MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP
نویسندگان
چکیده
منابع مشابه
Perfect phylogenies via branchings in acyclic digraphs and a generalization of Dilworth's theorem
Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurović et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a given binary matrix into a bitwise OR of a set of rows so that the resulting matrix corresponds to a perfect phylogeny and has the minimum number of rows among all...
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MOTIVATION Recent studies sequenced tumor samples from the same progenitor at different development stages and showed that by taking into account the phylogeny of this development, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting. RESULTS We present SNV-PPILP, a...
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Computational methods for inferring haplotype information from genotype data are used in studying the association between genomic variation and medical condition. Recently, Gusfield proposed a haplotype inference method that is based on perfect phylogeny principles. A fundamental problem arises when one tries to apply this approach in the presence of missing genotype data, which is common in pr...
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در این پایان نامه یک مولد برای چند قاب یا ابر قاب تولید شده تحت عمل نمایش یکانی تصویر برای گروه های شمارش پذیر گسسته بررسی خواهد شد. مثال هایی از این قاب ها چند قاب های گابور، ابرقاب های گابور و قاب هایی برای زیرفضاهای انتقال پایاست. نشان می دهیم که مولد چند قاب تنک نرمال شده (ابرقاب) یکتا وجود دارد به طوری که مینیمم فاصله را از ان دارد. همچنین مسایل مشابه برای قاب های دوگان مطرح شده و برخی ...
15 صفحه اولDating phylogenies with sequentially sampled tips.
We develop a Bayesian Markov chain Monte Carlo (MCMC) algorithm for estimating divergence times using sequentially sampled molecular sequences. This type of data is commonly collected during viral epidemics and is sometimes available from different species in ancient DNA studies. We derive the distribution of ages of nodes in the tree under a birth-death-sequential-sampling (BDSS) model and use...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2018
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bty683