TY - JOUR AU - Wang, Y. K. AU - Bashashati, A. AU - Anglesio, M. S. AU - Cochrane, D. R. AU - Grewal, D. S. AU - Ha, G. PY - 2017 DA - 2017// TI - Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes JO - Nat Genet VL - 49 UR - https://doi.org/10.1038/ng.3849 DO - 10.1038/ng.3849 ID - Wang2017 ER - TY - JOUR AU - Xia, R. AU - Lin, Y. AU - Zhou, J. AU - Geng, T. AU - Bing, F. AU - Tang, J. PY - 2018 DA - 2018// TI - Phylogenetic reconstruction for copy-number evolution problems JO - IEEE/ACM Trans Comput Biol Bioinform VL - 16 UR - https://doi.org/10.1109/TCBB.2018.2829698 DO - 10.1109/TCBB.2018.2829698 ID - Xia2018 ER - TY - JOUR AU - Toosi, H. AU - Moeini, A. AU - Hajirasouliha, I. PY - 2019 DA - 2019// TI - BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples JO - BMC Bioinform VL - 20 UR - https://doi.org/10.1186/s12859-019-2824-3 DO - 10.1186/s12859-019-2824-3 ID - Toosi2019 ER - TY - JOUR AU - Stolzer, M. AU - Siewert, K. AU - Lai, H. AU - Xu, M. AU - Durand, D. PY - 2015 DA - 2015// TI - Event inference in multidomain families with phylogenetic reconciliation JO - BMC Bioinform VL - 16 UR - https://doi.org/10.1186/1471-2105-16-S14-S8 DO - 10.1186/1471-2105-16-S14-S8 ID - Stolzer2015 ER - TY - JOUR AU - Karpov, N. AU - Malikic, S. AU - Rahman, M. K. AU - Sahinalp, S. C. PY - 2019 DA - 2019// TI - A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression JO - Algorithms Mol Biol VL - 14 UR - https://doi.org/10.1186/s13015-019-0152-9 DO - 10.1186/s13015-019-0152-9 ID - Karpov2019 ER - TY - STD TI - Pe’er I, Shamir R. The median problems for breakpoints are NP-complete. In: Electronic colloquim on computational complexity, report., vol. 71. Citeseer; 1998. p. 1–16. ID - ref6 ER - TY - STD TI - Caprara A. Formulations and hardness of multiple sorting by reversals. In: RECOMB, vol. 99. Citeseer; 1999. p. 84–93. ID - ref7 ER - TY - STD TI - Xu AW, Sankoff D. Decompositions of multiple breakpoint graphs and rapid exact solutions to the median problem. In: International workshop on algorithms in bioinformatics. Springer; 2008. p. 25–37. ID - ref8 ER - TY - JOUR AU - Xu, A. W. PY - 2009 DA - 2009// TI - A fast and exact algorithm for the median of three problem: a graph decomposition approach JO - J Comput Biol VL - 16 UR - https://doi.org/10.1089/cmb.2009.0087 DO - 10.1089/cmb.2009.0087 ID - Xu2009 ER - TY - STD TI - Xu AW, Moret BM. GASTS: parsimony scoring under rearrangements. In: International workshop on algorithms in bioinformatics. Springer; 2011. p. 351–363. ID - ref10 ER - TY - JOUR AU - Feijão, P. PY - 2015 DA - 2015// TI - Reconstruction of ancestral gene orders using intermediate genomes JO - BMC Bioinform VL - 16 UR - https://doi.org/10.1186/1471-2105-16-S14-S3 DO - 10.1186/1471-2105-16-S14-S3 ID - Feijão2015 ER - TY - STD TI - Feijão P, Mane A, Chauve C. A tractable variant of the single cut or join distance with duplicated genes. In: RECOMB international workshop on comparative genomics. Springer; 2017. p. 14–30. ID - ref12 ER - TY - STD TI - Mane AC, Lafond M, Feijão P, Chauve C. The rooted SCJ median with single gene duplications. In: RECOMB international conference on comparative genomics. Springer; 2018. p. 28–48. ID - ref13 ER - TY - JOUR AU - Hill, T. AU - Lundgren, A. AU - Fredriksson, R. AU - Schiöth, H. B. PY - 2005 DA - 2005// TI - Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins JO - Biochim Biophys Acta (BBA) Gen Subj VL - 1725 UR - https://doi.org/10.1016/j.bbagen.2005.04.027 DO - 10.1016/j.bbagen.2005.04.027 ID - Hill2005 ER - TY - JOUR AU - Gao, N. AU - Yang, N. AU - Tang, J. PY - 2013 DA - 2013// TI - Ancestral genome inference using a genetic algorithm approach JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0062156 DO - 10.1371/journal.pone.0062156 ID - Gao2013 ER - TY - JOUR AU - Gao, N. AU - Zhang, Y. AU - Feng, B. AU - Tang, J. PY - 2015 DA - 2015// TI - A cooperative co-evolutionary genetic algorithm for tree scoring and ancestral genome inference JO - IEEE/ACM Trans Comput Biol Bioinform VL - 12 UR - https://doi.org/10.1109/TCBB.2015.2430860 DO - 10.1109/TCBB.2015.2430860 ID - Gao2015 ER - TY - JOUR AU - Xia, R. AU - Lin, Y. AU - Zhou, J. AU - Feng, B. AU - Tang, J. PY - 2018 DA - 2018// TI - A median solver and phylogenetic inference based on double-cut-and-join sorting JO - J Comput Biol VL - 25 UR - https://doi.org/10.1089/cmb.2017.0157 DO - 10.1089/cmb.2017.0157 ID - Xia2018 ER - TY - STD TI - Sun J, Feng B, Xu W. Particle swarm optimization with particles having quantum behavior. In: Proceedings of the 2004 congress on evolutionary computation (IEEE Cat. No. 04TH8753). vol. 1. IEEE; 2004. p. 325–331. ID - ref18 ER - TY - JOUR AU - Yancopoulos, S. AU - Attie, O. AU - Friedberg, R. PY - 2005 DA - 2005// TI - Efficient sorting of genomic permutations by translocation, inversion and block interchange JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti535 DO - 10.1093/bioinformatics/bti535 ID - Yancopoulos2005 ER - TY - STD TI - Bergeron A, Mixtacki J, Stoye J. A unifying view of genome rearrangements. In: International workshop on algorithms in bioinformatics. Springer; 2006. p. 163–173. ID - ref20 ER - TY - STD TI - Braga MD, Stoye J. Counting all DCJ sorting scenarios. In: RECOMB international workshop on comparative genomics. Springer; 2009. p. 36–47. ID - ref21 ER - TY - STD TI - Xu S, Mu X, Discrete Ma J, Optimization quantum-behaved particle swarm, for 2-D maximum entropic multilevel thresholding image segmentation. In: 2015 Chinese Automation Congress (CAC). IEEE; 2015. p. 651–656. ID - ref22 ER - TY - JOUR AU - Li, L. AU - Jiao, L. AU - Zhao, J. AU - Shang, R. AU - Gong, M. PY - 2017 DA - 2017// TI - Quantum-behaved discrete multi-objective particle swarm optimization for complex network clustering JO - Pattern Recogn VL - 63 UR - https://doi.org/10.1016/j.patcog.2016.09.013 DO - 10.1016/j.patcog.2016.09.013 ID - Li2017 ER - TY - JOUR AU - Lukemire, J. AU - Mandal, A. AU - Wong, W. K. PY - 2019 DA - 2019// TI - d-qpso: a quantum-behaved particle swarm technique for finding d-optimal designs with discrete and continuous factors and a binary response JO - Technometrics VL - 61 UR - https://doi.org/10.1080/00401706.2018.1439405 DO - 10.1080/00401706.2018.1439405 ID - Lukemire2019 ER - TY - STD TI - Lai X, Hao J, Yue D, Gao H. A diversification-based quantum particle swarm optimization algorithm for the multidimensional knapsack problem. In: 2018 5th IEEE international conference on cloud computing and intelligence systems (CCIS). IEEE; 2019. p. 315–319. ID - ref25 ER - TY - STD TI - Sun J, Xu W, Fang W, Chai Z. Quantum-behaved particle swarm optimization with binary encoding. In: International conference on adaptive and natural computing algorithms. Springer; 2007. p. 376–385. ID - ref26 ER - TY - JOUR AU - Clark, A. AU - Eisen, M. AU - Smith, D. PY - 2007 DA - 2007// TI - Evolution of genes and genomes on the drosophila phylogeny JO - Nature VL - 450 UR - https://doi.org/10.1038/nature06341 DO - 10.1038/nature06341 ID - Clark2007 ER -