EURASIP journal on bioinformatics & systems biology最新文献

{"title":"From microscopy data to in silico environments for in vivo-oriented simulations.","authors":"Noriko Hiroi1,&nbsp;Michael Klann,&nbsp;Keisuke Iba,&nbsp;Pablo de Heras Ciechomski,&nbsp;Shuji Yamashita,&nbsp;Akito Tabira,&nbsp;Takahiro Okuhara,&nbsp;Takeshi Kubojima,&nbsp;Yasunori Okada,&nbsp;Kotaro Oka,&nbsp;Robin Mange,&nbsp;Michael Unger,&nbsp;Akira Funahashi,&nbsp;Heinz Koeppl","doi":"10.1186/1687-4153-2012-7","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-7","url":null,"abstract":"<p><strong>Abstract: </strong>: In our previous study, we introduced a combination methodology of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM), which is powerful to investigate the effect of intracellular environment to biochemical reaction processes. Now, we developed a reconstruction method of realistic simulation spaces based on our TEM images. Interactive raytracing visualization of this space allows the perception of the overall 3D structure, which is not directly accessible from 2D TEM images. Simulation results show that the diffusion in such generated structures strongly depends on image post-processing. Frayed structures corresponding to noisy images hinder the diffusion much stronger than smooth surfaces from denoised images. This means that the correct identification of noise or structure is significant to reconstruct appropriate reaction environment in silico in order to estimate realistic behaviors of reactants in vivo. Static structures lead to anomalous diffusion due to the partial confinement. In contrast, mobile crowding agents do not lead to anomalous diffusion at moderate crowding levels. By varying the mobility of these non-reactive obstacles (NRO), we estimated the relationship between NRO diffusion coefficient (Dnro) and the anomaly in the tracer diffusion (α). For Dnro=21.96 to 44.49 μm2/s, the simulation results match the anomaly obtained from FCS measurements. This range of the diffusion coefficient from simulations is compatible with the range of the diffusion coefficient of structural proteins in the cytoplasm. In addition, we investigated the relationship between the radius of NRO and anomalous diffusion coefficient of tracers by the comparison between different simulations. The radius of NRO has to be 58 nm when the polymer moves with the same diffusion speed as a reactant, which is close to the radius of functional protein complexes in a cell.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2012-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30719475","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":"Phase computations and phase models for discrete molecular oscillators.","authors":"Onder Suvak,&nbsp;Alper Demir","doi":"10.1186/1687-4153-2012-6","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-6","url":null,"abstract":"<p><strong>Background: </strong>Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigorous and useful definition for phase is based on the so-called isochrons of oscillators. Phase computation techniques for continuous oscillators that are based on isochrons have been used for characterizing the behavior of various types of oscillators under the influence of perturbations such as noise.</p><p><strong>Results: </strong>In this article, we extend the applicability of these phase computation methods to biochemical oscillators as discrete molecular systems, upon the information obtained from a continuous-state approximation of such oscillators. In particular, we describe techniques for computing the instantaneous phase of discrete, molecular oscillators for stochastic simulation algorithm generated sample paths. We comment on the accuracies and derive certain measures for assessing the feasibilities of the proposed phase computation methods. Phase computation experiments on the sample paths of well-known biological oscillators validate our analyses.</p><p><strong>Conclusions: </strong>The impact of noise that arises from the discrete and random nature of the mechanisms that make up molecular oscillators can be characterized based on the phase computation techniques proposed in this article. The concept of isochrons is the natural choice upon which the phase notion of oscillators can be founded. The isochron-theoretic phase computation methods that we propose can be applied to discrete molecular oscillators of any dimension, provided that the oscillatory behavior observed in discrete-state does not vanish in a continuous-state approximation. Analysis of the full versatility of phase noise phenomena in molecular oscillators will be possible if a proper phase model theory is developed, without resorting to such approximations.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2012-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30681747","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":"Modeling stochasticity and variability in gene regulatory networks.","authors":"David Murrugarra,&nbsp;Alan Veliz-Cuba,&nbsp;Boris Aguilar,&nbsp;Seda Arat,&nbsp;Reinhard Laubenbacher","doi":"10.1186/1687-4153-2012-5","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-5","url":null,"abstract":"<p><p> Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This article contributes an approach as an alternative to these classical settings. Within the discrete paradigm, where genes, proteins, and other molecular components of gene regulatory networks are modeled as discrete variables and are assigned as logical rules describing their regulation through interactions with other components. Stochasticity is modeled at the biological function level under the assumption that even if the expression levels of the input nodes of an update rule guarantee activation or degradation there is a probability that the process will not occur due to stochastic effects. This approach allows a finer analysis of discrete models and provides a natural setup for cell population simulations to study cell-to-cell variability. We applied our methods to two of the most studied regulatory networks, the outcome of lambda phage infection of bacteria and the p53-mdm2 complex.