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EURASIP journal on bioinformatics & systems biology最新文献

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Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems. 生化反应系统中罕见事件的加权次反应方法及参数选择。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-07-25 DOI: 10.1186/1687-4153-2011-797251
Zhouyi Xu, Xiaodong Cai
{"title":"Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems.","authors":"Zhouyi Xu,&nbsp;Xiaodong Cai","doi":"10.1186/1687-4153-2011-797251","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-797251","url":null,"abstract":"<p><p> The weighted stochastic simulation algorithm (wSSA) recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for efficient estimation of the probability of rare events in biochemical reaction systems. In this paper, we first apply the importance sampling technique to the next reaction method (NRM) of the stochastic simulation algorithm and develop a weighted NRM (wNRM). We then develop a systematic method for selecting the values of importance sampling parameters, which can be applied to both the wSSA and the wNRM. Numerical results demonstrate that our parameter selection method can substantially improve the performance of the wSSA and the wNRM in terms of simulation efficiency and accuracy.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2011-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-797251","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30134860","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
Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation. 低剂量IL-1刺激后NFκB信号通路的建模时间延迟。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-06-17 DOI: 10.1186/1687-4153-2011-3
Johannes Witt, Sandra Barisic, Oliver Sawodny, Michael Ederer, Dagmar Kulms, Thomas Sauter
{"title":"Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation.","authors":"Johannes Witt,&nbsp;Sandra Barisic,&nbsp;Oliver Sawodny,&nbsp;Michael Ederer,&nbsp;Dagmar Kulms,&nbsp;Thomas Sauter","doi":"10.1186/1687-4153-2011-3","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-3","url":null,"abstract":"<p><p> Stimulation of human epithelial cells with IL-1 (10 ng/ml) + UVB radiation results in sustained NFκB activation caused by continuous IKKβ phosphorylation. We have recently published a strictly reduced ordinary differential equation model elucidating the involved mechanisms. Here, we compare model extensions for low IL-1 doses (0.5 ng/ml), where delayed IKKβ phosphorylation is observed. The extended model including a positive regulatory element, most likely auto-ubiquitination of TRAF6, reproduces the observed experimental data most convincingly. The extension is shown to be consistent with the original model and contains very sensitive processes which may serve as potential intervention targets.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2011-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30134859","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: 5
A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana. 拟南芥叶片碳水化合物代谢的系统生物学分析方法。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-06-17 DOI: 10.1186/1687-4153-2011-2
Sebastian Henkel, Thomas Nägele, Imke Hörmiller, Thomas Sauter, Oliver Sawodny, Michael Ederer, Arnd G Heyer
{"title":"A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana.","authors":"Sebastian Henkel,&nbsp;Thomas Nägele,&nbsp;Imke Hörmiller,&nbsp;Thomas Sauter,&nbsp;Oliver Sawodny,&nbsp;Michael Ederer,&nbsp;Arnd G Heyer","doi":"10.1186/1687-4153-2011-2","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-2","url":null,"abstract":"<p><p> Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we present a systems biology approach to analyse any possible regulatory principle that operates such futile cycles based on experimental data for sucrose (Scr) cycling in photosynthetically active leaves of the model plant Arabidopsis thaliana. Kinetic parameters of enzymatic steps in Scr cycling were identified by fitting model simulations to experimental data. A statistical analysis of the kinetic parameters and calculated flux rates allowed for estimation of the variability and supported the predictability of the model. A principal component analysis of the parameter results revealed the identifiability of the model parameters. We investigated the stability properties of Scr cycling and found that feedback inhibition of enzymes catalysing metabolite interconversions at different steps of the cycle have differential influence on stability. Applying this observation to futile cycling of Scr in leaf cells points to the enzyme hexokinase as an important regulator, while the step of Scr degradation by invertases appears subordinate.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2011-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30134858","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: 23
Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks. 用于基因调控网络逆向工程的概率多项式动力学系统。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-06-06 DOI: 10.1186/1687-4153-2011-1
Elena S Dimitrova, Indranil Mitra, Abdul Salam Jarrah
