Publications

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2020

Brown, D.G., and M. Owen, "Mean and Variance of Phylogenetic Trees", Systematic Biology, vol. 69, issue 1, 01/2020.

2019

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.
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.
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.
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.
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.
Doxey, A.C., M.J. Mansfield, and B. Lobb, "Exploring the evolution of virulence factors through bioinformatic data mining", mSystems. 4:e00162-19, 2019.
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.
Guan, S., M. Moran, and B. Ma, "Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning", Molecular Cellular Proteomics, 2019.
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.

2018

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.
Tran, N.H., X. Zhang, and M. Li, " Deep Omics", Proteomics. 18:2. 1700319. (Cover page story), 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.
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.
Doxey, A.C., M.J. Mansfield, and C. Montecucco, "Discovery of novel bacterial toxins by genomics and computational biology", Toxicon. 147:2-12, 2018.
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.

2017

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.
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.
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.
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.
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.
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.
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.
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.
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.

2016

Ma, B., "De novo Peptide Sequencing", Proteome Informatics, 15-38. Royal Society of Chemistry Publishing, 2016.
Kari, L., S. Konstantinidis, S. Kopecki, and S. Solis-Reyes, "Additive methods for genomic signatures", BMC Bioinformatics, 17:313, 2016.
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.
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.
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.
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.
Lobb, B., and A.C. Doxey, "Novel function discovery through sequence and structural data mining", Current Opinion in Structural Biology. 38:53-61, 2016.
Chen, Z., B. Ma, and L. Wang, "Randomized Fixed-Parameter Algorithms for the Closest String Problem", Algorithmica 74(1): 466-484, 2016.

2015

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.
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.
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.
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.
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.
Mansfield, M., J. Adams, and A.C. Doxey, "Botulinum neurotoxin homologs in non-Clostridium species", FEBS Letters. 589:342-8, 2015.
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.
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.
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.
Ma, B., "Novor: Real-Time Peptide de Novo Sequencing Software", Journal of American Society of Mass Spectrometry 26 (11), 1885-1894, 2015.
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.
Marinier, E., D.G. Brown, and B.J. McConkey, "Pollux: platform-independent error correction of single and mixed genomes", BMC Bioinformatics 16:10, 2015.
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.

2014

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.
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.
Cui, X., S.C. Li, L. He, and M. Li, " Fingerprinting protein structures effectively and efficieintly", Bioinformatics,30:7 949-955, 2014.
Wooley, J., M. Li, L. Wong, and JBCB, " The first decade", Journal of Bioinformatics and Computational Biology 12:03, 2014.
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.
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.
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.
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.
DasGupta, B., X. He, M. Li, J. Tromp, and L. Zhang, "Nearest neighbor interchange and related distances", Encyclopedia of Algorithms, Springer, 2014.
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.
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.

2013

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.
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.
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.
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.
Brown, D.G., and J. Truszkowski, "Fast error-tolerant quartet phylogeny algorithms", Theoretical Computer Science 483: 104-114, 2013.
Dexter, D., and D.G. Brown, "Fast half-sibling population reconstruction: theory and algorithms", Algorithms for Molecular Biology 8: 20, 2013.
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.
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.
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.
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.
Doxey, A.C., and B.J. McConkey, "Prediction of molecular mimicry candidates in human pathogenic bacteria", Virulence. 4:453-66, 2013.
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.
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.
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.
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.
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.

2012

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Ma, B., and R. Johnson, "De Novo Sequencing and Homology Searching. Molecular & Cellular Proteomics 11", DOI 10.1074/mcp.O111.014902, 2012.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Truszkowski, J., Y. Hao, and D.G. Brown, "Towards a practical O(n log n) phylogeny algorithm", Algorithms in Molecular Biology 7:32, 2012.

