Publications

Sort by: Author Type Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

Ackerman, M., D.G. Brown, and D. Loker, "Effects of rooting via outgroups on ingroup topology in phylogeny", Proceedings of the International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 7 pages, 2012.
Ackerman, M., D.G. Brown, and D. Loker, "Effects of rooting via outgroups on ingroup topology in phylogeny", International Journal of Bioinformatics Research and Applications 10(4/5): 426-446, 2014.
Adams, J., M.J. Mansfield, D.J. Richard, and A.C. Doxey, "Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function", Bioinformatics. 33:1338-1345, 2017.
Alhaider, A., A. Abdelgader, A. Turjoman, K. Newell, S. Hunsucker, B. Shan, B. Ma, D. Gibson, and M. Duncan, "Through the Eye of an Electrospray Needle: Mass Spectrometric Identification of the Major Peptides & Proteins in the Milk of the One Humped Camel (Camelus dromedarius)", Journal of Mass Spectrometry. 48 (7), 779-794, 2013.
Alipanahi, B., N. Krislock, H. Wolkowicz, A. Ghodsi, L. Donaldson, and M. Li, "Protein Structure by Semidefinite Facial Reduction", RECOMB 2012. pp. 1-11, Barcelona, Spain, 2012.
Alipanahi, B., X. Gao, E. Karakoc, L. Donaldson, and M. Li, "PICKY: a novel SVM-based NMR spectra peak picking method", ISMB, 2009.
Alipanahi, B., N. Krislock, H. Wolkowicz, A. Ghodsi, L. Donaldson, and M. Li, " Determining protein structures from NOESY distance constraints by semidefinite programming", J. Computat. Biol., 20:4 296-310, 2013.
Alipanahi, B., X. Gao, E. Karakoc, F. Balbach, S.C. Li, G. Feng, L. Donaldson, and M. Li, "Error tolerant NMR backbone resonance assignment for automated structure generation", J. Bioinform Computat. Biol., 1V26, 2011.
Alipanahi, B., X. Gao, E. Karakoc, L. Donaldson, and M. Li, "PICKY: a novel SVD-based NMR spectra peak picking method", Bioinformatics. ISMB'09 Special issue. 25: i268-i275, 2009.

B

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.

