EURASIP journal on bioinformatics & systems biology最新文献

{"title":"The prediction of virus mutation using neural networks and rough set techniques.","authors":"Mostafa A Salama,&nbsp;Aboul Ella Hassanien,&nbsp;Ahmad Mostafa","doi":"10.1186/s13637-016-0042-0","DOIUrl":"https://doi.org/10.1186/s13637-016-0042-0","url":null,"abstract":"<p><p>Viral evolution remains to be a main obstacle in the effectiveness of antiviral treatments. The ability to predict this evolution will help in the early detection of drug-resistant strains and will potentially facilitate the design of more efficient antiviral treatments. Various tools has been utilized in genome studies to achieve this goal. One of these tools is machine learning, which facilitates the study of structure-activity relationships, secondary and tertiary structure evolution prediction, and sequence error correction. This work proposes a novel machine learning technique for the prediction of the possible point mutations that appear on alignments of primary RNA sequence structure. It predicts the genotype of each nucleotide in the RNA sequence, and proves that a nucleotide in an RNA sequence changes based on the other nucleotides in the sequence. Neural networks technique is utilized in order to predict new strains, then a rough set theory based algorithm is introduced to extract these point mutation patterns. This algorithm is applied on a number of aligned RNA isolates time-series species of the Newcastle virus. Two different data sets from two sources are used in the validation of these techniques. The results show that the accuracy of this technique in predicting the nucleotides in the new generation is as high as 75 %. The mutation rules are visualized for the analysis of the correlation between different nucleotides in the same RNA sequence.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2016 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2016-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13637-016-0042-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34544083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment.","authors":"Yijie Wang,&nbsp;Xiaoning Qian","doi":"10.1186/s13637-016-0041-1","DOIUrl":"https://doi.org/10.1186/s13637-016-0041-1","url":null,"abstract":"<p><p>With increasingly \"big\" data available in biomedical research, deriving accurate and reproducible biology knowledge from such big data imposes enormous computational challenges. In this paper, motivated by recently developed stochastic block coordinate algorithms, we propose a highly scalable randomized block coordinate Frank-Wolfe algorithm for convex optimization with general compact convex constraints, which has diverse applications in analyzing biomedical data for better understanding cellular and disease mechanisms. We focus on implementing the derived stochastic block coordinate algorithm to align protein-protein interaction networks for identifying conserved functional pathways based on the IsoRank framework. Our derived stochastic block coordinate Frank-Wolfe (SBCFW) algorithm has the convergence guarantee and naturally leads to the decreased computational cost (time and space) for each iteration. Our experiments for querying conserved functional protein complexes in yeast networks confirm the effectiveness of this technique for analyzing large-scale biological networks.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2016 1","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2016-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13637-016-0041-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34429398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning.","authors":"Antti Larjo,&nbsp;Harri Lähdesmäki","doi":"10.1186/s13637-015-0024-7","DOIUrl":"https://doi.org/10.1186/s13637-015-0024-7","url":null,"abstract":"<p><p>Bayesian networks have become popular for modeling probabilistic relationships between entities. As their structure can also be given a causal interpretation about the studied system, they can be used to learn, for example, regulatory relationships of genes or proteins in biological networks and pathways. Inference of the Bayesian network structure is complicated by the size of the model structure space, necessitating the use of optimization methods or sampling techniques, such Markov Chain Monte Carlo (MCMC) methods. However, convergence of MCMC chains is in many cases slow and can become even a harder issue as the dataset size grows. We show here how to improve convergence in the Bayesian network structure space by using an adjustable proposal distribution with the possibility to propose a wide range of steps in the structure space, and demonstrate improved network structure inference by analyzing phosphoprotein data from the human primary T cell signaling network.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2015 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2015-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13637-015-0024-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34832523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty.","authors":"Mohammadmahdi R Yousefi,&nbsp;Edward R Dougherty","doi":"10.1186/1687-4153-2014-6","DOIUrl":"https://doi.org/10.1186/1687-4153-2014-6","url":null,"abstract":"<p><p>Perfect knowledge of the underlying state transition probabilities is necessary for designing an optimal intervention strategy for a given Markovian genetic regulatory network. However, in many practical situations, the complex nature of the network and/or identification costs limit the availability of such perfect knowledge. To address this difficulty, we propose to take a Bayesian approach and represent the system of interest as an uncertainty class of several models, each assigned some probability, which reflects our prior knowledge about the system. We define the objective function to be the expected cost relative to the probability distribution over the uncertainty class and formulate an optimal Bayesian robust intervention policy minimizing this cost function. The resulting policy may not be optimal for a fixed element within the uncertainty class, but it is optimal when averaged across the uncertainly class. Furthermore, starting from a prior probability distribution over the uncertainty class and collecting samples from the process over time, one can update the prior distribution to a posterior and find the corresponding optimal Bayesian robust policy relative to the posterior distribution. Therefore, the optimal intervention policy is essentially nonstationary and adaptive. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2014-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2014-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32242551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of gene network robustness based on saturated fixed point attractors.","authors":"Genyuan Li,&nbsp;Herschel Rabitz","doi":"10.1186/1687-4153-2014-4","DOIUrl":"https://doi.org/10.1186/1687-4153-2014-4","url":null,"abstract":"<p><p>The analysis of gene network robustness to noise and mutation is important for fundamental and practical reasons. Robustness refers to the stability of the equilibrium expression state of a gene network to variations of the initial expression state and network topology. Numerical simulation of these variations is commonly used for the assessment of robustness. Since there exists a great number of possible gene network topologies and initial states, even millions of simulations may be still too small to give reliable results. When the initial and equilibrium expression states are restricted to being saturated (i.e., their elements can only take values 1 or -1 corresponding to maximum activation and maximum repression of genes), an analytical gene network robustness assessment is possible. We present this analytical treatment based on determination of the saturated fixed point attractors for sigmoidal function models. The analysis can determine (a) for a given network, which and how many saturated equilibrium states exist and which and how many saturated initial states converge to each of these saturated equilibrium states and (b) for a given saturated equilibrium state or a given pair of saturated equilibrium and initial states, which and how many gene networks, referred to as viable, share this saturated equilibrium state or the pair of saturated equilibrium and initial states. We also show that the viable networks sharing a given saturated equilibrium state must follow certain patterns. These capabilities of the analytical treatment make it possible to properly define and accurately determine robustness to noise and mutation for gene networks. Previous network research conclusions drawn from performing millions of simulations follow directly from the results of our analytical treatment. Furthermore, the analytical results provide criteria for the identification of model validity and suggest modified models of gene network dynamics. The yeast cell-cycle network is used as an illustration of the practical application of this analytical treatment. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2014-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2014-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32192610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracking of time-varying genomic regulatory networks with a LASSO-Kalman smoother.","authors":"Jehandad Khan,&nbsp;Nidhal Bouaynaya,&nbsp;Hassan M Fathallah-Shaykh","doi":"10.1186/1687-4153-2014-3","DOIUrl":"https://doi.org/10.1186/1687-4153-2014-3","url":null,"abstract":"<p><p>: It is widely accepted that cellular requirements and environmental conditions dictate the architecture of genetic regulatory networks. Nonetheless, the status quo in regulatory network modeling and analysis assumes an invariant network topology over time. In this paper, we refocus on a dynamic perspective of genetic networks, one that can uncover substantial topological changes in network structure during biological processes such as developmental growth. We propose a novel outlook on the inference of time-varying genetic networks, from a limited number of noisy observations, by formulating the network estimation as a target tracking problem. We overcome the limited number of observations (small n large p problem) by performing tracking in a compressed domain. Assuming linear dynamics, we derive the LASSO-Kalman smoother, which recursively computes the minimum mean-square sparse estimate of the network connectivity at each time point. The LASSO operator, motivated by the sparsity of the genetic regulatory networks, allows simultaneous signal recovery and compression, thereby reducing the amount of required observations. The smoothing improves the estimation by incorporating all observations. We track the time-varying networks during the life cycle of the Drosophila melanogaster. The recovered networks show that few genes are permanent, whereas most are transient, acting only during specific developmental phases of the organism. