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Journal of Computational Biology: a Journal of Computational Molecular Cell Biology

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https://www.readbyqxmd.com/read/27901606/protein-folding-prediction-in-a-cubic-lattice-in-hydrophobic-polar-model
#1
Nicola Yanev, Metodi Traykov, Peter Milanov, Borislav Yurukov
The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the most popular protein structure prediction methods, called Hydrophobic-Polar (HP) model, is based on the observation that in polar environment hydrophobic amino acids are in the core of the molecule-in contact between them and more polar amino acids are in contact with the polar environment...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27901586/long-single-molecule-reads-can-resolve-the-complexity-of-the-influenza-virus-composed-of-rare-closely-related-mutant-variants
#2
Alexander Artyomenko, Nicholas C Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous "swarm" of mutant variants. The long read length 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 article, we present two single-nucleotide variants (2SNV), a method able to tolerate the high error rate of the single-molecule protocol and reconstruct mutant variants...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892712/variability-in-metagenomic-count-data-and-its-influence-on-the-identification-of-differentially-abundant-genes
#3
Viktor Jonsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892695/defining-low-dimensional-projections-to-guide-protein-conformational-sampling
#4
Anastasia Novinskaya, Didier Devaurs, Mark Moll, Lydia E Kavraki
Exploring the conformational space of proteins is critical to characterize their functions. Numerous methods have been proposed to sample a protein's conformational space, including techniques developed in the field of robotics and known as sampling-based motion-planning algorithms (or sampling-based planners). However, these algorithms suffer from the curse of dimensionality when applied to large proteins. Many sampling-based planners attempt to mitigate this issue by keeping track of sampling density to guide conformational sampling toward unexplored regions of the conformational space...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892693/a-graph-approach-to-mining-biological-patterns-in-the-binding-interfaces
#5
Wen Cheng, Changhui Yan
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, we present a graph-mining method for discovering biological patterns in the protein-RNA interfaces. We represented known protein-RNA interfaces using graphs and then discovered graph patterns enriched in the interfaces. Comparison of the discovered graph patterns with UniProt annotations showed that the graph patterns had a significant overlap with residue sites that had been proven crucial for the RNA binding by experimental methods...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27870559/combinatorial-methods-for-epistasis-and-dominance
#6
Serge Sverdlov, Elizabeth Thompson
We develop computational tools for the analysis of nonlinear genotype-phenotype relationships with epistasis among multiple loci or dominance interactions among multiple alleles within the same locus. Theory distinguishes between separable traits, with removable epistasis, and traits with essential epistasis. Separable traits can be transformed to a natural scale where additive methods apply. The methods we present solve for the natural scale, exactly when possible and approximately when not. Through graph methods, our methods allow for enumeration, counting, or sampling of distinct trait architectures satisfying constraints from the separability theory...
November 21, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27835030/a-mad-bayes-algorithm-for-state-space-inference-and-clustering-with-application-to-querying-large-collections-of-chip-seq-data-sets
#7
Chandler Zuo, Kailei Chen, Sündüz Keleş
Current analytic approaches for querying large collections of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from multiple cell types rely on individual analysis of each data set (i.e., peak calling) independently. This approach discards the fact that functional elements are frequently shared among related cell types and leads to overestimation of the extent of divergence between different ChIP-seq samples. Methods geared toward multisample investigations have limited applicability in settings that aim to integrate 100s to 1000s of ChIP-seq data sets for query loci (e...
November 11, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27828710/improving-bloom-filter-performance-on-sequence-data-using-k-mer-bloom-filters
#8
David Pellow, Darya Filippova, Carl Kingsford
Using a sequence's k-mer content rather than the full sequence directly has enabled significant performance improvements in several sequencing applications, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. As k-mer sets often reach hundreds of millions of elements, traditional data structures are often impractical for k-mer set storage, and Bloom filters (BFs) and their variants are used instead. BFs reduce the memory footprint required to store millions of k-mers while allowing for fast set containment queries, at the cost of a low false positive rate (FPR)...
November 9, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27788022/on-computing-breakpoint-distances-for-genomes-with-duplicate-genes
#9
Mingfu Shao, Bernard M E Moret
A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always efficiently compute) a variety of distance measures, but the problem is NP-hard under most models when genomes contain duplicate genes. To tackle duplicate genes, three formulations (exemplar, maximum matching, and any matching) have been proposed, all of which aim to build a matching between homologous genes so as to minimize some distance measure...
