Publications

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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.

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