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2012-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30670850","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 visual analytics approach for models of heterogeneous cell populations.","authors":"Jan Hasenauer,&nbsp;Julian Heinrich,&nbsp;Malgorzata Doszczak,&nbsp;Peter Scheurich,&nbsp;Daniel Weiskopf,&nbsp;Frank Allgöwer","doi":"10.1186/1687-4153-2012-4","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-4","url":null,"abstract":"<p><p> In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in most populations of primary cells, cancer cells, and stem cells. Unfortunately, tools for in-depth analysis of population models are still missing. This problem originates from the complexity of population models. Particularly important are methods to determine the source of heterogeneity (e.g., genetics or epigenetic differences) and to select potential (bio-)markers. We propose an analysis based on visual analytics to tackle this problem. Our approach combines parallel-coordinates plots, used for a visual assessment of the high-dimensional dependencies, and nonlinear support vector machines, for the quantification of effects. The method can be employed to study qualitative and quantitative differences among cells. To illustrate the different components, we perform a case study using the proapoptotic signal transduction pathway involved in cellular apoptosis.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2012-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30657447","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 novel cost function to estimate parameters of oscillatory biochemical systems.","authors":"Seyedbehzad Nabavi,&nbsp;Cranos M Williams","doi":"10.1186/1687-4153-2012-3","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-3","url":null,"abstract":"<p><p> Oscillatory pathways are among the most important classes of biochemical systems with examples ranging from circadian rhythms and cell cycle maintenance. Mathematical modeling of these highly interconnected biochemical networks is needed to meet numerous objectives such as investigating, predicting and controlling the dynamics of these systems. Identifying the kinetic rate parameters is essential for fully modeling these and other biological processes. These kinetic parameters, however, are not usually available from measurements and most of them have to be estimated by parameter fitting techniques. One of the issues with estimating kinetic parameters in oscillatory systems is the irregularities in the least square (LS) cost function surface used to estimate these parameters, which is caused by the periodicity of the measurements. These irregularities result in numerous local minima, which limit the performance of even some of the most robust global optimization algorithms. We proposed a parameter estimation framework to address these issues that integrates temporal information with periodic information embedded in the measurements used to estimate these parameters. This periodic information is used to build a proposed cost function with better surface properties leading to fewer local minima and better performance of global optimization algorithms. We verified for three oscillatory biochemical systems that our proposed cost function results in an increased ability to estimate accurate kinetic parameters as compared to the traditional LS cost function. We combine this cost function with an improved noise removal approach that leverages periodic characteristics embedded in the measurements to effectively reduce noise. The results provide strong evidence on the efficacy of this noise removal approach over the previous commonly used wavelet hard-thresholding noise removal methods. This proposed optimization framework results in more accurate kinetic parameters that will eventually lead to biochemical models that are more precise, predictable, and controllable.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2012-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30619698","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":"Determination of minimal transcriptional signatures of compounds for target prediction.","authors":"Florian Nigsch,&nbsp;Janna Hutz,&nbsp;Ben Cornett,&nbsp;Douglas W Selinger,&nbsp;Gregory McAllister,&nbsp;Somnath Bandyopadhyay,&nbsp;Joseph Loureiro,&nbsp;Jeremy L Jenkins","doi":"10.1186/1687-4153-2012-2","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-2","url":null,"abstract":"<p><p> The identification of molecular target and mechanism of action of compounds is a key hurdle in drug discovery. Multiplexed techniques for bead-based expression profiling allow the measurement of transcriptional signatures of compound-treated cells in high-throughput mode. Such profiles can be used to gain insight into compounds' mode of action and the protein targets they are modulating. Through the proxy of target prediction from such gene signatures we explored important aspects of the use of transcriptional profiles to capture biological variability of perturbed cellular assays. We found that signatures derived from expression data and signatures derived from biological interaction networks performed equally well, and we showed that gene signatures can be optimised using a genetic algorithm. Gene signatures of approximately 128 genes seemed to be most generic, capturing a maximum of the perturbation inflicted on cells through compound treatment. Moreover, we found evidence for oxidative phosphorylation to be one of the most general ways to capture compound perturbation.