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

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https://www.readbyqxmd.com/read/28437136/enumeration-of-ancestral-configurations-for-matching-gene-trees-and-species-trees
#1
Filippo Disanto, Noah A Rosenberg
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the recursive computation of the conditional probability under the multispecies coalescent model of a gene tree topology given a species tree, the cost of this computation being affected by the number of ancestral configurations of the gene tree in the species tree. For matching gene trees and species trees, we obtain enumerative results on ancestral configurations...
April 24, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28418726/u50-a-new-metric-for-measuring-assembly-output-based-on-non-overlapping-target-specific-contigs
#2
Christina J Castro, Terry Fei Fan Ng
Advances in next-generation sequencing technologies enable routine genome sequencing, generating millions of short reads. A crucial step for full genome analysis is the de novo assembly, and currently, performance of different assembly methods is measured by a metric called N50. However, the N50 value can produce skewed, inaccurate results when complex data are analyzed, especially for viral and microbial datasets. To provide a better assessment of assembly output, we developed a new metric called U50. The U50 identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to the N50 metric...
April 18, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414553/gd-rda-a-new-regularized-discriminant-analysis-for-high-dimensional-data
#3
Yan Zhou, Baoxue Zhang, Gaorong Li, Tiejun Tong, Xiang Wan
High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identification of which type of diseases a new patient belongs to has been recognized as an important problem. For high-dimensional small sample size data, the classical discriminant methods suffer from the singularity problem and are, therefore, no longer applicable in practice. In this article, we propose a geometric diagonalization method for the regularized discriminant analysis. We then consider a bias correction to further improve the proposed method...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414531/a-system-architecture-for-efficient-transmission-of-massive-dna-sequencing-data
#4
Mahmut Şamİl Sağiroğlu, M Oğuzhan Külekcİ
The DNA sequencing data analysis pipelines require significant computational resources. In that sense, cloud computing infrastructures appear as a natural choice for this processing. However, the first practical difficulty in reaching the cloud computing services is the transmission of the massive DNA sequencing data from where they are produced to where they will be processed. The daily practice here begins with compressing the data in FASTQ file format, and then sending these data via fast data transmission protocols...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414526/assessing-the-impact-of-assemblers-on-virus-detection-in-a-de-novo-metagenomic-analysis-pipeline
#5
Daniel J White, Jing Wang, Richard J Hall
Applying high-throughput sequencing to pathogen discovery is a relatively new field, the objective of which is to find disease-causing agents when little or no background information on disease is available. Key steps in the process are the generation of millions of sequence reads from an infected tissue sample, followed by assembly of these reads into longer, contiguous stretches of nucleotide sequences, and then identification of the contigs by matching them to known databases, such as those stored at GenBank or Ensembl...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414521/representations-of-search-spaces-in-the-problem-of-mutational-pressure-optimization-according-to-protein-coding-sequences
#6
Paweł Błażej, Małgorzata Wnętrzak, Małgorzata Grabińska, Paweł Mackiewicz
The proper representation of the search space is the fundamental step in every optimization task, because it has a decisive impact on the quality of potential solutions. In particular, this problem appears when the search spaces are nonstandard and complex, with the large number of candidate solutions that differ from classical forms usually investigated. One of such spaces is the set of continuous-time, homogenous, and stationary Markov processes. They are commonly used to describe biological phenomena, for example, mutations in DNA sequences and their evolution...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28414515/zseq-an-approach-for-preprocessing-next-generation-sequencing-data
#7
Abedalrhman Alkhateeb, Luis Rueda
Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28375654/loopx-a-graphical-user-interface-based-database-for-comprehensive-analysis-and-comparative-evaluation-of-loops-from-protein-structures
#8
Rajashekar Varma Kadumuri, Ramakrishna Vadrevu
Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops...
April 4, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28355123/gffview-a-web-server-for-parsing-and-visualizing-annotation-information-of-eukaryotic-genome
#9
Feilong Deng, Shi-Yi Chen, Zhou-Lin Wu, Yongsong Hu, Xianbo Jia, Song-Jia Lai
Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization...