C

Capellini, T.D., H. Chen, J. Cao, A.C. Doxey, K. Kiapour, M. Schoor, and D.M. Kingsley, "The locus of selection on common GDF5 height and arthritis risk variants in humans", Nature Genetics. 49:1202-1210, 2017.
Chen, Z., B. Ma, and L. Wang, " Randomized and Parameterized Algorithms for the Closest String Problem", The 25th Symposium on Combinatorial Pattern Matching. 100-109, 2014.
Chen, Z., B. Ma, and L. Wang, " A Three-String Approach to the Closest String Problem", The 16th International Computing and Combinatorics Conference. 449-458, 2010.
Chen, X., S. Kwong, and M. Li, "A compression algorithm for DNA sequences and its application in genome comparison", In GIW'99 (best paper award), Tokyo, Japan, Dec. 1999, pp. 51-61,and in RECOMB'00. Tokyo, Japan, p. 107, 2000.
Chen, Z., B. Ma, and L. Wang, "Randomized Fixed-Parameter Algorithms for the Closest String Problem", Algorithmica 74(1): 466-484, 2016.
Chen, Z., B. Ma, and L. Wang, "A Three-String Approach to the Closest String Problem", Journal of Computer and System Sciences 78(1): 164-178, 2012.
Chen, S., B. Ma, and K. Zhang, " On the Similarity Metric and the Distance Metric", Theoretical Computer Science 410(24-25): 2365-2376, 2009.
Chen, X., M. Li, B. Ma, and J. Tromp, "DNACompress: fast and effective DNA sequence compression", Bioinformatics. 18, 1696-1698, 2002.
Chen, X., S. Kwong, and M. Li, "A compression algorithm for DNA Sequences", IEEE Engineering in Medicine and Biology Magazine, (Special Issue on Bioinformatics) 20:4, 61-66, 2001.
Cheng, Z., J.F. Li, Y. Niu, X.C. Zhang, O.Z. Woody, Y. Xiong, S. Djonovic, Y. Millet, J. Bush, and B.J. McConkey, "Pathogen-secreted proteases activate a novel plant immune pathway", Nature, 521:213, 2015.
Cheng, Z., O.Z. Woody, B.J. McConkey, and B.R. Glick, "Combined effects of the plant growth-promoting bacterium Pseudomonas putida UW4 and salinity stress on the Brassica napus proteome", Applied Soil Ecology,61:255-263, 2012.
Cheng, Z., B.J. McConkey, and B.R. Glick, "Proteomic studies of plant-bacterial interactions", Soil Biology and Biochemistry, 42:1673-1684, 2010.
Chow, B.A., S.W. Donahue, M.R. Vaughan, B.J. McConkey, and M.M. Vijayan, "Serum immune-related proteins are differentially expressed during hibernation in the American black bear", PLoS One, 8:e66119, 2013.
Consortium, S. japonica G., D.G. Brown, and M. Li, "The Schistosoma japonicum genome reveals features of host-parasite interplay", Nature 460: 345-352, 2009.
Consortium, R. Genome Seq, and B. Ma, "Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution", Nature 428: 493-521, 2004.
Consortium, M. Genome, D.G. Brown, M. Li, and B. Ma, "Initial sequencing and comparative analysis of the mouse genome", Nature,409:6822, 520-522, 2002.
Consortium, I. Human Geno, and D.G. Brown, "Initial sequencing and analysis of the human genome", Nature 409: 860-921 (Member of genome analysis group), 2001.
Csuros, M., and B. Ma, "Rapid homology search with two-stage extension and daughter seeds", The Eleventh International Computing and Combinatorics Conference. 104-114, 2005.
Csuros, M., and B. Ma, " Rapid Homology Search with Neighbor Seeds", Algorithmica. 48(2): 187-202, 2007.
Cui, X.F., S.C. Li, D.B. Bu, and M. Li, "Towards reliable automatic protein structure alignment", WABI 2013 Sept. 2-4, Sophia Antipolis, France, pp. 18-32, 2013.
Cui, X.F., S.C. Li, D.B. Bu, B. Alipanahi, and M. Li, "How accurately can we model protein structures with dihedral angles?", WABI 2012, Sept. 10-12, Ljubljana, Slovenia, pp. 274-287, 2012.
Cui, X., T. Vinar, B. Brejova, D. Shasha, and M. Li, "Homology search for genes", ISMB, 2007.
Cui, X., S.C. Li, L. He, and M. Li, " Fingerprinting protein structures effectively and efficieintly", Bioinformatics,30:7 949-955, 2014.
Cui, X.F., S.C. Li, D.B. Bu, B. Alipanahi, and M. Li, "Protein structure idealization: How accurately is it possible to model protein structures with dihedral angles?", Alg. of Molecular Biology, 8:5, 2013.
