Titlebook: Research in Computational Molecular Biology; 20th Annual Conferen Mona Singh Conference proceedings 2016 Springer International Publishing

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MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flowsvering the species and their abundances in an HTS sample are based on genome-specific markers, which can lead to skewed results, especially at species level. We present MetaFlow, the first method based on coverage analysis across entire genomes that also scales to HTS samples. We formulated this pro

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LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General En the sequence and conformation of at most two residues. Although modeling of . and of . significantly increases the accuracy of protein design, previous methods to model these phenomena add a significant asymptotic cost to design calculations. We now remove this cost by modeling continuous flexibili

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Improving Bloom Filter Performance on Sequence Data Using ,-mer Bloom Filterstions, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. Since .-mer sets often reach hundreds of millions of elements, traditional data structures are impractical for .-mer set storage, and Bloom filters and their vari

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Safe and Complete Contig Assembly Via Omnitigs of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph . (e.g. a de Bruijn, or a string grap

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Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closegth offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this paper, we present 2SNV, a method able to to

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Structural Variation Detection with Read Pair Information—An Improved Null-Hypothesis Reduces Biasment length for detection. After aligning read-pairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model li

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