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222
Modeling and simulation of genetic regulatory systems: A literature review
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 738 (14 self)
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In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rulebased formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.
Probabilistic Boolean networks: a rulebased uncertainty model for gene regulatory networks
, 2002
"... Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selec ..."
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Cited by 391 (59 self)
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Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selection; and (iv ) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes.
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
 Bioinformatics
, 2003
"... Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few doze ..."
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Cited by 174 (5 self)
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Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few dozen time points during a cell cycle. Most previous studies have assessed the inference results on real gene expression data by comparing predicted genetic regulatory interactions with those known from the biological literature. This approach is controversial due to the absence of known gold standards, which renders the estimation of the sensitivity and specificity, that is, the true and (complementary) false detection rate, unreliable and difficult. The objective of the present study is to test the viability of the Bayesian network paradigm in a realistic simulation study. First, gene expression data are simulated from a realistic biological network involving DNAs, mRNAs, inactive protein monomers and active protein dimers. Then, interaction networks are inferred from these data in a reverse engineering approach, using Bayesian networks and Bayesian learning with Markov chain Monte Carlo.
Results: The simulation results are presented as receiver operator characteristics curves. This allows estimating the proportion of spurious gene interactions incurred for a specified target proportion of recovered true interactions. The findings demonstrate how the network inference performance varies with the training set size, the degree of inadequacy of prior assumptions, the experimental sampling strategy and the inclusion of further, sequencebased information.
A comparison of genetic network models
 In Pac. Symp. Biocomputing
, 2001
"... The inference of genetic interactions from measured expression data is one of the most challenging tasks of modern functional genomics. When successful, the learned network of regulatory interactions yields a wealth of useful information. An inferred genetic network contains information about the p ..."
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Cited by 97 (5 self)
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The inference of genetic interactions from measured expression data is one of the most challenging tasks of modern functional genomics. When successful, the learned network of regulatory interactions yields a wealth of useful information. An inferred genetic network contains information about the pathway to which a gene belongs and which genes it interacts with. Furthermore, it explains the gene's function in terms of how it influences other genes and indicates which genes are pathway initiators and therefore potential drug targets. Obviously, such wealth comes at a price and that of genetic network modeling is that it is an extremely complex task. Therefore, it is necessary to develop sophisticated computational tools that are able to extract relevant information from a limited set of microarray measurements and integrate this with different information sources, to come up with reliable hypotheses of a genetic regulatory network. Thus far, a multitude of modeling approaches has been proposed for discovering genetic networks. However, it is unclear what the advantages and disadvantages of each of the different approaches are and how their results can be compared. In this review, genetic network models are put in a historical perspective that explains why certain models were introduced. Various modeling assumptions and their consequences are also highlighted. In addition, an overview of the principal differences and similarities between the approaches is given by considering the qualitative properties of the chosen models and their learning strategies. In pharmacogenomics and related areas, a lot of research is directed towards discovering, understanding and/or controlling the outcome of some particular biological pathway. Numerous examples exist where the manipulation of a key enzyme in such a pathway did not lead to the desired effect We know that the structure of complex genetic and biochemical networks lies hidden in the sequence information of our DNA but it is far from trivial to predict gene expression from the sequence code alone. The current availability of microarray measurements of thousands of gene expression levels during the course of an experiment or after the knockout of a gene provides a wealth of complementary information that may be exploited to unravel the complex interplay between genes. It now becomes possible to start answering some of the truly challenging questions in systems biology. For example, is it possible to model these genetic interactions as a large network of interacting elements and can these interactions be effectively learned from measured expression data? Since Kauffman Although the behavior and properties of artificial networks match the observations made in real biological systems well, the field of genetic network modeling has yet to reach its full maturity. The automatic discovery of genetic networks from expression data alone is far from trivial because of the combinatorial nature of the problem and the poor information content of 1 For reasons of brevity, the authors consistently refer only to the first author of each reference.
Gene networks inference using dynamic Bayesian networks
 Bioinformatics
, 2003
"... This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly wel ..."
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Cited by 94 (0 self)
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This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly well suited to tackle the stochastic nature of gene regulation and gene expression measurement. Parameters of the model are learned through a penalized likelihood maximization implemented through an extended version of EM algorithm. Our approach is tested against experimental data relative to the S.O.S. DNA Repair network of the Escherichia coli bacterium. It appears to be able to extract the main regulations between the genes involved in this network. An added missing variable is found to model the main protein of the network. Good prediction abilities on unlearned data are observed. These first results are very promising: they show the power of the learning algorithm and the ability of the model to capture gene interactions.
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks
 In Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 03
, 2003
"... We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including proteinprotein interactions, proteinDNA interactions, binding site information, existing literature and so on. Unfortunately, m ..."
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Cited by 80 (6 self)
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We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including proteinprotein interactions, proteinDNA interactions, binding site information, existing literature and so on. Unfortunately, microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the tradeoff between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application. 1.
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data
 Biosystems
, 2003
"... Abstract. We propose a dynamic Bayesian network and nonparametric regression model for constructing a gene network from time series microarray gene expression data. The proposed method can overcome a shortcoming of the Bayesian network model in the sense of the construction of cyclic regulations. Th ..."
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Cited by 78 (12 self)
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Abstract. We propose a dynamic Bayesian network and nonparametric regression model for constructing a gene network from time series microarray gene expression data. The proposed method can overcome a shortcoming of the Bayesian network model in the sense of the construction of cyclic regulations. The proposed method can analyze the microarray data as continuous data and can capture even nonlinear relations among genes. It can be expected that this model will give a deeper insight into the complicated biological systems. We also derive a new criterion for evaluating an estimated network from Bayes approach. We demonstrate the effectiveness of our method by analyzing Saccharomyces cerevisiae gene expression data. 1
Modelling regulatory pathways in E. coli from time series expression profiles
, 2002
"... Motivation: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression profiles ..."
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Cited by 66 (1 self)
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Motivation: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression profiles. Few analysis techniques, however, are well suited to modelling such time series data.
Modeling Tcell activation using gene expression profiling and state space modeling
 Bioinformatics
, 2004
"... Motivation: We have used statespace models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a wellestablished model of Tcell activation. State space models are a class of dynamic Bayesian networks that assume that the obse ..."
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Cited by 63 (3 self)
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Motivation: We have used statespace models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a wellestablished model of Tcell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics.These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. Results: Bootstrap confidence intervals are developed for parameters representing ‘gene–gene ’ interactions over time. Our models represent the dynamics of Tcell activation and provide a methodology for the development of rational and experimentally testable hypotheses. Availability: Supplementary data and Matlab computer source code will be made available on the web at the URL given below.
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network
 Proc. 1st IEEE Computer Society Bioinformatics Conference
, 2002
"... We propose a new statistical method for constructing a genetic network from microarray gene expression data by using a Bayesian network. An essential point of Bayesian network construction is in the estimation of the conditional distribution of each random variable. We consider fitting nonparametric ..."
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Cited by 51 (19 self)
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We propose a new statistical method for constructing a genetic network from microarray gene expression data by using a Bayesian network. An essential point of Bayesian network construction is in the estimation of the conditional distribution of each random variable. We consider fitting nonparametric regression models with heterogeneous error variances to the microarray gene expression data to capture the nonlinear structures between genes. A problem still remains to be solved in selecting an optimal graph, which gives the best representation of the system among genes. We theoretically derive a new graph selection criterion from Bayes approach in general situations. The proposed method includes previous methods based on Bayesian networks. We demonstrate the effectiveness of the proposed method through the analysis of Saccharomyces cerevisiae gene expression data newly obtained by disrupting 100 genes. 1.