Cui, X.F., S.C. Li, D.B. Bu, and M. Li, "Towards reliable automatic protein structure alignment", Nucleic Acids Research, 37:12, 1-7, 2013.
Cui, X., T. Vinar, B. Brejova, D. Shasha, and M. Li, "Homology search for genes", Bioinformatics 23, i97-i103, 2007.

D

D'Alessio, M., R. Nordeste, A.C. Doxey, and T.C. Charles, "Transcriptome analysis of polyhydroxybutyrate cycle mutants reveals discrete loci connecting nitrogen utilization and carbon storage in Sinorhizobium meliloti", mSystems. 2:e00035-17, 2017.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, L. Wang, and L. Zhang, "Computing distances between evolutionary trees", In Handbook in Combinatorial Optimization, 1999.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, "On distances between phylogenetic trees", Proc. 8th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'97), New Orleans, 1997.
DasGupta, B., T. Jiang, S. Kannan, M. Li, and Z. Sweedyk, "On the complexity and approximation of syntenic distance", In Proc. 1st Symp. on Computational Molecular Biology (RECOMB'97) Santa Fe, 1997.
DasGupta, B., X. He, M. Li, J. Tromp, and L. Zhang, "Nearest neighbor interchange and related distances", Encyclopedia of Algorithms, Springer, 2014.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, "On computing the neares t neighbor interchange distance", in D.Z. Du, P.M. Pardalos and J. Wang (eds.), Proceedings of the DIMACS Workshop on Discrete Problems with Medical Applications, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, AmericanMathematical Society, Vol. 55, pp. 125-143, 2000.
DasGupta, B., X. He, T. Jiang, M. Li, and J. Tromp, "On the linear-cost subtree-transfer distance between phylogenetic trees", Algorithmica, 25, 176-195, 1999.
DasGupta, B., T. Jiang, S. Kannan, M. Li, and Z. Sweedyk, "On the complexity and approximation of syntenic distance", Discrete Applied Mathematics (special issue in computational biology), 88:1-3,59-82, 1998.
Deng, X., G. Li, Z. Li, B. Ma, and L. Wang, " Genetic Design of Drug without Side Effects", SIAM Journal on Computing 32(4): 1073-1090, 2003.
Deng, X., G. Li, Z. Li, B. Ma, and L. Wang, " A PTAS for Distinguishing (Sub)string Selection", The 29th International Colloquium on Automata, Languages, and Programming. 740-751, 2002.
Dexter, D., and D.G. Brown, "Fast half-sibling population reconstruction: theory and algorithms", Algorithms for Molecular Biology 8: 20, 2013.
Doxey, A.C., M.J. Mansfield, and B. Lobb, "Exploring the evolution of virulence factors through bioinformatic data mining", mSystems. 4:e00162-19, 2019.
Doxey, A.C., M.J. Mansfield, and C. Montecucco, "Discovery of novel bacterial toxins by genomics and computational biology", Toxicon. 147:2-12, 2018.
Doxey, A.C., D. Kurtz, L. Sauder, M.D.J. Lynch, and J.D. Neufeld, "Aquatic metagenomes implicate Thaumarchaeaota in global cobalamin production", ISME Journal. 9:461-71, 2015.
Doxey, A.C., and B.J. McConkey, "Prediction of molecular mimicry candidates in human pathogenic bacteria", Virulence. 4:453-66, 2013.
Doxey, A.C., Z. Cheng, B.A. Moffatt, and B.J. McConkey, "Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d", BMC Structural Biology. 10:23, 2010.
Doxey, A.C., M.D.J. Lynch, K.M. Muller, E.M. Meiering, and B.J. McConkey, "Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster", BMC evolutionary biology, 8:316, 2008.
Doxey, A.C., M.W. Yaish, B.A. Moffatt, M. Griffith, and B.J. McConkey, "Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states", Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ, 2007.
Doxey, A.C., M.W. Yaish, M. Griffith, and B.J. McConkey, "Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions", Nature biotechnology, 24:852, 2006.
Duncker, B.P., I.N. Chesnokov, and B.J. McConkey, "The origin recognition complex protein family", Genome biology.10:214, 2009.

