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

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https://www.readbyqxmd.com/read/29461874/grohar-automated-visualization-of-genome-scale-metabolic-models-and-their-pathways
#1
Miha Moškon, Nikolaj Zimic, Miha Mraz
Genome-scale metabolic models (GEMs) have become a powerful tool for the investigation of the entire metabolism of the organism in silico. These models are, however, often extremely hard to reconstruct and also difficult to apply to the selected problem. Visualization of the GEM allows us to easier comprehend the model, to perform its graphical analysis, to find and correct the faulty relations, to identify the parts of the system with a designated function, etc. Even though several approaches for the automatic visualization of GEMs have been proposed, metabolic maps are still manually drawn or at least require large amount of manual curation...
February 20, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29461862/superbubbles-ultrabubbles-and-cacti
#2
Benedict Paten, Jordan M Eizenga, Yohei M Rosen, Adam M Novak, Erik Garrison, Glenn Hickey
A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can be considered to represent the set of possible sequences at a location in a genome. Bidirected and biedged graphs are a generalization of digraphs that are increasingly being used to more fully represent genome assembly and variation problems. In this study, we define snarls and ultrabubbles, generalizations of superbubbles for bidirected and biedged graphs, and give an efficient algorithm for the detection of these more general structures...
February 20, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29451395/determining-the-consistency-of-resolved-triplets-and-fan-triplets
#3
Jesper Jansson, Andrzej Lingas, Ramesh Rajaby, Wing-Kin Sung
The [Formula: see text] Consistency problem takes as input two sets [Formula: see text] and [Formula: see text] of resolved triplets and two sets [Formula: see text] and [Formula: see text] of fan triplets, and asks for a distinctly leaf-labeled tree that contains all elements in [Formula: see text] and no elements in [Formula: see text] as embedded subtrees, if such a tree exists. This article presents a detailed characterization of how the computational complexity of the problem changes under various restrictions...
February 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29297699/on-the-search-for-retrotransposons-alternative-protocols-to-obtain-sequences-to-learn-profile-hidden-markov-models
#4
Carlos N Fischer, Victor De A Campos, Victor H Barella
Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class...
January 3, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29293371/popstr-inference-of-admixed-population-structure-based-on-single-nucleotide-polymorphisms-and-copy-number-variations
#5
Jaeil Ahn, Brian Conkright, Simina M Boca, Subha Madhavan
Statistical approaches for population structure estimation have been predominantly driven by a particular data type, single-nucleotide polymorphisms (SNPs). However, in the presence of weak identifiability in SNPs, population structure estimation can suffer from undesirable accuracy loss. Copy number variations (CNVs) are genomic structural variants with loci that are commonly shared within a specific population and thus provide valuable information for estimation of the ancestry of sampled populations. We develop a Bayesian joint modeling framework of SNPs and CNVs, called POPSTR, to better understand population structure than approaches that use SNPs solely...
January 2, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29272149/a-novel-real-time-genome-comparison-method-using-discrete-wavelet-transform
#6
Hsin-Hsiung Huang, Senthil B Girimurugan
Real-time genome comparison is important for identifying unknown species and clustering organisms. We propose a novel method that can represent genome sequences of different lengths as a 12-dimensional numerical vector in real time for this purpose. Given a genome sequence, a binary indicator sequence of each nucleotide base location is computed, and then discrete wavelet transform is applied to these four binary indicator sequences to attain the respective power spectra. Afterward, moments of the power spectra are calculated...
December 22, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29272145/finding-statistically-significant-repeats-in-nucleic-acids-and-proteins
#7
Ana M Jelovic, Nenad S Mitic, Samira Eshafah, Milos V Beljanski
DNA repeats have great importance for biological research and a large number of tools for determining repeats have been developed. Herein we define a method for extracting a statistically significant subset of a determined set of repeats. Our aim was to identify a subset of repeats in the input sequences that are not expected to occur with a number of their appearances in a random sequence of the same length. It is expected that results obtained in such manner would reduce the quantity of processed material and could thereby represent a more important biological signal...
December 22, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29267011/everyone-is-a-protagonist-residue-conformational-preferences-in-high-resolution-protein-structures
#8
Rodrigo Ligabue-Braun, Bruno Borguesan, Hugo Verli, Mathias J Krause, Márcio Dorn
In many structural bioinformatics problems, there is a broad range of unanswered questions about protein dynamics and amino acid properties. Proteins are not strictly static objects, but rather populate ensembles of conformations. One way to understand these particularities is to analyze the information available in experimental databases. The Ramachandran plot, despite being more than half a century old, remains an utterly useful tool in the study of protein conformation. Based on its assumptions, we inspected a large data set (11,130 protein structures, amounting to 5,255,768 residues) and discriminated the conformational preferences of each residue type regarding their secondary structure participation...
December 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29265882/survival-forests-with-r-squared-splitting-rules
#9
Hong Wang, Xiaolin Chen, Gang Li
In modeling censored data, survival forest models are a competitive nonparametric alternative to traditional parametric or semiparametric models when the function forms are possibly misspecified or the underlying assumptions are violated. In this work, we propose a survival forest approach with trees constructed using a novel pseudo R2 splitting rules. By studying the well-known benchmark data sets, we find that the proposed model generally outperforms popular survival models such as random survival forest with different splitting rules, Cox proportional hazard model, and generalized boosted model in terms of C-index metric...
