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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., 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.
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Badger, J., P. Kearney, M. Li, J. Tsang, and T. Jiang , "Selecting the branches for an evolutionary tree: a polynomial time approximation scheme " , Journal of Algorithms, 51, 1-14 , 2004.
Bennett, C.H., P. Gacs, M. Li, P. Vitanyi, and W. Zurek , "Information Distance " , IEEE Trans. Inform. Theory, 44:4, 1407-1423 , 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.
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 B. Ma , "Closest String with Outliers " , The 9th Asia Pacific Bioinformatics Conference. BMC Bioinformatics 12(Suppl 1): S55 , 2011.
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.
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. , "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 , "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.
Bu, D., M. Li, S.C. Li, J. Qian, and J. Xu , "Finding compact structural motifs " , Theoretical Computer Science, 410:30-32, 2834-2839 , 2009.
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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, 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.
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.
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.
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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., 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 , " A PTAS for Distinguishing (Sub)string Selection " , The 29th International Colloquium on Automata, Languages, and Programming. 740-751 , 2002.
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.
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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.
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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.
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.
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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.
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.
Kisman, D., M. Li, B. Ma, and L. Wang , "tPatternHunter: Gapped, Fast and Sensitive Translated Homology Search " , Bioinformatics, 21:4, 542-544 , 2005.
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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., 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, 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., X. Chen, X. Li, B. Ma, and P. Vitanyi , "The Similarity Metric " , IEEE Transaction Information Theory 50: 3250-3264 , 2004.
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.
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, 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., 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.
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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.
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.
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.
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.
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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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.
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.
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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.
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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.
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Wooley, J., M. Li, L. Wong, and JBCB , " The first decade " , Journal of Bioinformatics and Computational Biology 12:03 , 2014.
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Xu, J., M. Li, G. Lin, D. Kim, and Y. Xu , "Protein threading by linear programming " , PSB'03, Hawaii, pp 264-275 , 2003.
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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.
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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, 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.
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.