E

Eyal, E., R. Najmanovich, B.J. McConkey, M. Edelman, and V. Sobolev, "Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins", Journal of computational chemistry. 25:712-724, 2004.

G

Gao, X., D. Bu, S. Li, M. Li, and J. Xu, "Consensus contact prediction by linear programming", CSB'2007. San Diego, CA, 2007.
Gao, X., D. Bu, S.C. Li, J. Xu, and M. Li, "FragQA: predicting local fragment quality of a sequence-structure alignment", In GIW'2007. Best paper award. Singapore, 2007.
Gao, X., D. Bu, J. Xu, and M. Li, "Improving consensus contact prediction via server correlation reduction", BMC Structural Biology. 9:28, 1-14, 2009.
Gao, X., J. Xu, S.C. Li, and M. Li, "Predicting local quality of a sequence-structure alignment", J. Bioinform & Computat. Biol., 7:5 789-810, 2009.
Gidvani, R.D., P. Sudmant, G. Li, L.F. DaSilva, B.J. McConkey, B.P. Duncker, and B.P. Ingalls, "A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations", BMC systems biology, 6:78, 2012.
Guan, S., M. Moran, and B. Ma, "Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning", Molecular Cellular Proteomics, 2019.
Gusfield, D., Y. Frid, and D.G. Brown, "Integer programming formulations and computations solving phylogenetic and population genetic problems with missing or genotypic data", Proceedings of the 2007 Conference on Computing and Combinatorics (COCOON), 51-64, 2007.
Guturu, H., A.C. Doxey, A.M. Wenger, and G. Bejerano, "Structure-aided prediction of transcription factor complexes in conserved non-coding elements", Philosophical Transactions of the Royal Society B. 368:20130029. Co-first authors, 2013.

H

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.

I

Ibrahima, A., L. Yang, C. Johnstonc, X. Liu, B. Ma, and N.A. Magarvey, "Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery", PNAS 109:19196-19201, 2012.
Ingalls, B.P., B.P. Duncker, D.R. Kim, and B.J. McConkey, "Systems level modeling of the cell cycle using budding yeast", Cancer informatics. 3:357-70, 2007.

