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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
Identification of CpG islands in DNA sequences using statistically optimal null filters
Springer Science and Business Media LLC - Tập 2012 - Trang 1-14 - 2012
Rajasekhar Kakumani, Omair Ahmad, Vijay Devabhaktuni
CpG dinucleotide clusters also referred to as CpG islands (CGIs) are usually located in the promoter regions of genes in a deoxyribonucleic acid (DNA) sequence. CGIs play a crucial role in gene expression and cell differentiation, as such, they are normally used as gene markers. The earlier CGI identification methods used the rich CpG dinucleotide content in CGIs, as a characteristic measure to id...... hiện toàn bộ
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation
Springer Science and Business Media LLC - Tập 2011 Số 1 - Trang 572876 - 2011
Henrik Mannerström, Olli Yli‐Harja, Alexandra B. Ribeiro
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
The post-genomic era of biological network alignment
Springer Science and Business Media LLC - Tập 2015 - Trang 1-19 - 2015
Fazle E Faisal, Lei Meng, Joseph Crawford, Tijana Milenković
Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by geno...... hiện toàn bộ
Gene Selection for Multiclass Prediction by Weighted Fisher Criterion
Springer Science and Business Media LLC - - 2007
Jianhua Xuan, Yue Wang, Yibin Dong, Yuanjian Feng, Bin Wang, Javed Khan, Maria Bakay, Zuyi Wang, Lauren M. Pachman, Sara T. Winokur, Yiwen Chen, Robert Clarke, Eric P. Hoffman
Adaptive Dynamics of Regulatory Networks: Size Matters
Springer Science and Business Media LLC - - 2009
Dirk Repsilber, Thomas Martinetz, Mats Björklund
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
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