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2012-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30607587","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 top-down approach to classify enzyme functional classes and sub-classes using random forest.","authors":"Chetan Kumar,&nbsp;Alok Choudhary","doi":"10.1186/1687-4153-2012-1","DOIUrl":"https://doi.org/10.1186/1687-4153-2012-1","url":null,"abstract":"<p><p> Advancements in sequencing technologies have witnessed an exponential rise in the number of newly found enzymes. Enzymes are proteins that catalyze bio-chemical reactions and play an important role in metabolic pathways. Commonly, function of such enzymes is determined by experiments that can be time consuming and costly. Hence, a need for a computing method is felt that can distinguish protein enzyme sequences from those of non-enzymes and reliably predict the function of the former. To address this problem, approaches that cluster enzymes based on their sequence and structural similarity have been presented. But, these approaches are known to fail for proteins that perform the same function and are dissimilar in their sequence and structure. In this article, we present a supervised machine learning model to predict the function class and sub-class of enzymes based on a set of 73 sequence-derived features. The functional classes are as defined by International Union of Biochemistry and Molecular Biology. Using an efficient data mining algorithm called random forest, we construct a top-down three layer model where the top layer classifies a query protein sequence as an enzyme or non-enzyme, the second layer predicts the main function class and bottom layer further predicts the sub-function class. The model reported overall classification accuracy of 94.87% for the first level, 87.7% for the second, and 84.25% for the bottom level. Our results compare very well with existing methods, and in many cases report better performance. Using feature selection methods, we have shown the biological relevance of a few of the top rank attributes.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2012 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2012-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2012-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30494874","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":"Detecting controlling nodes of boolean regulatory networks.","authors":"Steffen Schober,&nbsp;David Kracht,&nbsp;Reinhard Heckel,&nbsp;Martin Bossert","doi":"10.1186/1687-4153-2011-6","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-6","url":null,"abstract":"<p><p> Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show that functions found in Boolean regulatory networks belong to certain classes of functions, for example, the unate functions. It turns out that these classes have specific properties in the Fourier domain. That motivates us to study the problem of detecting controlling nodes in classes of Boolean networks using spectral techniques. We consider networks with unbalanced functions and functions of an average sensitivity less than 23k, where k is the number of controlling variables for a function. Further, we consider the class of 1-low networks which include unate networks, linear threshold networks, and networks with nested canalyzing functions. We show that the application of spectral learning algorithms leads to both better time and sample complexity for the detection of controlling nodes compared with algorithms based on exhaustive search. For a particular algorithm, we state analytical upper bounds on the number of samples needed to find the controlling nodes of the Boolean functions. Further, improved algorithms for detecting controlling nodes in large-scale unate networks are given and numerically studied.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2011-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30199263","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":"Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models.","authors":"Syed Murtuza Baker,&nbsp;C Hart Poskar,&nbsp;Björn H Junker","doi":"10.1186/1687-4153-2011-7","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-7","url":null,"abstract":"<p><p> In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2011-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30200695","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":"Measuring and analyzing tissue specificity of human genes and protein complexes.","authors":"Dorothea Emig,&nbsp;Tim Kacprowski,&nbsp;Mario Albrecht","doi":"10.1186/1687-4153-2011-5","DOIUrl":"https://doi.org/10.1186/1687-4153-2011-5","url":null,"abstract":"<p><p> Proteins and their interactions are essential for the survival of each human cell. Knowledge of their tissue occurrence is important for understanding biological processes. Therefore, we analyzed microarray and high-throughput RNA-sequencing data to identify tissue-specific and universally expressed genes. Gene expression data were used to investigate the presence of proteins, protein interactions and protein complexes in different tissues. Our comparison shows that the detection of tissue-specific genes and proteins strongly depends on the applied measurement technique. We found that microarrays are less sensitive for low expressed genes than high-throughput sequencing. Functional analyses based on microarray data are thus biased towards high expressed genes. This also means that previous biological findings based on microarrays might have to be re-examined using high-throughput sequencing results.</p>","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":" ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2011-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1687-4153-2011-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30185097","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}