Book
Brown, D.G., M. Li, and B. Ma , "The Homology Search Methods " , In The Practical Bioinformatician, edited by Limsoon Wong. World Scientific , 2004.
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.
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.
Conference Paper
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 , "Protein Structure by Semidefinite Facial Reduction " , RECOMB 2012. pp. 1-11, Barcelona, Spain , 2012.
Conference Proceedings
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.
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.
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.
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.
Xu, J., M. Li, G. Lin, D. Kim, and Y. Xu , "Protein threading by linear programming " , PSB'03, Hawaii, pp 264-275 , 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.
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.
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.
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.
Journal Article
Magazine Article
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Boucher, C., and B. Ma , "Closest String with Outliers " , The 9th Asia Pacific Bioinformatics Conference. BMC Bioinformatics 12(Suppl 1): S55 , 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.
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.
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.
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.
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.
Kisman, D., M. Li, B. Ma, and L. Wang , "tPatternHunter: Gapped, Fast and Sensitive Translated Homology Search " , Bioinformatics, 21:4, 542-544 , 2005.
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 , "Homology search methods " , In The Practical Bioinformatician. L. Wong Ed. World Scientific, 217-244 , 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.
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.
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.
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.
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.
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.
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.