Titlebook: Research in Computational Molecular Biology; 13th Annual Internat Serafim Batzoglou Conference proceedings 2009 Springer-Verlag Berlin Heid

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Storage and Retrieval of Individual Genomes, length .. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tr

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Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology,r ODEs is that seemingly minor changes in initial conditions or parameters can lead to radically different behaviors. This is problematic because in general it is never possible to know/measure the precise state of any biological system due to measurement errors. The parameter synthesis problem is t

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Spatial Clustering of Multivariate Genomic and Epigenomic Information,ry and epigenetics marks on a global scale. This new experimental methodology was recently applied to map multiple histone marks and genomic factors, characterizing patterns of genome organization and discovering interactions among processes of epigenetic reprogramming during cellular differentiatio

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A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microa biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answ

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Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes,These studies have typically been based high-cost library generation and Sanger sequencing; however, recent introduction of next-generation sequencing (NGS) technologies is changing how research in this area is conducted in a significant way. Highthroughput sequencing technologies such as 454, Illum

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Optimizing PCR Assays for DNA Based Cancer Diagnostics,umor cells are frequently admixed with normal cells, particularly in early stage tumor samples, and thus the samples contain a high background of normal DNA. Detection is further confounded by the fact that the rearrangement boundaries are not conserved across individuals, and might vary over hundre

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The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Prs that extend the utility of the multi-state perfect phylogeny model: . where some entries in the input are missing and the question is whether (bounded) values for the missing data can be imputed so that the resulting data has a multi-state perfect phylogeny; . where we want to minimize the number