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

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https://www.readbyqxmd.com/read/28294640/evoligo-a-novel-software-to-design-and-group-libraries-of-oligonucleotides-applicable-for-nucleic-acid-based-experiments
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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/28177780/calculating-higher-order-moments-of-phylogenetic-stochastic-mapping-summaries-in-linear-time
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28177649/evolutionary-relationships-and-taxa-specific-conserved-signature-indels-among-cellulases-of-archaea-bacteria-and-eukarya
#11
Lebin Thomas, Hari Ram, Ved Pal Singh
The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28128642/multitask-matrix-completion-for-learning-protein-interactions-across-diseases
#12
Meghana Kshirsagar, Keerthiram Murugesan, Jaime G Carbonell, Judith Klein-Seetharaman
Disease-causing pathogens such as viruses introduce their proteins into the host cells in which they interact with the host's proteins, enabling the virus to replicate inside the host. These interactions between pathogen and host proteins are key to understanding infectious diseases. Often multiple diseases involve phylogenetically related or biologically similar pathogens. Here we present a multitask learning method to jointly model interactions between human proteins and three different but related viruses: Hepatitis C, Ebola virus, and Influenza A...
January 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28056190/flexible-modeling-of-genetic-effects-on-function-valued-traits
#13
Nicolo Fusi, Jennifer Listgarten
Genome-wide association studies commonly examine one trait at a time. Occasionally they examine several related traits with the hope of increasing power; in such a setting, the traits are not generally smoothly varying in any way such as time or space. However, for function-valued traits, the trait is often smoothly varying along the axis of interest, such as space or time. For instance, in the case of longitudinal traits such as growth curves, the axis of interest is time; for spatially varying traits such as chromatin accessibility, it would be position along the genome...
January 5, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28056180/clonality-inference-from-single-tumor-samples-using-low-coverage-sequence-data
#14
Nilgun Donmez, Salem Malikic, Alexander W Wyatt, Martin E Gleave, Colin C Collins, S Cenk Sahinalp
Inference of intra-tumor heterogeneity can provide valuable insight into cancer evolution. Somatic mutations detected by sequencing can help estimate the purity of a tumor sample and reconstruct its subclonal composition. Although several methods have been developed to infer intra-tumor heterogeneity, the majority of these tools rely on variant allele frequencies as estimated via ultra-deep sequencing from multiple samples of the same tumor. In practice, obtaining sequencing data from a large number of samples per patient is only feasible in a few cancer types such as liquid tumors, or in rare cases involving solid tumors selected for research...
January 5, 2017: 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...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27661099/an-enumerative-combinatorics-model-for-fragmentation-patterns-in-rna-sequencing-provides-insights-into-nonuniformity-of-the-expected-fragment-starting-point-and-coverage-profile
#16
Celine Prakash, Arndt Von Haeseler
RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27608300/cautionary-tales-of-inapproximability
#17
David Budden, Mitchell Jones
Modeling biology as classical problems in computer science allows researchers to leverage the wealth of theoretical advancements in this field. Despite countless studies presenting heuristics that report improvement on specific benchmarking data, there has been comparatively little focus on exploring the theoretical bounds on the performance of practical (polynomial-time) algorithms. Conversely, theoretical studies tend to overstate the generalizability of their conclusions to physical biological processes...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27513917/ompcontact-an-outer-membrane-protein-inter-barrel-residue-contact-prediction-method
#18
Li Zhang, Han Wang, Lun Yan, Lingtao Su, Dong Xu
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these functions. Because experimental structures are scarce, predicted 3D structures are more adapted to OMP research instead, and the inter-barrel residue contact is becoming one of the most remarkable features, improving prediction accuracy by describing the structural information of OMPs...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27494258/nias-server-neighbors-influence-of-amino-acids-and-secondary-structures-in-proteins
#19
Bruno Borguesan, Mario Inostroza-Ponta, Márcio Dorn
The exponential growth in the number of experimentally determined three-dimensional protein structures provide a new and relevant knowledge about the conformation of amino acids in proteins. Only a few of probability densities of amino acids are publicly available for use in structure validation and prediction methods. NIAS (Neighbors Influence of Amino acids and Secondary structures) is a web-based tool used to extract information about conformational preferences of amino acid residues and secondary structures in experimental-determined protein templates...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27494114/nonparametric-model-of-smooth-muscle-force-production-during-electrical-stimulation
#20
Marc Cole, Steffen Eikenberry, Takahide Kato, Roman A Sandler, Stanley M Yamashiro, Vasilis Z Marmarelis
A nonparametric model of smooth muscle tension response to electrical stimulation was estimated using the Laguerre expansion technique of nonlinear system kernel estimation. The experimental data consisted of force responses of smooth muscle to energy-matched alternating single pulse and burst current stimuli. The burst stimuli led to at least a 10-fold increase in peak force in smooth muscle from Mytilus edulis, despite the constant energy constraint. A linear model did not fit the data. However, a second-order model fit the data accurately, so the higher-order models were not required to fit the data...
March 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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