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Measuring and analyzing tissue specificity of human genes and protein complexes
Springer Science and Business Media LLC - Tập 2011 - Trang 1-6 - 2011
Dorothea Emig, Tim Kacprowski, Mario Albrecht
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...... hiện toàn bộ
Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data
Springer Science and Business Media LLC - Tập 2008 - Trang 1-12 - 2008
Wentao Zhao, Erchin Serpedin, Edward R Dougherty
Recent advances in high-throughput DNA microarrays and chromatin immunoprecipitation (ChIP) assays have enabled the learning of the structure and functionality of genetic regulatory networks. In light of these heterogeneous data sets, this paper proposes a novel approach for reconstruction of genetic regulatory networks based on the posterior probabilities of gene regulations. Built within the fra...... hiện toàn bộ
A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks
Springer Science and Business Media LLC - Tập 2007 - Trang 1-11 - 2007
Nestor Walter Trepode, Hugo Aguirre Armelin, Michael Bittner, Junior Barrera, Marco Dimas Gubitoso, Ronaldo Fumio Hashimoto
The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical behavior displaying the degree of robustness typical of the biological cell cycle. The structure of our PGN model was inspired in well-established biological facts such as the existence of in...... hiện toàn bộ
A novel cost function to estimate parameters of oscillatory biochemical systems
Springer Science and Business Media LLC - Tập 2012 - Trang 1-17 - 2012
Seyedbehzad Nabavi, Cranos M Williams
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 ...... hiện toàn bộ
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods
Springer Science and Business Media LLC - - 2015
Jie Hou, Gary Stacey, Jianlin Cheng
Abstract Soybean (Glycine max) is a major source of vegetable oil and protein for both animal and human consumption. The completion of soybean genome sequence led to a number of transcriptomic studies (RNA-seq), which provide a resource for gene discovery and functional analysis. Several data-driven (e.g., based on gene expressi...... hiện toàn bộ
Inferring Time-Varying Network Topologies from Gene Expression Data
Springer Science and Business Media LLC - Tập 2007 - Trang 1-12 - 2007
Arvind Rao, Alfred O Hero, David J States, James Douglas Engel
Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has been a need to infer and represent networks in a dynamic, that is, time-varying fashion, in order to account for different cellular states affecting the interactions amongst genes. In this work,...... hiện toàn bộ
Bayesian estimation of the discrete coefficient of determination
Springer Science and Business Media LLC - Tập 2016 - Trang 1-19 - 2016
Ting Chen, Ulisses M. Braga-Neto
The discrete coefficient of determination (CoD) measures the nonlinear interaction between discrete predictor and target variables and has had far-reaching applications in Genomic Signal Processing. Previous work has addressed the inference of the discrete CoD using classical parametric and nonparametric approaches. In this paper, we introduce a Bayesian framework for the inference of the discrete...... hiện toàn bộ
TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites
Springer Science and Business Media LLC - Tập 2010 - Trang 1-15 - 2010
Michael P. Weir, Michael D. Rice
Relative individual information is a measurement that scores the quality of DNA- and RNA-binding sites for biological machines. The development of analytical approaches to increase the power of this scoring method will improve its utility in evaluating the functions of motifs. In this study, the scoring method was applied to potential translation initiation sites in Drosophila to compute Translati...... hiện toàn bộ
A Bayesian Network View on Nested Effects Models
Springer Science and Business Media LLC - Tập 2009 - Trang 1-8 - 2008
Cordula Zeller, Holger Fröhlich, Achim Tresch
Nested effects models (NEMs) are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the signalling pathway. We give a more flexible formulation of NEMs in the language of Bayesian networks. Our framework constitutes a natural generalization of the original NEM model, since it exp...... hiện toàn bộ
Relations between the set-complexity and the structure of graphs and their sub-graphs
Springer Science and Business Media LLC - Tập 2012 - Trang 1-10 - 2012
Tomasz M Ignac, Nikita A Sakhanenko, David J Galas
We describe some new conceptual tools for the rigorous, mathematical description of the “set-complexity” of graphs. This set-complexity has been shown previously to be a useful measure for analyzing some biological networks, and in discussing biological information in a quantitative fashion. The advances described here allow us to define some significant relationships between the set-complexity me...... hiện toàn bộ
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