systems Bioinformatics Conference (CSB), 211-222, 2006.
Brown, D.G., and I.M. Harrower, "A new integer programming formulation for the pure parsimony problem in haplotype analysis", Proceedings of WABI, 254-265, 2004.
Brown, D.G., "Multiple vector seeds for protein alignment", Proceedings of WABI, 170-181, 2004.
Brown, D.G., and A.K. Hudek, "New algorithms for multiple DNA sequence alignment", Proceedings of WABI, 314-325, 2004.
Brown, D.G., "A probabilistic analysis of a greedy algorithm arising from computational biology", Proceedings of the 2001 ACM/SIAM Symposium on Discrete Algorithms (SODA), pp 208, 206 (misprinted in proceedings), 2001.
Brown, D.G., T.J. Vision, and S.D. Tanksley, "Selective mapping: a discrete optimization approach to selecting a population subset for use in a high-density genetic mapping project", Proceedings of SODA, 419-428, 2000.
Brown, D.G., and M. Owen, "Mean and Variance of Phylogenetic Trees", Systematic Biology, vol. 69, issue 1, 01/2020.
Brown, D.G., and J. Truszkowski, "Fast error-tolerant quartet phylogeny algorithms", Theoretical Computer Science 483: 104-114, 2013.
Brown, D.G., and J. Truszkowski, "LSHPlace: Fast phylogenetic placement using locality-sensitive hashing", Proceedings of the Pacific Symposium in Biocomputing (PSB), 310-319, 2013.
Brown, D.G., and D. Golod, "Decoding HMMs using the k best paths: algorithms and applications", BMC Bioinformatics 11 (Suppl 1): S28, 2010.
Brown, D.G., and J. Truszkowski, "New decoding algorithms for hidden Markov models using distance measures on state paths", BMC Bioinformatics 11 (Suppl 1): S40, 2010.
Brown, D.G., and D. Golod, "A tutorial of techniques for improving standard hidden Markov model algorithms", Journal of Bioinformatics and Computational Biology 7: 737-754, 2009.
Brown, D.G., and I.M. Harrower, "Integer programming approaches to haplotype inference by pure parsimony", IEEE ACM Transactions on Computational Biology and Bioinformatics, 3(2):141-154, 2006.
Brown, D.G., "Multiple seeds for protein alignment", IEEE ACM Transactions on Bioinformatics and Computational Biology 2: 29-38 (Special issue for the best papers of the 2004 Workshop on Algorithms in Bioinformatics), 2005.
Brown, D.G., M. Li, and B. Ma, "A Tutorial of Recent Developments in the Seeding of Local Alignment", Journal of Bioinformatics and Computational Biology 2(4): 819-842, 2004.
Brown, D.G., M. Li, and B. Ma, "Homology search methods", In The Practical Bioinformatician. L. Wong Ed. World Scientific, 217-244, 2004.
Bryant, D., V. Berry, P. Kearney, T. Jiang, M. Li, T. Wareham, and H. Zhang, "A practical algorithm for recovering the best supported edges of an evolutionary tree", Proc. 11th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'2000), pp. 287--296, 2000.
Bryant, D., J. Tsang, P. Kearney, and M. Li, "Computing the quartet difference between two trees", Proc. 11th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'2000), pp. 285--286, 2000.
Bu, D., S.C. Li, and M. Li, " Clustering 100,000 potein structure decoys in minutes", IEEE/ACM Trans. Comput. Biol. Bioinf. 9:3, 765-773, 2012.
Bu, F., X. Zhu, and M. Li, "A New Multiword Expression Metric and Its Applications", J. Comput. Sci. Tech.,26:1, 3-13, 2011.
Bu, D., M. Li, S.C. Li, J. Qian, and J. Xu, "Finding compact structural motifs", Theoretical Computer Science, 410:30-32, 2834-2839, 2009.

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