J

Jaitly, D., P. Kearney, G. Lin, and B. Ma, "Methods for Reconstructing the History of Tandem Repeats and their Application to the Human Genome", Invited paper, Journal of Computer and System Sciences 65(3): 494-507, 2002.
Jameson, E., A.C. Doxey, R. Airs, K.J. Purdy, J.C. Murrell, and Y. Chen, "Metagenomic datamining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems", Microbial Genomics. 2(9). (DOI 10.1099/mgen.0.000080), 2016.
Jang, R., X. Gao, and M. Li, "Towards automated structure-based assignment", RECOMB 2010, pp. 189-207. Lisbon, Portugal, vol. April 25-28 2010, 2010.
Jang, R., X. Gao, and M. Li, " Towards fully automated structure-based NMR assignment of 15N-labeled proteins from automatically picked peaks", Special Issue for RECOMB 2010, J. Comput. Biol.,18:3, 374-363, 2011.
Jiang, T., and M. Li, "Shortest common superstring", Chapter 8 in Pattern matching algorithms, pp. 237-266, 1997.
Jiang, T., and M. Li, "Optimization problems in molecular biology", In Advances in Optimization and Approximation, edited by D.Z. Du and J. Sun, Kluwer Academic Publishers, pp. 195-216, 1994.
Jiang, T., G. Lin, B. Ma, and K. Zhang, " The Longest Common Subsequence Problem for Arc-Annotated Sequences", The 11th Symposium on Combinatorial Pattern Matching. 154-165, 2000.
Jiang, T., P. Kearney, and M. Li, "Orchestrating quartets: approximation and data correction", Proc. 39th IEEE Symp. Foundation of Computer Science (FOCS'98), Palo Alto, California, pp. 416-425, 1998.
Jiang, T., and M. Li, "On the approximation of shortest common supersequences and longest common subsequences", Proc. 21st International Colloquium on Automata, Languages, and Programming (ICALP'94), pp. 191-202, 1994.
Jiang, T., and M. Li, "Approximating shortest superstrings with constraints", Proc. 3rd Workshop on Algorithms and Data Structures (WAD'93), Montreal, pp. 385-396, 1993.
Jiang, T., and M. Li, "On the complexity of learning strings and sequences", Proc. 4th ACM Conf. Computational Learning Theory (COLT'91), Santa Cruz., pp. 367-274, 1991.
Jiang, T., G. Lin, B. Ma, and K. Zhang, " The Longest Common Subsequence Problem for Arc-Annotated Sequences", Journal of Discrete Algorithms 2(2): 257-270, 2004.
Jiang, T., G. Lin, B. Ma, and K. Zhang, "A General Edit Distance between Two RNA Structures", Journal of Computational Biology 9(2): 371-388, 2002.
Jiang, T., P. Kearney, and M. Li, "A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application", SIAM J. Computing, 30:6, 1942-1961, 2001.
Jiang, T., P. Kearney, and M. Li, "Some open questions in computational molecular biology", Journal of Algorithms, 34:1(2000), 194-201; and SIGACT News, 30:3, 43-49, 1999.
Jiang, T., and M. Li, "DNA sequencing and string learning", Math. Syst. Theory, 29, 387-405, 1996.
Jiang, T., and M. Li, "On the approximation of shortest common supersequences and longest common subsequences", SIAM J. Comput., 24:5, 1122-1139, 1995.
Jiang, T., and M. Li, "Approximating shortest superstrings with constraints", Theoret. Comput. Sci., 134, 473-491, 1994.
Jiang, T., and M. Li, "On the complexity of learning strings and sequences", Theoretical Computer Science, 119, 363-371, 1993.
Jiang, T., M. Li, and D. Du, "A note on shortest common superstrings with flipping", Inform. Process. Lett., 44:4, 195-199, 1992.
Jiao, Y.S., M. Li, and J.Y. Xu, "On the k-Closest Substring and k-Consensus Pattern problems", CPM'04, Istanbul, Turkey, 2004.
Johnston, C., M. Skinnider, M. Wyatt, X. Li, L. Yang, D. Zechel, B. Ma, and N. Magarvey, "An Automated Genomes-to-Natural Products Platform (GNP)", Nature Communications. DOI: 10.1038/ncomms9421, 2015.

K

Kabashi, E., P.N. Valdmanis, P. Dion, D. Spiegelman, B.J. McConkey, C.V. Velde, J.P. Bouchard, L. Lacomblez, K. Pochigaeva, F. Salachas, et al., "TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis", Nature genetics. 40:572, 2008.
Karamichalis, R., and L. Kari, "ModMaps3D: An interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences", Bioinformatics, 2017.
Karamichalis, R., L. Kari, S. Konstantinidis, and S. Kopecki, "An investigation into inter- and intragenomic variations of graphic genomic signatures", BMC Bioinformatics, 16:246, 2015.
Kari, L., S. Konstantinidis, S. Kopecki, and S. Solis-Reyes, "Additive methods for genomic signatures", BMC Bioinformatics, 17:313, 2016.
Kari, L., K. Hill, A. Sayem, R. Karamichalis, N. Bryans, K. Davis, and N. Dattani, "Mapping the space of genomic signatures", PLOS ONE 10(5): e0119815. doi:10.1371/journal.pone.0119815, 2015.
Kearney, P., J.I. Munro, and D. Phillips, "Efficient generation of uniform samples from phylogenetic trees", Proceedings of the 2003 Workshop on Algorithms in Bioinformatics (WABI), pp 177-189, 2003.
Kearney, P., M. Li, J. Tsang, and T. Jiang, "Recovering branches on the tree of life: an approximation algorithm", Proc. 10th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'99), pp. 537-546, 1999.
Kececioglu, J., M. Li, and J. Tromp, "Reconstructing a DNA sequence from erroneous copies", Proc. 6th International Workshop on Algorithmic Learning Theory (ALT'95), Fukuoka, Japan, pp. 151-152. , 1995.
Kececioglu, J., M. Li, and J. Tromp, "Reconstucting a DNA sequence from erroneous copies", Theoretical Computer Science, 185:1, 3-13, 1997.
Keich, U., M. Li, B. Ma, and J. Tromp, "On spaced seeds for similarity search", Discrete Applied Math.138, 253-263, 2004.
Kim, D.R., R.D. Gidvani, B.P. Ingalls, B.P. Duncker, and B.J. McConkey, "Differential chromatin proteomics of the MMS-induced DNA damage response in yeast", Proteome science, 9:62, 2011.
Kisman, D., M. Li, B. Ma, and L. Wang, "tPatternHunter: Gapped, Fast and Sensitive Translated Homology Search", Bioinformatics, 21:4, 542-544, 2005.

