EURASIP journal on bioinformatics & systems biology最新文献_第8页

A bayesian analysis for identifying DNA copy number variations using a compound poisson process. 用复合泊松过程鉴定DNA拷贝数变异的贝叶斯分析。

EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 Epub Date: 2010-09-27 DOI: 10.1155/2010/268513

Jie Chen, Ayten Yiğiter, Yu-Ping Wang, Hong-Wen Deng

{"title":"A bayesian analysis for identifying DNA copy number variations using a compound poisson process.","authors":"Jie Chen, Ayten Yiğiter, Yu-Ping Wang, Hong-Wen Deng","doi":"10.1155/2010/268513","DOIUrl":"https://doi.org/10.1155/2010/268513","url":null,"abstract":"To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH) technique is often used for detecting DNA copy number variants (CNVs). Various methods have been developed for gaining CNVs information based on aCGH data. However, most of these methods make use of the log-intensity ratios in aCGH data without taking advantage of other information such as the DNA probe (e.g., biomarker) positions/distances contained in the data. Motivated by the specific features of aCGH data, we developed a novel method that takes into account the estimation of a change point or locus of the CNV in aCGH data with its associated biomarker position on the chromosome using a compound Poisson process. We used a Bayesian approach to derive the posterior probability for the estimation of the CNV locus. To detect loci of multiple CNVs in the data, a sliding window process combined with our derived Bayesian posterior probability was proposed. To evaluate the performance of the method in the estimation of the CNV locus, we first performed simulation studies. Finally, we applied our approach to real data from aCGH experiments, demonstrating its applicability.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"268513"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2010/268513","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29376054","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}

引用次数: 3

TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites. 黑腹果蝇翻译起始位点的概率评分。

EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 DOI: 10.1155/2010/814127

Michael P Weir, Michael D Rice

引用次数: 6

A hypothesis test for equality of bayesian network models. 贝叶斯网络模型等价性的假设检验。

EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 Epub Date: 2010-10-12 DOI: 10.1155/2010/947564

Anthony Almudevar

{"title":"A hypothesis test for equality of bayesian network models.","authors":"Anthony Almudevar","doi":"10.1155/2010/947564","DOIUrl":"https://doi.org/10.1155/2010/947564","url":null,"abstract":"Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately fit models can be directly compared, but it is difficult to assign statistical significance to any observed differences. There would therefore be an advantage to the development of a rigorous hypothesis test for homogeneity of network structure. In this paper, a generalized likelihood ratio test based on Bayesian network models is developed, with significance level estimated using permutation replications. In order to be computationally feasible, a number of algorithms are introduced. First, a method for approximating multivariate distributions due to Chow and Liu (1968) is adapted, permitting the polynomial-time calculation of a maximum likelihood Bayesian network with maximum indegree of one. Second, sequential testing principles are applied to the permutation test, allowing significant reduction of computation time while preserving reported error rates used in multiple testing. The method is applied to gene-set analysis, using two sets of experimental data, and some advantage to a pathway modelling approach to this problem is reported.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"947564"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2010/947564","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29390854","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}

引用次数: 9

How to improve postgenomic knowledge discovery using imputation. 如何利用归算改进后基因组知识发现。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 DOI: 10.1155/2009/717136

Muhammad Shoaib B Sehgal, Iqbal Gondal, Laurence S Dooley, Ross Coppel

{"title":"How to improve postgenomic knowledge discovery using imputation.","authors":"Muhammad Shoaib B Sehgal, Iqbal Gondal, Laurence S Dooley, Ross Coppel","doi":"10.1155/2009/717136","DOIUrl":"https://doi.org/10.1155/2009/717136","url":null,"abstract":"While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignore or regard erroneous gene readings as missing values, though this assumption can exert a major influence upon postgenomic knowledge discovery methods like gene selection and gene regulatory network (GRN) reconstruction. This has been the catalyst for a raft of new flexible imputation algorithms including local least square impute and the recent heuristic collateral missing value imputation, which exploit the biological transactional behaviour of functionally correlated genes to afford accurate missing value estimation. This paper examines the influence of missing value imputation techniques upon postgenomic knowledge inference methods with results for various algorithms consistently corroborating that instead of ignoring missing values, recycling microarray data by flexible and robust imputation can provide substantial performance benefits for subsequent downstream procedures.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"717136"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/717136","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9785776","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}

引用次数: 9

Functional classification of genome-scale metabolic networks. 基因组尺度代谢网络的功能分类。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2009-03-17 DOI: 10.1155/2009/570456