{"title":"Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks.","authors":"Elena S Dimitrova, Indranil Mitra, Abdul Salam Jarrah","doi":"10.1186/1687-4153-2011-1","DOIUrl":"10.1186/1687-4153-2011-1","url":null,"abstract":"<p><p> Elucidating the structure and/or dynamics of gene regulatory networks from experimental data is a major goal of systems biology. Stochastic models have the potential to absorb noise, account for un-certainty, and help avoid data overfitting. Within the frame work of probabilistic polynomial dynamical systems, we present an algorithm for the reverse engineering of any gene regulatory network as a discrete, probabilistic polynomial dynamical system. The resulting stochastic model is assembled from all minimal models in the model space and the probability assignment is based on partitioning the model space according to the likeliness with which a minimal model explains the observed data. We used this method to identify stochastic models for two published synthetic network models. In both cases, the generated model retains the key features of the original model and compares favorably to the resulting models from other algorithms.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2011-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9479167","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
Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D. 体外神经元生长的建模:模拟工具NETMORPH和CX3D的比较。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-01-01 Epub Date: 2011-03-08 DOI: 10.1155/2011/616382
J Aćimović, T Mäki-Marttunen, R Havela, H Teppola, M-L Linne
{"title":"Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D.","authors":"J Aćimović,&nbsp;T Mäki-Marttunen,&nbsp;R Havela,&nbsp;H Teppola,&nbsp;M-L Linne","doi":"10.1155/2011/616382","DOIUrl":"https://doi.org/10.1155/2011/616382","url":null,"abstract":"<p><p>We simulate the growth of neuronal networks using the two recently published tools, NETMORPH and CX3D. The goals of the work are (1) to examine and compare the simulation tools, (2) to construct a model of growth of neocortical cultures, and (3) to characterize the changes in network connectivity during growth, using standard graph theoretic methods. Parameters for the neocortical culture are chosen after consulting both the experimental and the computational work presented in the literature. The first (three) weeks in culture are known to be a time of development of extensive dendritic and axonal arbors and establishment of synaptic connections between the neurons. We simulate the growth of networks from day 1 to day 21. It is shown that for the properly selected parameters, the simulators can reproduce the experimentally obtained connectivity. The selected graph theoretic methods can capture the structural changes during growth.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 ","pages":"616382"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/616382","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29768323","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: 19
Inference of kinetic parameters of delayed stochastic models of gene expression using a markov chain approximation. 用马尔可夫链近似推断基因表达延迟随机模型的动力学参数。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-01-01 Epub Date: 2010-12-29 DOI: 10.1155/2011/572876
Henrik Mannerstrom, Olli Yli-Harja, Andre S Ribeiro
{"title":"Inference of kinetic parameters of delayed stochastic models of gene expression using a markov chain approximation.","authors":"Henrik Mannerstrom,&nbsp;Olli Yli-Harja,&nbsp;Andre S Ribeiro","doi":"10.1155/2011/572876","DOIUrl":"https://doi.org/10.1155/2011/572876","url":null,"abstract":"We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription using the delayed stochastic modelling strategy and realistic parameter values for rate of transcription initiation and RNA degradation. From the model, we generate time series of RNA levels at the single molecule level, from which we use the method to infer the duration of the promoter open complex formation. This is found to be possible even when adding external Gaussian noise to the RNA levels.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 ","pages":"572876"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/572876","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29599325","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: 6
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models. 导致突触可塑性的信号转导建模:五种模型的评价和比较。
EURASIP journal on bioinformatics & systems biology Pub Date : 2011-01-01 Epub Date: 2011-03-29 DOI: 10.1155/2011/797250
Tiina Manninen, Katri Hituri, Eeva Toivari, Marja-Leena Linne
{"title":"Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models.","authors":"Tiina Manninen,&nbsp;Katri Hituri,&nbsp;Eeva Toivari,&nbsp;Marja-Leena Linne","doi":"10.1155/2011/797250","DOIUrl":"https://doi.org/10.1155/2011/797250","url":null,"abstract":"<p><p>An essential phenomenon of the functional brain is synaptic plasticity which is associated with changes in the strength of synapses between neurons. These changes are affected by both extracellular and intracellular mechanisms. For example, intracellular phosphorylation-dephosphorylation cycles have been shown to possess a special role in synaptic plasticity. We, here, provide the first computational comparison of models for synaptic plasticity by evaluating five models describing postsynaptic signal transduction networks. Our simulation results show that some of the models change their behavior completely due to varying total concentrations of protein kinase and phosphatase. Furthermore, the responses of the models vary when models are compared to each other. Based on our study, we conclude that there is a need for a general setup to objectively compare the models and an urgent demand for the minimum criteria that a computational model for synaptic plasticity needs to meet.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 ","pages":"797250"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/797250","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29873026","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: 11