L

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.

M

Ma, B., "De novo Peptide Sequencing", Proteome Informatics, 15-38. Royal Society of Chemistry Publishing, 2016.
Ma, B., and G. Lajoie, "De Novo Interpretation of Tandem Mass Spectra", In The Current Protocol in Bioinformatics. John Wiley & Sons, 2009.
Ma, B., "Peptide De Novo Sequencing with MS/MS", In Encyclopedia of Algorithms. Springer, 2008.
Ma, B., and X. Wu, " Maximum network flow of multiple description codes", First Workshop on Network Coding, Theory and Applications, 2005.
Ma, B., and L. Zhang, " Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Reconstruction of Ancestral States", The 7th Asia Pacific Bioinformatics Conference. 133-144, 2009.
Ma, B., and X. Sun, " More Efficient Algorithms for Closest String and Substring", The 12th International Conference on Research in Computational Molecular Biology. 396-409, 2008.
Ma, B., and H. Yao, " Seed Optimization Is No Easier Than Optimal Golomb Ruler Design", The 6th Asia Pacific Bioinformatics Conference. 133-144, 2008.
Ma, B., " Why Greed Works for Shortest Common Superstring Problem", The 19th Annual Symposium on Combinatorial Pattern Matching. 244-254, 2008.
Ma, B., L. Wu, and K. Zhang, "Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures", First International Workshop on Bioinformatics Research and Applications. 960-967, 2005.
Ma, B., and K. Zhang, "On the Longest Common Rigid Subsequence Problem", The Sixteenth Annual Symposium on Combinatorial Pattern Matching. 11-20, 2005.
Ma, B., and K. Zhang, "The similarity metric and the distance metric", The 6th Atlantic Symposium on Computational Biology and Genome Informatics, 2005.
Ma, B., Z. Wang, and K. Zhang, " Alignment between Two Multiple Alignments", The 14th Symposium on Combinatorial Pattern Matching. 254-265, 2003.
Ma, B., K. Zhang, and C. Liang, " An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum", The 14th Symposium on Combinatorial Pattern Matching. 266-278, 2003.
Ma, B., K. Zhang, G. Lajoie, A. Doherty-Kirby, C. Liang, and M. Li, "PEAKS: A powerful software tool for de novo sequencing of peptides from MS/MS data", 50th ASMS Conference, 2002.
Ma, B., " A Polynomial Time Approximation Scheme for the Closest Substring Problem", The 11th Symposium on Combinatorial Pattern Matching. 99-107, 2000.
Ma, B., L. Wang, and M. Li, "Fixed topology alignment with recombination", 9th Ann. Conf. on Combinatorial Pattern Matching, (CPM'98), 1998.
Ma, B., M. Li, and L. Zhang, "On Reconstructing Species Trees from Gene trees in Term of Duplications and Losses", The 2nd International Conference on Computational Molecular Biology. 182-191, 1998.
Ma, B., "Novor: Real-Time Peptide de Novo Sequencing Software", Journal of American Society of Mass Spectrometry 26 (11), 1885-1894, 2015.
Ma, B., and R. Johnson, "De Novo Sequencing and Homology Searching. Molecular & Cellular Proteomics 11", DOI 10.1074/mcp.O111.014902, 2012.
Ma, B., and X. Sun, " More Efficient Algorithm for Closest String and Substring Problems", SIAM J. Computing 39(4): 1432-1443, 2009.
Ma, B., "Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics", Journal of Computer Science and Technology 25(1): 107-123, 2009.
Ma, B., and H. Yao, "Seed Optimization for I.I.D. Similarities Is No Easier than Optimal Golomb Ruler Design", Information Processing Letter 109(19): 1120-1124, 2009.
Ma, B., "Why Greed Works for Shortest Common Superstring Problem", Theoretical Computer Science, 2009.
Ma, B., L. Xin, and K. Zhang, " A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method", Journal of Combinatorial Optimization 16(3): 293-306, 2008.
Ma, B., L. Wang, and M. Li, " Near Optimal Multiple Alignment within a Band in Polynomial Time", Journal of Computer Science and System Sciences 73(6): 997-1011, 2007.
Ma, B., and M. Li, "On the Complexity of Spaced Seeds", Journal of Computer Science and System Sciences 73(7): 1024-1034, 2007.
Ma, B., L. Wu, and K. Zhang, " Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures", Journal of Bioinformatics and Computational Biology 4(3): 709-720, 2006.
Ma, B., K. Zhang, and C. Liang, "An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum", Journal of Computer and System Sciences (70): 418-430, 2005.
Ma, B., K. Zhang, C. Hendrie, C. Liang, M. Li, A. Doherty-Kirby, and G. Lajoie, "PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS", Rapid Communications in Mass Spectrometry 20: 2337-2342, 2003.
Ma, B., J. Tromp, and M. Li, " PatternHunter: Faster and More Sensitive Homology Search", Bioinformatics 18: 440-445, 2002.
Ma, B., L. Wang, and K. Zhang, "Computing Similarity between RNA Structures", Theoretical Computer Sciences 276(1-2): 111-132, 2002.
Ma, B., L. Wang, and M. Li, "Fixed topology alignment with recombination", Discrete Applied Math. (Special Issue on Computational Molecular Biology), 104, 281-300, 2002.
Ma, B., M. Li, and L. Zhang, "From gene trees to species trees", SIAM J. Comput.,30:3, 729-752, 2000.
Ma, B., L. Wang, and L. Zhang, " Fitting Distances by Tree Metrics with Incremental Errors", Journal of Combinatorial Optimization 3: 213-225, 1999.
Mansfield, M.J., T. Wentz, S. Zhang, E.J. Lee, M. Dong, S. Sharma, and A.C. Doxey, "Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins", Scientific Reports. 9: 1634, 2019.
Mansfield, M., J. Adams, and A.C. Doxey, "Botulinum neurotoxin homologs in non-Clostridium species", FEBS Letters. 589:342-8, 2015.
Marinier, E., D.G. Brown, and B.J. McConkey, "Pollux: platform-independent error correction of single and mixed genomes", BMC Bioinformatics 16:10, 2015.
Masella, A.P., A.K. Bartram, J. Truszkowski, D.G. Brown, and J.D. Neufeld, "PANDAseq: paired-end assembler for illumina sequences", BMC Bioinformatics volume 13, Article number: 31, 2012.
Matthews, L.A., R. Selvaratnam, D.R. Jones, M. Akimoto, B.J. McConkey, G. Melacini, B.P. Duncker, and A. Guarn, "A novel non-canonical forkhead-associated (FHA) domain-binding interface mediates the interaction between Rad53 and Dbf4 proteins", Journal of Biological Chemistry, 289:2589-2599, 2014.
McConkey, B.J., "Theory and Applications of Proteomics", Academic Press, 2011.
McConkey, B.J., V. Sobolev, and M. Edelman, "Discrimination of native protein structures using atom-atom contact scoring", Proceedings of the National Academy of Sciences,100:3215-3220, 2003.
McConkey, B.J., V. Sobolev, and M. Edelman, "Quantification of protein surfaces volumes and atom-atom contacts using a constrained Voronoi procedure", Bioinformatics,18:1365-1373, 2002.
McConkey, B.J., P.G. Mezey, D.G. Dixon, and B.M. Greenberg, "Fractional simplex designs for interaction screening in complex mixtures", Biometrics, 56:824-832, 2000.
Mendler, K., H. Chen, D.H. Parks, B. Lobb, L.A. Hug, and A.C. Doxey, "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life", Nucleic Acids Research. 47: 4442-4448, 2019.
Meshram, M., S. Naderi, B.J. McConkey, B. Ingalls, J. Scharer, and H. Budman, "Modeling the coupled extracellular and intracellular environments in mammalian cell culture", Metabolic engineering, 19:57-68, 2013.
Meshram, M., S. Naderi, B.J. McConkey, H. Budman, J. Scharer, and B.P. Ingalls, "Population-based modeling of the progression of apoptosis in mammalian cell culture", Biotechnology and bioengineering 109:1193-1204, 2012.
Mooney, S.M., V. Talebian, M.K. Jolly, D. Jia, M. Gromala, H. Levine, and B.J. McConkey, "The GRHL2/ZEB feedback loop--A key axis in the regulation of EMT in breast cancer", Journal of cellular biochemistry, 118:2559-2570, 2017.

