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

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https://www.readbyqxmd.com/read/29792514/a-flow-procedure-for-linearization-of-genome-sequence-graphs
#1
David Haussler, Maciej Smuga-Otto, Jordan M Eizenga, Benedict Paten, Adam M Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of reference genomes is sufficiently diverse, the sequence graph implicitly contains all frequent human genetic variations, including translocations, inversions, deletions, and insertions. In representing a set of genomes as a sequence graph, one encounters certain challenges...
May 24, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29741956/a-secure-alignment-algorithm-for-mapping-short-reads-to-human-genome
#2
Yongan Zhao, Xiaofeng Wang, Haixu Tang
The elastic and inexpensive computing resources such as clouds have been recognized as a useful solution to analyzing massive human genomic data (e.g., acquired by using next-generation sequencers) in biomedical researches. However, outsourcing human genome computation to public or commercial clouds was hindered due to privacy concerns: even a small number of human genome sequences contain sufficient information for identifying the donor of the genomic data. This issue cannot be directly addressed by existing security and cryptographic techniques (such as homomorphic encryption), because they are too heavyweight to carry out practical genome computation tasks on massive data...
May 9, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29741924/efficient-modeling-and-simulation-of-space-dependent-biological-systems
#3
Elise Rosati, Morgan Madec, Jean-Baptiste Kammerer, Luc Hébrard, Christophe Lallement, Jacques Haiech
We recently demonstrated the possibility to model and to simulate biological functions using hardware description languages (HDLs) and associated simulators traditionally used for microelectronics. Nevertheless, those languages are not suitable to model and simulate space-dependent systems described by partial differential equations. However, in more and more applications space- and time-dependent models are unavoidable. For this purpose, we investigated a new modeling approach to simulate molecular diffusion on a mesoscopic scale still based on HDL...
May 9, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29741913/a-curated-target-gene-pool-assisting-early-disease-prediction-and-patient-specific-treatment-for-small-cell-lung-cancer
#4
Yan Dong, Hongbao Cao, Zhigang Liang
Hundreds of genes have been linked to small cell lung cancer (SCLC), presenting multiple levels of connections with the disease. The question is whether these genes are sufficient as genetic biomarkers for the early diagnosis and personalized treatment of SCLC. An SCLC genetic database was developed through comprehensive ResNet relationship data analysis, where 557 SCLC target genes were curated. Multiple levels of associations between these genes and SCLC were studied. Then, a sparse representation-based variable selection (SRVS) was employed for gene selection for four SCLC gene expression data sets, followed by a case-control classification...
May 9, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29708779/genome-wide-analysis-of-the-association-of-transposable-elements-with-gene-regulation-suggests-that-alu-elements-have-the-largest-overall-regulatory-impact
#5
Lu Zeng, Stephen M Pederson, Danfeng Cao, Zhipeng Qu, Zhiqiang Hu, David L Adelson, Chaochun Wei
Nearly half of the human genome is made up of transposable elements (TEs), and there is evidence that TEs are involved in gene regulation. In this study, we have integrated publicly available genomic, epigenetic, and transcriptomic data to investigate this in a genome-wide manner. A bootstrapping statistical method was applied to minimize confounder effects from different repeat types. Our results show that although most TE classes are primarily associated with reduced gene expression, Alu elements are associated with upregulated gene expression...
April 30, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29708767/a-fast-approximate-algorithm-for-mapping-long-reads-to-large-reference-databases
#6
Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M Phillippy
Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision...
April 30, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29694245/computational-analysis-of-cell-dynamics-in-videos-with-hierarchical-pooled-deep-convolutional-features
#7
Fengqian Pang, Heng Li, Yonggang Shi, Zhiwen Liu
Computational analysis of cellular appearance and its dynamics is used to investigate physiological properties of cells in biomedical research. In consideration of the great success of deep learning in video analysis, we first introduce two-stream convolutional networks (ConvNets) to automatically learn the biologically meaningful dynamics from raw live-cell videos. However, the two-stream ConvNets lack the ability to capture long-range video evolution. Therefore, a novel hierarchical pooling strategy is proposed to model the cell dynamics in a whole video, which is composed of trajectory pooling for short-term dynamics and rank pooling for long-range ones...
April 25, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29671616/a-parallel-multiobjective-metaheuristic-for-multiple-sequence-alignment
#8
Álvaro Rubio-Largo, Mauro Castelli, Leonardo Vanneschi, Miguel A Vega-Rodríguez
The alignment among three or more nucleotides/amino acids sequences at the same time is known as multiple sequence alignment (MSA), a nondeterministic polynomial time (NP)-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a multiobjective version of the MSA problem wherein the goal is to simultaneously optimize the accuracy and conservation of the alignment. A parallel version of the hybrid multiobjective memetic metaheuristics for MSA is proposed...
April 19, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29668315/approximation-algorithms-for-protein-folding-in-the-hydrophobic-polar-model-on-3d-hexagonal-prism-lattice
#9
Qianghui Guo, Jian Wang, Zhao Xu
In this article, we study approximation algorithms for the protein folding problem in the hydrophobic-polar (HP) model on three-dimensional (3D) hexagonal prism lattice. We present two approximation algorithms based on previous work on two-dimensional (2D) square, 3D cubic, and 2D hexagonal lattice HP models. The first algorithm produces folds in which the H-H contacts are mainly on or between the hexagonal planes, and has approximation ratio [Formula: see text]. While in the folds produced by the second algorithm, the H-H contacts are mainly on or between the zigzag square planes...
