The interactions among genes and their products are the key determinant of their functions. Discovering these interactions is critical in order to understand fundamental cellular processes and disease mechanisms, and is one of the major research areas in biology. Diseases such as cancer have their ...
In: Presented at the International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics); 2014 16. Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP. Network component analysis: Reconstruction of regulatory signals in biological systems. Proceedings of the ...
Space Ranger uses two different methods for clustering spots by expression similarity, both of which operate in the PCA representation.Graph-basedThe graph-based clustering algorithm consists of building a sparse nearest-neighbor graph (where spots are linked if they are among the k nearest Euclidean...
Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such ...
The method can best be thought of as an analysis approach, to guide and assist in the use of any of a wide range of available clustering algorithms. We call the new methodology consensus clustering, and in conjunction with resampling techniques, it provides for a method to represent the ...
One example is Monte Carlo methods and their extensions, which randomly change parameters and then enrich for changes that improve network performance [44, 45]. Another approach that has had great success is evolutionary algorithms [46]. Here, populations of gene circuits are ‘evolved’ in an ...
Mathematical models and algorithms are used to build these networks for their experimental testing. This allows to study more thoroughly the complex gene regulatory networks that are involved for example in the control of cell embryogenesis, cell differentiation, and tissue development. View chapter...
Ever since the development of high-throughput sequencing technologies, gene module detection methods have been a cornerstone for the biological interpretation of large gene compendia. Numerous approaches and algorithms have been proposed for the detection of gene modules through measuring gene expression3,...
(see “ methods ” section for details). to validate the performance of tsee, we compare it with three other dimensionality reduction algorithms, pca, tsne and ee. tsee outperforms other dimensionality reduction methods in visualization and structure preservation we apply the 4 dimensionality ...
Methods of Genetic Transfer Between Organisms The three main ways to transfer genes between bacterial organisms are conjugation, transduction, and transformation (Fig. 11-5). Bacterial conjugation is the bacterial equivalent of sexual reproduction or mating. To perform conjugation, one bacterium has to...