N

Nascimento, F.X., M.J. Rossi, C.R.F.S. Soares, B.J. McConkey, and B.R. Glick, "New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny evolution and ecological significance", PLoS One, 9:e99168, 2014.

P

Petrenko, P., D.A. Kurtz, B. Lobb, J.D. Neufeld, and A.C. Doxey, "MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes", BMC Biology. 13:92, 2015.
Petrenko, P., and A.C. Doxey, "mimicMe: a webserver for prediction and analysis of host-like proteins in microbial pathogens", Bioinformatics. 31:590-592, 2014.

Q

Qian, J., S.C. Li, D. Bu, M. Li, and J. Xu, "Finding compact structural motifs in many proteins", CPM, 2007.

R

Randhawa, G., K. Hill, L. Kari, and B.M.C. Genomics, "ML-DSP: Machine learning with Digital Signal Processing for ultrafast, accurate and scalable DNA sequence classification at all taxonomic levels", BMC Genomics, 20:267, 2019.

S

Shan, B., G. Lajoie, B. Ma, and K. Zhang, " Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry", The 5th Asia Pacific Bioinformatics Conference. 297-306, 2007.
Shan, B., K. Zhang, B. Ma, C. Zhang, and G. Lajoie, " An Algorithm for Determining Glycan Structures from MS/MS Spectra", International Conference on Bioinformatics and its Applications, 2004. In Advances in Bioinformatics and Its Applications, World Scientific, 414-425, 2005.
Shan, B., G. Lajoie, B. Ma, and K. Zhang, " Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry", Journal of Bioinformatics and Computational Biology 6(1): 77-91, 2008.
Shen, J., V. Pagala, A. Breuer, J. Peng, B. Ma, and X. Wang, "Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra", Journal of Proteome Research, 2018.
Solis-Reyes, S., M. Avino, A. Poon, and L. Kari, "An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-I genomes", PLOS ONE 13(11): e0206409, 2018.
Stearns, J.C., O.Z. Woody, B.J. McConkey, and B.R. Glick, "Effects of bacterial ACC deaminase on Brassica napus gene expression", Molecular Plant-Microbe Interactions, 25:668-676, 2012.
Sun, W., G. Lajoie, B. Ma, and K. Zhang, " A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry", International Symposium on Bioinformatics Research and Applications. 320-330, 2015.
Sun, W., Y. Liu, G. Lajoie, B. Ma, and K. Zhang, "An Improved Approach for N-linked Glycan Structure Identification from HCD MS/MS Spectra", IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB.2017.2701819, 2017.
Sun, W., M. Kuljanin, P. Pittock, B. Ma, K. Zhang, and G. Lajoie, "An Effective Approach for Glycan Structure De Novo Sequencing from HCD Spectra", IEEE transactions on nanobioscience 15 (2), 177-184, 2016.
Sun, S., F. Yang, Q. Yang, H. Zhang, Y. Wang, D. Bu, and B. Ma, "MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions", Journal of Proteome Research. DOI: 10.1021/pr300235v, 2012.

T

Tang, T., J. Xu, and M. Li, "Discovering sequence-structure motifs from protein segments and two applications", PSB'05. Hawaii, 2005.
Tran, N.H., R. Qiao, L. Xin, X. Chen, C. Lui, X. Zhang, B. Shan, A. Ghodsi, and M. Li, "Deep learning enables de novo peptide sequencing from data-independent acquisition mass spectrometry", Nature Methods, vol. Vol 16, 2019.
Tran, N.H., X. Zhang, and M. Li, " Deep Omics", Proteomics. 18:2. 1700319. (Cover page story), 2018.
Tran, N.H., X. Zhang, L. Xin, B. Shan, and M. Li, "De novo peptide sequencing by deep learning", Proc. National Academy of Sciences of the USA, 114(31), 8247-8252, 2017.
Tran, N.H., M.Z. Rahman, L. He, L. Xin, B. Shan, and M. Li, "Complete de novo assembly of monoclonal antibody sequences", Nature, Scientific Reports 6, doi:10.1038/srep31730, 2016.
Truszkowski, J., Y. Hao, and D.G. Brown, "Towards a practical O(n log n) phylogeny algorithm", Algorithms in Molecular Biology 7:32, 2012.

V

Vision, T.J., D.G. Brown, D.B. Shmoys, R.T. Durrett, and S.D. Tanksley, "Selective mapping: A strategy for optimizing the construction of linkage map", Genetics 155: 407-420, 2000.
Vision, T.J., D.G. Brown, and S.D. Tanksley, "The origins of genomic duplications in Arabidopsis", Science 290: 2114-2117, 2000.
Vogl, C., J. Badger, P. Kearney, M. Li, M. Clegg, and T. Jiang, "Probabilistic analysis indicates discordant gene trees in chloroplast evolution", J. Mol. Evol., 56:3, 330-340, 2003.