2011

Brown, D.G., and J. Truszkowski, "Fast error-tolerant quartet phylogeny algorithms", Proceedings of the Symposium on Combinatorial Pattern Matching (CPM), 147-161, 2011.
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.
Brown, D.G., and J. Truszkowski, "Toward a practical O(n log n) quartet phylogeny algorithm", Proceedings of WABI, 14-25, 2011.
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.
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.
Bu, F., X. Zhu, and M. Li, "A New Multiword Expression Metric and Its Applications", J. Comput. Sci. Tech.,26:1, 3-13, 2011.
Boucher, C., and B. Ma, "Closest String with Outliers", The 9th Asia Pacific Bioinformatics Conference. BMC Bioinformatics 12(Suppl 1): S55, 2011.
Woody, O.Z., and B.J. McConkey, "Detection and analysis of functional specialization in duplicated genes", Gene Duplication, 37-58, 2011.
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.
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.
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.
Ho, R., and B.J. McConkey, "Modulating glycosylation of recombinant monoclonal antibodies for therapeutic applications", Current topics in biotechnology. 6:57-69, 2011.
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.
McConkey, B.J., "Theory and Applications of Proteomics", Academic Press, 2011.

2010

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.
Brown, D.G., and T. Berger-Wolf, "Discovering kinship through small subsets", Proceedings of WABI, 111-123, 2010.
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.
Li, M., " Can we determine a protein structure quickly?", J. Comput. Sci. Tech. 25:1 95-106, 2010.
Zhao, Y., B. Alipanahi, S.C. Li, and M. Li, " Protein secondary structure prediction using NMR chemical shift data", JBCB 8:5, 2010.
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.
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.
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.
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.
Bansal, N., M. Lewenstein, B. Ma, and K. Zhang, "On the Longest Common Rigid Subsequence Problem", Algorithmica 56(2): 270-280, 2010.
Cheng, Z., B.J. McConkey, and B.R. Glick, "Proteomic studies of plant-bacterial interactions", Soil Biology and Biochemistry, 42:1673-1684, 2010.
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.
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.

2009

Ma, B., and G. Lajoie, "De Novo Interpretation of Tandem Mass Spectra", In The Current Protocol in Bioinformatics. John Wiley & Sons, 2009.
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.
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.
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.
Alipanahi, B., X. Gao, E. Karakoc, L. Donaldson, and M. Li, "PICKY: a novel SVM-based NMR spectra peak picking method", ISMB, 2009.
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.
Ma, B., and X. Sun, " More Efficient Algorithm for Closest String and Substring Problems", SIAM J. Computing 39(4): 1432-1443, 2009.
Chen, S., B. Ma, and K. Zhang, " On the Similarity Metric and the Distance Metric", Theoretical Computer Science 410(24-25): 2365-2376, 2009.
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.
Ma, B., "Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics", Journal of Computer Science and Technology 25(1): 107-123, 2009.
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.
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.
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.
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.
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.
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.
Duncker, B.P., I.N. Chesnokov, and B.J. McConkey, "The origin recognition complex protein family", Genome biology.10:214, 2009.
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.
Ma, B., "Why Greed Works for Shortest Common Superstring Problem", Theoretical Computer Science, 2009.

2008

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.
Ma, B., "Peptide De Novo Sequencing with MS/MS", In Encyclopedia of Algorithms. Springer, 2008.
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.
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.
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.
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.
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.
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.
Zhang, J., X. Gao, J. Xu, and M. Li, "Rapid and accurate side chain prediction with local backbone information", RECOMB'08, 2008.
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.
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.
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.
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.
Li, S.C., D. Bu, J. Xu, and M. Li, "Designing succinct structural alphabet", Bioinformatics, ISMB Special Issue, 2008.
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.
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.
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.
Lin, H., Z. Zhang, M.Q. Zhang, B. Ma, and M. Li, "ZOOM! Zillions of oligos mapped", Bioinformatics. 24:21, 2431-2437, 2008.

2007

Gao, X., D. Bu, S. Li, M. Li, and J. Xu, "Consensus contact prediction by linear programming", CSB'2007. San Diego, CA, 2007.
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.
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.
Boucher, C., D.G. Brown, and P. Church, "A graph clustering approach to weak motif recognition", Proceedings of WABI, 149-160, 2007.
Zhang, J., X. Chen, and M. Li, "Calculating exact p-value for structured motif", CPM, 2007.
Qian, J., S.C. Li, D. Bu, M. Li, and J. Xu, "Finding compact structural motifs in many proteins", CPM, 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.
Cui, X., T. Vinar, B. Brejova, D. Shasha, and M. Li, "Homology search for genes", ISMB, 2007.
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.
Zhang, Z., H. Lin, and M. Li, "MANGO: a new approach to multiple sequence alignment", CSB'2007. Best paper award. San Diego, CA, 2007.
Liu, J., B. Ma, and K. Zhang, " An Algorithm for Searching RNA Motifs in Genomic Sequences", Biomolecular Engineering 24: 343-350, 2007.
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.
Csuros, M., and B. Ma, " Rapid Homology Search with Neighbor Seeds", Algorithmica. 48(2): 187-202, 2007.
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.
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.
Cui, X., T. Vinar, B. Brejova, D. Shasha, and M. Li, "Homology search for genes", Bioinformatics 23, i97-i103, 2007.
Ma, B., and M. Li, "On the Complexity of Spaced Seeds", Journal of Computer Science and System Sciences 73(7): 1024-1034, 2007.
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.
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.