Oliver Ebenhöh, Thomas Handorf

{"title":"Functional classification of genome-scale metabolic networks.","authors":"Oliver Ebenhöh, Thomas Handorf","doi":"10.1155/2009/570456","DOIUrl":"https://doi.org/10.1155/2009/570456","url":null,"abstract":"We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are aerotolerant and/or photosynthetic. Despite differences in the underlying concepts, both measures display some common features. Closely related organisms often display a similar functional behavior and in both cases the functional measures appear to correlate with the considered classes of environments. Carbon utilization spectra and nutrient profiles are complementary approaches toward a functional classification of organism-wide metabolic networks. Both approaches contain different information and thus yield different clusterings, which are both different from the classical taxonomy of organisms. Our results indicate that a sophisticated combination of our approaches will allow for a quantitative description reflecting the lifestyles of organisms.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"570456"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/570456","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28056102","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}

引用次数: 15

Spectral preprocessing for clustering time-series gene expressions. 聚类时间序列基因表达的光谱预处理。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2009-04-08 DOI: 10.1155/2009/713248

Wentao Zhao, Erchin Serpedin, Edward R Dougherty

引用次数: 9

Assessing the exceptionality of coloured motifs in networks. 网络中有色图案的异常性评估。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2009-01-26 DOI: 10.1155/2009/616234

Sophie Schbath, Vincent Lacroix, Marie-France Sagot

{"title":"Assessing the exceptionality of coloured motifs in networks.","authors":"Sophie Schbath, Vincent Lacroix, Marie-France Sagot","doi":"10.1155/2009/616234","DOIUrl":"https://doi.org/10.1155/2009/616234","url":null,"abstract":"Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive P-values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound) Poisson and Gaussian approximations for the motif count distribution in Erdös-Rényi random graphs or on simulations in other models. We focus on a different definition of graph motifs that corresponds to coloured motifs. A coloured motif is a connected subgraph with fixed vertex colours but unspecified topology. Our work is the first analytical attempt to assess the exceptionality of coloured motifs in networks without any simulation. We first establish analytical formulae for the mean and the variance of the count of a coloured motif in an Erdös-Rényi random graph model. Using simulations under this model, we further show that a Pólya-Aeppli distribution better approximates the distribution of the motif count compared to Gaussian or Poisson distributions. The Pólya-Aeppli distribution, and more generally the compound Poisson distributions, are indeed well designed to model counts of clumping events. Altogether, these results enable to derive a P-value for a coloured motif, without spending time on simulations.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"616234"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/616234","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27964692","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}

引用次数: 0

Selection of statistical thresholds in graphical models. 图形模型中统计阈值的选择。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2010-03-04 DOI: 10.1155/2009/878013

Anthony Almudevar

引用次数: 4

Stochastic simulation of delay-induced circadian rhythms in Drosophila. 果蝇延迟诱导的昼夜节律的随机模拟。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2009-07-19 DOI: 10.1155/2009/386853

Zhouyi Xu, Xiaodong Cai

{"title":"Stochastic simulation of delay-induced circadian rhythms in Drosophila.","authors":"Zhouyi Xu, Xiaodong Cai","doi":"10.1155/2009/386853","DOIUrl":"https://doi.org/10.1155/2009/386853","url":null,"abstract":"Circadian rhythms are ubiquitous in all eukaryotes and some prokaryotes. Several computational models with or without time delays have been developed for circadian rhythms. Exact stochastic simulations have been carried out for several models without time delays, but no exact stochastic simulation has been done for models with delays. In this paper, we proposed a detailed and a reduced stochastic model with delays for circadian rhythms in Drosophila based on two deterministic models of Smolen et al. and employed exact stochastic simulation to simulate circadian oscillations. Our simulations showed that both models can produce sustained oscillations and that the oscillation is robust to noise in the sense that there is very little variability in oscillation period although there are significant random fluctuations in oscillation peaks. Moreover, although average time delays are essential to simulation of oscillation, random changes in time delays within certain range around fixed average time delay cause little variability in the oscillation period. Our simulation results also showed that both models are robust to parameter variations and that oscillation can be entrained by light/dark circles. Our simulations further demonstrated that within a reasonable range around the experimental result, the rates that dclock and per promoters switch back and forth between activated and repressed sites have little impact on oscillation period.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"386853"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/386853","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28407846","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}

引用次数: 1

Network structure and biological function: reconstruction, modeling, and statistical approaches. 网络结构和生物功能:重建、建模和统计方法。

EURASIP journal on bioinformatics & systems biology Pub Date : 2009-01-01 Epub Date: 2009-06-11 DOI: 10.1155/2009/714985

Joachim Selbig, Matthias Steinfath, Dirk Repsilber

引用次数: 3