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2014-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2014-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32107151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effective gene prediction by high resolution frequency estimator based on least-norm solution technique.","authors":"Manidipa Roy, Soma Barman","doi":"10.1186/1687-4153-2014-2","DOIUrl":"10.1186/1687-4153-2014-2","url":null,"abstract":"<p><p>Linear algebraic concept of subspace plays a significant role in the recent techniques of spectrum estimation. In this article, the authors have utilized the noise subspace concept for finding hidden periodicities in DNA sequence. With the vast growth of genomic sequences, the demand to identify accurately the protein-coding regions in DNA is increasingly rising. Several techniques of DNA feature extraction which involves various cross fields have come up in the recent past, among which application of digital signal processing tools is of prime importance. It is known that coding segments have a 3-base periodicity, while non-coding regions do not have this unique feature. One of the most important spectrum analysis techniques based on the concept of subspace is the least-norm method. The least-norm estimator developed in this paper shows sharp period-3 peaks in coding regions completely eliminating background noise. Comparison of proposed method with existing sliding discrete Fourier transform (SDFT) method popularly known as modified periodogram method has been drawn on several genes from various organisms and the results show that the proposed method has better as well as an effective approach towards gene prediction. Resolution, quality factor, sensitivity, specificity, miss rate, and wrong rate are used to establish superiority of least-norm gene prediction method over existing method. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2014-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31998149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A 2D graphical representation of the sequences of DNA based on triplets and its application.","authors":"Sai Zou, Lei Wang, Junfeng Wang","doi":"10.1186/1687-4153-2014-1","DOIUrl":"10.1186/1687-4153-2014-1","url":null,"abstract":"<p><p>In this paper, we first present a new concept of 'weight' for 64 triplets and define a different weight for each kind of triplet. Then, we give a novel 2D graphical representation for DNA sequences, which can transform a DNA sequence into a plot set to facilitate quantitative comparisons of DNA sequences. Thereafter, associating with a newly designed measure of similarity, we introduce a novel approach to make similarities/dissimilarities analysis of DNA sequences. Finally, the applications in similarities/dissimilarities analysis of the complete coding sequences of β-globin genes of 11 species illustrate the utilities of our newly proposed method. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2014-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31994803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.","authors":"Alexandros Iliadis,&nbsp;Dimitris Anastassiou,&nbsp;Xiaodong Wang","doi":"10.1186/1687-4153-2014-7","DOIUrl":"https://doi.org/10.1186/1687-4153-2014-7","url":null,"abstract":"<p><p>Copy number variations (CNVs) are abundant in the human genome. They have been associated with complex traits in genome-wide association studies (GWAS) and expected to continue playing an important role in identifying the etiology of disease phenotypes. As a result of current high throughput whole-genome single-nucleotide polymorphism (SNP) arrays, we currently have datasets that simultaneously have integer copy numbers in CNV regions as well as SNP genotypes. At the same time, haplotypes that have been shown to offer advantages over genotypes in identifying disease traits even though available for SNP genotypes are largely not available for CNV/SNP data due to insufficient computational tools. We introduce a new framework for inferring haplotypes in CNV/SNP data using a sequential Monte Carlo sampling scheme 'Tree-Based Deterministic Sampling CNV' (TDSCNV). We compare our method with polyHap(v2.0), the only currently available software able to perform inference in CNV/SNP genotypes, on datasets of varying number of markers. We have found that both algorithms show similar accuracy but TDSCNV is an order of magnitude faster while scaling linearly with the number of markers and number of individuals and thus could be the method of choice for haplotype inference in such datasets. Our method is implemented in the TDSCNV package which is available for download at http://www.ee.columbia.edu/~anastas/tdscnv. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2014-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32373692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regularized EM algorithm for sparse parameter estimation in nonlinear dynamic systems with application to gene regulatory network inference.","authors":"Bin Jia,&nbsp;Xiaodong Wang","doi":"10.1186/1687-4153-2014-5","DOIUrl":"https://doi.org/10.1186/1687-4153-2014-5","url":null,"abstract":"<p><p>Parameter estimation in dynamic systems finds applications in various disciplines, including system biology. The well-known expectation-maximization (EM) algorithm is a popular method and has been widely used to solve system identification and parameter estimation problems. However, the conventional EM algorithm cannot exploit the sparsity. On the other hand, in gene regulatory network inference problems, the parameters to be estimated often exhibit sparse structure. In this paper, a regularized expectation-maximization (rEM) algorithm for sparse parameter estimation in nonlinear dynamic systems is proposed that is based on the maximum a posteriori (MAP) estimation and can incorporate the sparse prior. The expectation step involves the forward Gaussian approximation filtering and the backward Gaussian approximation smoothing. The maximization step employs a re-weighted iterative thresholding method. The proposed algorithm is then applied to gene regulatory network inference. Results based on both synthetic and real data show the effectiveness of the proposed algorithm. </p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2014 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2014-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32243163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}