Polynomial-time algorithm for controllability test of a class of boolean biological networks. 一类布尔生物网络可控性测试的多项式时间算法。
EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 Epub Date: 2010-08-25 DOI: 10.1155/2010/210685
Koichi Kobayashi, Jun-Ichi Imura, Kunihiko Hiraishi
{"title":"Polynomial-time algorithm for controllability test of a class of boolean biological networks.","authors":"Koichi Kobayashi, Jun-Ichi Imura, Kunihiko Hiraishi","doi":"10.1155/2010/210685","DOIUrl":"10.1155/2010/210685","url":null,"abstract":"<p><p>In recent years, Boolean-network-model-based approaches to dynamical analysis of complex biological networks such as gene regulatory networks have been extensively studied. One of the fundamental problems in control theory of such networks is the problem of determining whether a given substance quantity can be arbitrarily controlled by operating the other substance quantities, which we call the controllability problem. This paper proposes a polynomial-time algorithm for solving this problem. Although the algorithm is based on a sufficient condition for controllability, it is easily computable for a wider class of large-scale biological networks compared with the existing approaches. A key to this success in our approach is to give up computing Boolean operations in a rigorous way and to exploit an adjacency matrix of a directed graph induced by a Boolean network. By applying the proposed approach to a neurotransmitter signaling pathway, it is shown that it is effective.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29314960","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
A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics. 一种用于疾病发现和视觉分析的新型FES-k-Means聚类算法。
EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 Epub Date: 2010-06-27 DOI: 10.1155/2010/746021
Tonny J Oyana
{"title":"A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics.","authors":"Tonny J Oyana","doi":"10.1155/2010/746021","DOIUrl":"https://doi.org/10.1155/2010/746021","url":null,"abstract":"<p><p>The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique-the Fast, Efficient, and Scalable k-means algorithm (FES-k-means). The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This two-step approach of data training prior to clustering provides a solid foundation for knowledge discovery and data mining, otherwise unclaimed by clustering methods alone. The benefits of this method are that it produces clusters similar to the original k-means method at a much faster rate as shown by runtime comparison data; and it provides efficient analysis of large geospatial data with implications for disease mechanism discovery. From a disease mechanism discovery perspective, it is hypothesized that the linear-like pattern of elevated blood lead levels discovered in the city of Chicago may be spatially linked to the city's water service lines.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2010/746021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29170737","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: 11
Progression analysis and stage discovery in continuous physiological processes using image computing. 用图像计算连续生理过程的进展分析和阶段发现。
EURASIP journal on bioinformatics & systems biology Pub Date : 2010-01-01 Epub Date: 2010-06-30 DOI: 10.1155/2010/107036
Lior Shamir, Salim Rahimi, Nikita Orlov, Luigi Ferrucci, Ilya G Goldberg
{"title":"Progression analysis and stage discovery in continuous physiological processes using image computing.","authors":"Lior Shamir,&nbsp;Salim Rahimi,&nbsp;Nikita Orlov,&nbsp;Luigi Ferrucci,&nbsp;Ilya G Goldberg","doi":"10.1155/2010/107036","DOIUrl":"https://doi.org/10.1155/2010/107036","url":null,"abstract":"<p><p>We propose an image computing-based method for quantitative analysis of continuous physiological processes that can be sensed by medical imaging and demonstrate its application to the analysis of morphological alterations of the bone structure, which correlate with the progression of osteoarthritis (OA). The purpose of the analysis is to quantitatively estimate OA progression in a fashion that can assist in understanding the pathophysiology of the disease. Ultimately, the texture analysis will be able to provide an alternative OA scoring method, which can potentially reflect the progression of the disease in a more direct fashion compared to the existing clinically utilized classification schemes based on radiology. This method can be useful not just for studying the nature of OA, but also for developing and testing the effect of drugs and treatments. While in this paper we demonstrate the application of the method to osteoarthritis, its generality makes it suitable for the analysis of other progressive clinical conditions that can be diagnosed and prognosed by using medical imaging.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"107036"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2010/107036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29155480","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: 12
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