October 27, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27759426/interaction-based-feature-selection-for-uncovering-cancer-driver-genes-through-copy-number-driven-expression-level
#10
Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene...
October 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27749096/safe-and-complete-contig-assembly-through-omnitigs
#11
Alexandru I Tomescu, Paul Medvedev
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs-a set 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 remains: given a genome graph G (e.g., a de Bruijn, or a string graph), what are all the strings that can be safely reported from G as contigs? In this article, we answer this question using a model in which the genome is a circular covering walk...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27748625/machine-learning-approaches-for-predicting-protein-complex-similarity
#12
Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interactions (e.g., Van der Waals, electrostatic, and desolvation forces) and the similarity of a conformation to its native structure, the precise nature of this relationship is not known. Existing protein-protein docking methods typically formulate this relationship as a weighted sum of selected terms and calibrate their weights by using a training set to evaluate and rank candidate complexes...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27726445/accurate-recovery-of-ribosome-positions-reveals-slow-translation-of-wobble-pairing-codons-in-yeast
#13
Hao Wang, Joel McManus, Carl Kingsford
Ribosome profiling quantitatively captures ribosome locations during translation. The resulting profiles of ribosome locations are widely used to study translational speed. However, an accurate estimation of the ribosome location depends on identifying the A-site from ribosome profiling reads, a problem that was previously unsolved. Here, we propose a novel method to estimate the ribosome A-site positions from high-coverage ribosome profiling reads. Our model allows more reads to be used, accurately explains the 3-nt periodicity of ribosome profiling reads from various lengths, and recovers consistent ribosome positions across different lengths...
October 11, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27710115/cross-validation-of-data-compatibility-between-small-angle-x-ray-scattering-and-cryo-electron-microscopy
#14
Jin Seob Kim, Bijan Afsari, Gregory S Chirikjian
Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a three-dimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27710048/fastbill-an-improved-tool-for-prediction-of-cis-regulatory-modules
#15
Bartek Wilczynski, Jerzy Tiuryn
Here, we provide a new software tool, called FastBill, for prediction of evolutionarily conserved cis-regulatory modules. It improves on the previous version of our program, called Billboard, by improving the statistical significance calculation. It is also faster than the original Billboard, allowing for large-scale analyses, including multiple informant species. We illustrate the utility of FastBill by performing a large-scale computational experiment of enhancer prediction in the promoter area of more than 150 Drosophila melanogaster genes that possess annotated experimentally verified enhancers...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27710035/using-variable-length-aligned-fragment-pairs-and-an-improved-transition-function-for-flexible-protein-structure-alignment
#16
Hu Cao, Yonggang Lu
With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27704866/sorting-by-cuts-joins-and-whole-chromosome-duplications
#17
Ron Zeira, Ron Shamir
Genome rearrangement problems have been extensively studied due to their importance in biology. Most studied models assumed a single copy per gene. However, in reality, duplicated genes are common, most notably in cancer. In this study, we make a step toward handling duplicated genes by considering a model that allows the atomic operations of cut, join, and whole chromosome duplication. Given two linear genomes, [Formula: see text] with one copy per gene and [Formula: see text] with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming [Formula: see text] into [Formula: see text] such that all intermediate genomes are linear...
October 5, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27681505/new-algorithm-and-software-bnomics-for-inferring-and-visualizing-bayesian-networks-from-heterogeneous-big-biological-and-genetic-data
#18
Grigoriy Gogoshin, Eric Boerwinkle, Andrei S Rodin
Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs...
September 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27681371/lute-local-unpruned-tuple-expansion-accurate-continuously-flexible-protein-design-with-general-energy-functions-and-rigid-rotamer-like-efficiency
#19
Mark A Hallen, Jonathan D Jou, Bruce R Donald
Most protein design algorithms search over discrete conformations and an energy function that is residue-pairwise, that is, a sum of terms that depend on the sequence and conformation of at most two residues. Although modeling of continuous flexibility and of non-residue-pairwise energies 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 flexibility and non-residue-pairwise energies in a form suitable for direct input to highly efficient, discrete combinatorial optimization algorithms such as DEE/A* or branch-width minimization...
September 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27681236/structural-variation-detection-with-read-pair-information-an-improved-null-hypothesis-reduces-bias
#20
Kristoffer Sahlin, Mattias Frånberg, Lars Arvestad
Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment 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 limits statistical analysis of identifying variants and propose a new model by adapting a model we have previously introduced for contig scaffolding, which agrees with data...
September 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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