Titlebook: Research in Computational Molecular Biology; 16th Annual Internat Benny Chor Conference proceedings 2012 Springer-Verlag Berlin Heidelberg

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TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq,led TrueSight, that combines information from (i) RNA-seq read mapping quality and (ii) coding potential from the reference genome sequences into a unified model that utilizes semi-supervised learning to precisely identify splice junctions.

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Protein Structure by Semidefinite Facial Reduction,ve of these methods is to minimize the error of deviating from the NOE distance constraints. However, this objective function is highly nonconvex and, consequently, difficult to optimize. Euclidean distance geometry methods based on semidefinite programming (SDP) provide a natural formulation for th

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Charge Group Partitioning in Biomolecular Simulation, fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, inc

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Increased Methylation Variation in Epigenetic Domains across Cancer Types,ed regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal tissue, in colon, lung, breast, thy

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Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising, and use our approach to address a new problem that we call .. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its e

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Quantifying the Dynamics of Coupled Networks of Switches and Oscillators,components (represented as nodes) in networks. For example, models of coupled switches have been applied to model systems such as neuronal synapses and gene regulatory networks. Similarly, models of coupled oscillators along networks have been used to model synchronization of oscillators which has b

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lobSTR: A Short Tandem Repeat Profiler for Personal Genomes,es that comprise hundreds of thousands of loci in the human genome. The repetitive structure of these loci makes them prone to replication slippage events [5] that can reach a rate of 1/500 mutations per locus per generation [8], 200,000 fold higher than the rate of . single nucleotide polymorphims

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