W

Wang, T., and B. Ma, "Adjacent Y-ion Ratio Distributions and Its Application in Peptide Sequencing", The 14th Asia Pacific Bioinformatics Conference, Yokohama, Japan, 2018.
Wang, T., and B. Ma, "Adjacent Y-ion Ratio Distributions and Its Application in Peptide Sequencing", IEEE/ACM Transactions on Computational Biology and Bioinformatics 16 (1), 43-51, 2018.
Wang, H.C., J. Badger, P. Kearney, and M. Li, "Analysis of codon usage patterns of microbial genomes with self-organizing map: methods and applications to genome exploration", Mol. Biol. Evol., 18:5, 792--800, 2001.
Wang, L., B. Ma, and M. Li, " Fixed Topology Alignment with Recombination", Discrete Applied Mathematics (special issue on computational molecular biology), 104: 281-300, 2000.
Whelan, F.J., C.J. Meehan, G.B. Golding, B.J. McConkey, and D.M.E. Bowdish, "The evolution of the class A scavenger receptors", BMC evolutionary biology, 12:227, 2012.
Woody, O.Z., and B.J. McConkey, "Detection and analysis of functional specialization in duplicated genes", Gene Duplication, 37-58, 2011.
Woody, O.Z., A.C. Doxey, and B.J. McConkey, "Assessing the evolution of gene expression using microarray data", Evolutionary Bioinformatics. 4:EBO.S628, 2008.
Wooley, J., M. Li, L. Wong, and JBCB, " The first decade", Journal of Bioinformatics and Computational Biology 12:03, 2014.
Wu, Z., G. Lajoie, and B. Ma, " MSDash: Mass Spectrometry Database and Search", The 7th Annual International Conference on Computational Systems Bioinformatics. 63-71, 2008.

X

Xin, L., B. Ma, and K. Zhang, " A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method", The 13th Annual International Computing and Combinatorics Conference. 40-50, 2007.
Xu, C., and B. Ma, "Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing", Computational System Bioinformatics Conference. 361-369, 2006.
Xu, J., L. Yu, and M. Li, "Consensus fold recognition by predicted model quality", APBC'05, Singapore, 2005.
Xu, E.W., D.G. Brown, and P. Kearney, "The use of functional domains to improve transmembrane protein topology prediction", Proceedings of APBC, 105-116, 2005.
Xu, J., D.G. Brown, M. Li, and B. Ma, " Optimizing Multiple Spaced Seeds for Homology Search", The 15th Symposium on Combinatorial Pattern Matching. 47-58, 2004.
Xu, J., M. Li, G. Lin, D. Kim, and Y. Xu, "Protein threading by linear programming", PSB'03, Hawaii, pp 264-275, 2003.
Xu, J., M. Li, D. Kim, and Y. Xu, "RAPTOR: optimal protein threading by linear programming", Journal of Bioinformatics and Computational Biology,1:1, 95-118, 2003.
Xu, J., D.G. Brown, M. Li, and B. Ma, " Optimizing Multiple Spaced Seeds for Homology Search", Journal of Computational Biology. 13(7): 1355-1368, 2006.
Xu, C., and B. Ma, " Review of software for computational peptide identification from MS/MS data", Drug Discovery Today 11(13/14): 595-600, 2006.
Xu, E.W., P. Kearney, and D.G. Brown, "The use of functional domains to improve transmembrane protein topology prediction", Journal of Bioinformatics and Computational Biology 4:109-113, 2006.
Xu, J., M. Li, and Y. Xu, "Protein Threading by Linear Programming: Theoretical Analysis and Computational Results", Journal of Combinatorial Optimization. 8:4, 403--418, 2004.
Xu, J., and M. Li, "Assessing RAPTOR's new linear programming approach for fold recognition in CAFASP3", PROTEINS: Structure, Function, and Genetics, 53(S6):579-584. Invited paper by CASP5 organizer, 2003.

Y

Yang, L., A. Ibrahim, C.W. Johnston, M.A. Skinnider, B. Ma, and N.A. Magarvey, "Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm", Chemistry & Biology 22 (9), 1259-1269, 2015.
Yao, D., J. Wang, Y. Lu, N. Noble, H. Sun, X. Zhu, N. Lin, D. Payan, M. Li, and K. Qu, "PathwayFinder: paving the way towards automatic pathway extraction", In The Second Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand, 2004.
Yuasa, S., Z. Chen, B. Ma, and L. Wang, "Designing and Implementing Algorithms for the Closest String Problem", International Workshop on Frontiers in Algorithmics. 79-90, 2017.

Z

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.

Publications search