March 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294640/evoligo-a-novel-software-to-design-and-group-libraries-of-oligonucleotides-applicable-for-nucleic-acid-based-experiments
#10
Marek C Milewski, Karol Kamel, Anna Kurzynska-Kokorniak, Marcin K Chmielewski, Marek Figlerowicz
Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294634/extracting-genes-involved-in-disease-from-a-connected-network-of-perturbed-biological-processes
#11
Rajat Anand, Samrat Chatterjee
Metabolic disorders such as obesity and diabetes are nowadays regarded as diseases affecting majority of population. These diseases develop gradually over time in an individual. Recently, systematic experiments tracking disease progression are conducted giving a high-throughput complex data. There is a pressing need for developing methods to analyze this complex data to capture the disease mechanism at molecular level. Diseases usually develop through perturbations of biological processes in an organism. In this study, we have tried to capture the interlinking between different biological processes that work together to regulate the disease phenotype...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294630/peak-integrating-curated-and-noisy-prior-knowledge-in-gene-regulatory-network-inference
#12
Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S Heath
With abundance of biological data, computational prediction of gene regulatory networks (GRNs) from gene expression data has become more feasible. Although incorporating other prior knowledge (PK), along with gene expression data, greatly improves prediction accuracy, the overall accuracy is still low. PK in GRN inference can be categorized into noisy and curated. In noisy PK, relations between genes do not necessarily correspond to regulatory relations and are thus considered inaccurate by inference algorithms such as transcription factor binding and protein-protein interactions...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28287829/influence-of-oscillatory-enzyme-activity-on-the-reaction-kinetics-mathematical-model
#13
Aldona Krupska
In this article, the model of a simple kinetic reaction process with an oscillating change in enzyme activity modulated by cosine-like function is considered. The model includes one substrate and one intermediate product in the reversible and irreversible enzymatic processes. The results obtained by numerical solutions show the small oscillations of enzyme-substrate complex with the phase shift in the steady state with respect to the oscillatory activity of enzyme. This phase shift decreases and tends to zero in dependence on the increasing activity of the enzyme periodic action...
March 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28287821/a-particle-swarm-optimization-based-approach-with-local-search-for-predicting-protein-folding
#14
Cheng-Hong Yang, Yu-Shiun Lin, Li-Yeh Chuang, Hsueh-Wei Chang
The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model...
March 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28281787/selection-probability-for-rare-variant-association-studies
#15
Gira Lee, Hokeun Sun
In human genome research, genetic association studies of rare variants have been widely studied since the advent of high-throughput DNA sequencing platforms. However, detection of outcome-related rare variants still remains a statistically challenging problem because the number of observed genetic mutations is extremely rare. Recently, a power set-based statistical selection procedure has been proposed to locate both risk and protective rare variants within the outcome-related genes or genetic regions. Although it can perform an individual selection of rare variants, the procedure has a limitation that it cannot measure the certainty of selected rare variants...
March 10, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28437135/d3gb-an-interactive-genome-browser-for-r-python-and-wordpress
#16
David Barrios, Carlos Prieto
Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web...
February 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177780/calculating-higher-order-moments-of-phylogenetic-stochastic-mapping-summaries-in-linear-time
#17
Amrit Dhar, Vladimir N Minin
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the evolutionary process on the phylogeny and, unlike parsimony-based mapping, conditions on the observed data to randomly draw substitution mappings that do not necessarily require the minimum number of events on a tree. Most stochastic mapping applications simulate substitution mappings only to estimate the mean and/or variance of two commonly used mapping summaries: the number of particular types of substitutions (labeled substitution counts) and the time spent in a particular group of states (labeled dwelling times) on the tree...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177752/a-computational-approach-to-studying-protein-folding-problems-considering-the-crucial-role-of-the-intracellular-environment
#18
Pedro P González-Pérez, Daniel J Orta, Irving Peña, Eduardo C Flores, José U Ramírez, Hiram I Beltrán, Salomón J Alas
Intracellular protein folding (PF) is performed in a highly inhomogeneous, crowded, and correlated environment. Due to this inherent complexity, the study and understanding of PF phenomena is a fundamental issue in the field of computational systems biology. In particular, it is important to use a modeled medium that accurately reflects PF in natural systems. In the current study, we present a simulation wherein PF is carried out within an inhomogeneous modeled medium. Simulation resources included a two-dimensional hydrophobic-polar (HP) model, evolutionary algorithms, and the dual site-bond model...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177699/comparing-phylogenetic-trees-by-matching-nodes-using-the-transfer-distance-between-partitions
#19
Damian Bogdanowicz, Krzysztof Giaro
Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177654/phenotype-analysis-method-for-identification-of-gene-functions-involved-in-asymmetric-division-of-caenorhabditis-elegans
#20
Sihai Yang, Xianhua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa, Yenwei Chen
In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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