December 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29265879/mutation-mechanisms-of-human-breast-cancer
#10
Lingling Li, Tianhai Tian, Xinan Zhang
Cancer is a class of diseases caused by the accumulation of gene mutations. All mutated genes constitute a genetic network for cancer progression. It is very helpful for tumor diagnosis and therapy if we know how many mutated genes are needed for human breast cancer. In this article, we investigate the mutation mechanisms of human breast cancer by modeling the data of surveillance, epidemiology, and end results registry. The data are age-specific incidence rates of breast cancer of females in the United States...
December 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185807/icon-mic-implementing-a-cpu-mic-collaboration-parallel-framework-for-icon-on-tianhe-2-supercomputer
#11
Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang
Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185805/an-optimized-method-for-bayesian-connectivity-change-point-model
#12
Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan
The brain undergoes functional dynamic changes at all times. Investigating functional dynamics has been recently verified to be helpful for detecting psychological conditions and powerful for analyzing disease-related abnormalities of the brain. This article aims to detect functional dynamics. Specifically, we focus on how to effectively distinguish corresponding functional connectivity and change points from functional magnetic resonance imaging (fMRI) data. By combining Bayesian connectivity change point model (BCCPM), a modified genetic algorithm (GA) is presented to optimize the evolutionary procedure toward the most probable distributions of real change points in fMRI...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185804/theory-of-morphogenesis
#13
Andrey Minarsky, Nadya Morozova, Robert Penner, Christophe Soulé
A model of morphogenesis is proposed based on seven explicit postulates. The mathematical import and biological significance of the postulates are explored and discussed.
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185792/metres-an-efficient-database-for-genomic-applications
#14
Jordi Vilaplana, Rui Alves, Francesc Solsona, Jordi Mateo, Ivan Teixidó, Marc Pifarré
MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29172679/in-silico-approach-to-investigate-the-structural-and-functional-attributes-of-familial-hypercholesterolemia-variants-reported-in-the-saudi-population
#15
Fatima A Morad, Omran M Rashidi, Saida S Sadath, Faisal A Al-Allaf, Mohammad Athar, Mohamed N Alama, Sherif E Edris, Nabeel S Bondagji, Noor A Shaik, Babajan Banaganapalli, Zuhier Awan
Familial hypercholesterolemia (FH) is a metabolic disorder that leads primarily to premature cardiovascular diseases, the main cause of mortality in Saudi Arabia (SA). FH is underreported and underdiagnosed in SA with statistical evidence of high expected prevalence in such a consanguineous community. Lacking knowledge of which and how these alterations are actually impacting lipid metabolism is one of the main reasons why FH is insufficiently diagnosed in the region. The aim of this study was to develop a fast prediction approach using an integrated bioinformatics method for future screening of the potential causative variants from national registries...
November 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29172668/symmetrical-parameterization-of-rigid-body-transformations-for-biomolecular-structures
#16
Jin Seob Kim, Gregory S Chirikjian
Assessing preferred relative rigid body position and orientation is important in the description of biomolecular structures (such as proteins) and their interactions. In this article, we extend and apply the "symmetrical parameterization," which we recently introduced in the kinematics community, to address problems in structural biology. We also review parameterization methods that are widely used in structural biology to describe relative rigid body motions (in particular, orientations) as a basis for comparison...
November 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29313736/quantification-of-twist-from-the-central-lines-of-%C3%AE-strands
#17
Tunazzina Islam, Michael Poteat, Jing He
Since the discovery of right-handed twist of a β-strand, many studies have been conducted to understand the twist. Given the atomic structure of a protein, twist angles have been defined using atomic positions of the backbone. However, limited study is available to characterize twist when the atomic positions are not available, but the central lines of β-strands are. Recent studies in cryoelectron microscopy show that it is possible to predict the central lines of β-strands from a medium-resolution density map...
January 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29313735/viral-capsid-assembly-a-quantified-uncertainty-approach
#18
Nathan Clement, Muhibur Rasheed, Chandrajit Lal Bajaj
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This article presents a statistical-ensemble-based approach that samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations...
January 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29313734/special-issue-preface-the-9th-computational-structural-bioinformatics-workshop
#19
Jing He, Kamal Al Nasr, Weitao Sun, Yonggang Lu
No abstract text is available yet for this article.
January 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29140728/sample-based-models-of-protein-energy-landscapes-and-slow-structural-rearrangements
#20
Tatiana Maximova, Zijing Zhang, Daniel B Carr, Erion Plaku, Amarda Shehu
Proteins often undergo slow structural rearrangements that involve several angstroms and surpass the nanosecond timescale. These spatiotemporal scales challenge physics-based simulations and open the way to sample-based models of structural dynamics. This article improves an understanding of current capabilities and limitations of sample-based models of dynamics. Borrowing from widely used concepts in evolutionary computation, this article introduces two conflicting aspects of sampling capability and quantifies them via statistical (and graphical) analysis tools...
November 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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