2006

Xu, C., and B. Ma, "Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing", Computational System Bioinformatics Conference. 361-369, 2006.
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.
Li, M., B. Ma, and L. Zhang, "Superiority and complexity of the spaced seeds", The 17th Symposium on Discrete Algorithms. 444-453, 2006.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2005

Ma, B., and X. Wu, " Maximum network flow of multiple description codes", First Workshop on Network Coding, Theory and Applications, 2005.
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.
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.
Brejova, B., D.G. Brown, M. Li, and T. Vinar, "Clone of ExonHunter: a comprehensive approach to gene finding", ISMB'2005 Michigan, 2005.
Xu, J., L. Yu, and M. Li, "Consensus fold recognition by predicted model quality", APBC'05, Singapore, 2005.
Tang, T., J. Xu, and M. Li, "Discovering sequence-structure motifs from protein segments and two applications", PSB'05. Hawaii, 2005.
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.
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.
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.
Ma, B., and K. Zhang, "The similarity metric and the distance metric", The 6th Atlantic Symposium on Computational Biology and Genome Informatics, 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.
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.
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.
Hudek, A.K., and D.G. Brown, "Ancestral sequence alignment under optimal conditions", BMC Bioinformatics 6:273, 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.
Brejova, B., D.G. Brown, M. Li, and T. Vinar, "ExonHunter: a comprehensive approach to gene finding", Bioinformatics 21:S1, i57-i65, 2005.
Liu, J., and M. Li, "Finding cancer biomarkers from mass spectrometry data by decision lists", Journal of Computational Biology. 12:7, 969-977, 2005.
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.
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.
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.
Kisman, D., M. Li, B. Ma, and L. Wang, "tPatternHunter: Gapped, Fast and Sensitive Translated Homology Search", Bioinformatics, 21:4, 542-544, 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.

2004

Brown, D.G., M. Li, and B. Ma, "The Homology Search Methods", In The Practical Bioinformatician, edited by Limsoon Wong. World Scientific, 2004.
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.
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.
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.
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.
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.
Jiao, Y.S., M. Li, and J.Y. Xu, "On the k-Closest Substring and k-Consensus Pattern problems", CPM'04, Istanbul, Turkey, 2004.
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.
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.
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.
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.
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.
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.
Consortium, R. Genome Seq, and B. Ma, "Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution", Nature 428: 493-521, 2004.
Brown, D.G., M. Li, and B. Ma, "Homology search methods", In The Practical Bioinformatician. L. Wong Ed. World Scientific, 217-244, 2004.
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.
Keich, U., M. Li, B. Ma, and J. Tromp, "On spaced seeds for similarity search", Discrete Applied Math.138, 253-263, 2004.
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.
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.
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.
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.
Li, M., X. Chen, X. Li, B. Ma, and P. Vitanyi, "The Similarity Metric", IEEE Transaction Information Theory 50: 3250-3264, 2004.

2003

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.
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.
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.
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.
Benson, G., and R. Page, "Algorithms in Bioinformatics", Third International Workshop, Proceedings of WABI 2003, Budapest, Hungary, 2003.
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.
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.
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.
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.
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.
Bennett, C.H., M. Li, and B. Ma, "Chain letters and evolutionary histories", Scientific American, 288:6200 (feature article), 76-81, 2003.
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.
Lanctot, J. K., M. Li, B. Ma, S. Wang, and L. Zhang, "Distinguishing String Search Problems", Information and Computation 185: 41-55, 2003.
Zhang, L., B. Ma, L. Wang, and Y. Xu, "Greedy Method for Inferring Tandem Duplication History", Bioinformatics. 19(12): 1497-1504, 2003.
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.
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.

