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PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem., , , , , , , , , and 7 other author(s). Bioinform., 36 (Supplement-1): i169-i176 (2020)Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data., , , , , , , , , and 1 other author(s). RECOMB, volume 11467 of Lecture Notes in Computer Science, page 174-189. Springer, (2019)A primal-dual trust region algorithm for nonlinear optimization., and . Math. Program., 100 (1): 49-94 (2004)A quasi-Newton trust-region method.. Math. Program., 100 (3): 447-470 (2004)Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data., , , , , , , , , and 5 other author(s). Bioinform., 37 (24): 4704-4711 (2021)Users Guide for SnadiOpt: A Package Adding Automatic Differentiation to Snopt, , and . CoRR, (2001)WindowMasker: window-based masker for sequenced genomes., , , and . Bioinform., 22 (2): 134-141 (2006)A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences., , , and . J. Comput. Biol., 13 (5): 1028-1040 (2006)The effectiveness of position- and composition-specific gap costs for protein similarity searches., , , and . ISMB, page 15-23. (2008)Using an iterative linear solver in an interior-point method for generating support vector machines., and . Comput. Optim. Appl., 47 (3): 431-453 (2010)