April 18, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29668310/human-splice-site-prediction-with-deep-neural-networks
#10
Tatsuhiko Naito
Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site...
April 18, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29668304/a-method-for-predicting-protein-complexes-from-dynamic-weighted-protein-protein-interaction-networks
#11
Lizhen Liu, Xiaowu Sun, Wei Song, Chao Du
Predicting protein complexes from protein-protein interaction (PPI) network is of great significance to recognize the structure and function of cells. A protein may interact with different proteins under different time or conditions. Existing approaches only utilize static PPI network data that may lose much temporal biological information. First, this article proposed a novel method that combines gene expression data at different time points with traditional static PPI network to construct different dynamic subnetworks...
April 18, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658784/fast-metagenomic-binning-via-hashing-and-bayesian-clustering
#12
Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
We introduce GATTACA, a framework for fast unsupervised binning of metagenomic contigs. Similar to recent approaches, GATTACA clusters contigs based on their coverage profiles across a large cohort of metagenomic samples; however, unlike previous methods that rely on read mapping, GATTACA quickly estimates these profiles from kmer counts stored in a compact index. This approach can result in over an order of magnitude speedup, while matching the accuracy of earlier methods on synthetic and real data benchmarks...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658782/phylogenetic-copy-number-factorization-of-multiple-tumor-samples
#13
Simone Zaccaria, Mohammed El-Kebir, Gunnar W Klau, Benjamin J Raphael
Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658778/shrangesim-simulation-of-single-nucleotide-polymorphism-clusters-in-next-generation-sequencing-data
#14
Markus Boenn
Genomic variations are in the focus of research to uncover mechanisms of host-pathogen interactions and diseases such as cancer. Nowadays, next-generation sequencing (NGS) data are analyzed through dedicated pipelines to detect them. Surrogate NGS data in conjunction with genomic variations help to evaluate pipelines and validate their outcomes, fostering selection of proper tools for a given scientific question. I describe how existing approaches for simulating NGS data in conjunction with genomic variations fail to model local enrichments of single nucleotide polymorphisms (SNPs), so called SNP clusters...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658777/simple-comparative-analyses-of-differentially-expressed-gene-lists-may-overestimate-gene-overlap
#15
Chelsea M Lawhorn, Rachel Schomaker, Jonathan T Rowell, Olav Rueppell
Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658776/toward-recovering-allele-specific-cancer-genome-graphs
#16
Ashok Rajaraman, Jian Ma
Integrated analysis of structural variants (SVs) and copy number alterations in aneuploid cancer genomes is key to understanding tumor genome complexity. A recently developed algorithm, Weaver, can estimate, for the first time, allele-specific copy number of SVs and their interconnectivity in aneuploid cancer genomes. However, one major limitation is that not all SVs identified by Weaver are phased. In this article, we develop a general convex programming framework that predicts the interconnectivity of unphased SVs with possibly noisy allele-specific copy number estimations as input...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29658774/a-simple-linear-space-algorithm-for-computing-nonoverlapping-inversion-and-transposition-distance-in-quadratic-average-time
#17
Xiaodong Wang, Lei Wang
In the sequence alignment problem, it is important to compare DNA sequences to retrieve relevant information and align these sequences. An inversion and a translocation are important operations in comparing DNA sequences in biosequence analysis. The alignment problem with nonoverlapping inversions and translocations is to find an alignment with nonoverlapping inversions and translocations for the given two strings X and Y. This problem has interesting application for finding a common sequence from two mutated sequences...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29653061/to-t-test-or-not-to-t-test-a-p-values-based-point-of-view-in-the-receiver-operating-characteristic-curve-framework
#18
Albert Vexler, Jihnhee Yu
A common statistical doctrine supported by many introductory courses and textbooks is that t-test type procedures based on normally distributed data points are anticipated to provide a standard in decision-making. In order to motivate scholars to examine this convention, we introduce a simple approach based on graphical tools of receiver operating characteristic (ROC) curve analysis, a well-established biostatistical methodology. In this context, we propose employing a p-values-based method, taking into account the stochastic nature of p-values...
April 13, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29641230/pypathway-python-package-for-biological-network-analysis-and-visualization
#19
Yang Xu, Xiao-Chun Luo
Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools...
April 11, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29641228/redo-rna-editing-detection-in-plant-organelles-based-on-variant-calling-results
#20
Shuangyang Wu, Wanfei Liu, Hasan Awad Aljohi, Sarah A Alromaih, Ibrahim O AlAnazi, Qiang Lin, Jun Yu, Songnian Hu
RNA editing is a post-transcriptional or cotranscriptional process that changes the sequence of the precursor transcript by substitutions, insertions, or deletions. Almost all of the land plants undergo RNA editing in organelles (plastids and mitochondria). Although several software tools have been developed to identify RNA editing events, there has been a great challenge to distinguish true RNA editing events from genome variation, sequencing errors, and other factors. Here we introduce REDO, a comprehensive application tool for identifying RNA editing events in plant organelles based on variant call format files from RNA-sequencing data...
April 11, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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