2002

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.
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.
Zhang, L., B. Ma, and L. Wang, "Efficient Methods for Inferring Tandem Duplication History", The 2nd Workshop on Algorithms in Bioinformatics. 97-111, 2002.
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.
Li, M., B. Ma, and L. Wang, " On the Closest String and Substring Problems", Journal of the ACM 49(2): 157-171, 2002.
Ma, B., J. Tromp, and M. Li, " PatternHunter: Faster and More Sensitive Homology Search", Bioinformatics 18: 440-445, 2002.
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.
Heffelfinger, G.S., "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling", OMICS, 6:4, 305-330, 2002.
Ma, B., L. Wang, and K. Zhang, "Computing Similarity between RNA Structures", Theoretical Computer Sciences 276(1-2): 111-132, 2002.
Chen, X., M. Li, B. Ma, and J. Tromp, "DNACompress: fast and effective DNA sequence compression", Bioinformatics. 18, 1696-1698, 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.
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.
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.
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.
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.

2001

Lin, G., B. Ma, and K. Zhang, " Edit Distance between Two RNA Structures", The 5th Conference on Computational Molecular Biology. 211-220, 2001.
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.
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.
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.
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.
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.
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.

2000

Ma, B., " A Polynomial Time Approximation Scheme for the Closest Substring Problem", The 11th Symposium on Combinatorial Pattern Matching. 99-107, 2000.
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.
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.
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.
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.
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.
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.
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.
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.
Ma, B., M. Li, and L. Zhang, "From gene trees to species trees", SIAM J. Comput.,30:3, 729-752, 2000.
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.
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.

1999

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.
Zhang, K., L. Wang, and B. Ma, " Computing Similarity between RNA Structures", The 10th Symposium on Combinatorial Pattern Matching. 281-293, 1999.
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.
Li, M., B. Ma, and L. Wang, "Finding similar regions in many sequences", Proc. 31st ACM Symp. Theory of Computing (STOC'99), Atlanta, 1999.
Berry, V., T. Jiang, P. Kearney, M. Li, and T. Wareham, "Quartet cleaning: improved algorithms and simulations", ESA'99, Prague, 1999.
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.
Ma, B., L. Wang, and L. Zhang, " Fitting Distances by Tree Metrics with Incremental Errors", Journal of Combinatorial Optimization 3: 213-225, 1999.
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.
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.
Li, M., and L. Zhang, "Twist-rotation transformations of binary trees and arithmetic expressions", Journal of Algorithms, 32, 155-166, 1999.

1998

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.
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.
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.
Bennett, C.H., P. Gacs, M. Li, P. Vitanyi, and W. Zurek, "Information Distance", IEEE Trans. Inform. Theory, 44:4, 1407-1423, 1998.
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.

1997

Jiang, T., and M. Li, "Shortest common superstring", Chapter 8 in Pattern matching algorithms, pp. 237-266, 1997.
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.
Kececioglu, J., M. Li, and J. Tromp, "Reconstucting a DNA sequence from erroneous copies", Theoretical Computer Science, 185:1, 3-13, 1997.

1996

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.
Jiang, T., and M. Li, "DNA sequencing and string learning", Math. Syst. Theory, 29, 387-405, 1996.
Li, M., J. Tromp, and L. Zhang, "On the nearest neighbour interchange distance between evolutionary trees", Journal of Theoretical Biology, 182, 463-467, 1996.

1995

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.
Jiang, T., and M. Li, "On the approximation of shortest common supersequences and longest common subsequences", SIAM J. Comput., 24:5, 1122-1139, 1995.

1994

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.
Li, M., and A. Viola, "Learning secondary structures of proteins", Proc. 6th International Conference on Computing and Information, Peterborough, Ontario, 1994.
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", Theoret. Comput. Sci., 134, 473-491, 1994.
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.

1993

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.
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.
Jiang, T., and M. Li, "On the complexity of learning strings and sequences", Theoretical Computer Science, 119, 363-371, 1993.

1992

Jiang, T., M. Li, and D. Du, "A note on shortest common superstrings with flipping", Inform. Process. Lett., 44:4, 195-199, 1992.

1991

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.
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.

1990

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.

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