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Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability
Springer Science and Business Media LLC - - 2008
Gang Wu, Ming-Yang Kao, Guohui Lin, Jia-Huai You
Inferring interaction type in gene regulatory networks using co-expression data
Springer Science and Business Media LLC - Tập 10 - Trang 1-11 - 2015
Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei, Gary D Bader
Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulatory interactions from genomics data, such as gene expression profiles; however, these approaches do not provide evidence about the regulation type (positive or negative sign) of the interaction...... hiện toàn bộ
On weighted k-mer dictionaries
Springer Science and Business Media LLC - Tập 18 - Trang 1-20 - 2023
Giulio Ermanno Pibiri
We consider the problem of representing a set of $$k$$ -mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a $$k$$ -mer is eff...... hiện toàn bộ
P-value based visualization of codon usage data
Springer Science and Business Media LLC - Tập 1 - Trang 1-7 - 2006
Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke, Stephan Waack
Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We h...... hiện toàn bộ
Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features
Springer Science and Business Media LLC - Tập 11 - Trang 1-12 - 2016
Prabina Kumar Meher, Tanmaya Kumar Sahu, A. R. Rao, S. D. Wahi
Identification of splice sites is essential for annotation of genes. Though existing approaches have achieved an acceptable level of accuracy, still there is a need for further improvement. Besides, most of the approaches are species-specific and hence it is required to develop approaches compatible across species. Each splice site sequence was transformed into a numeric vector of length 49, out o...... hiện toàn bộ
Module detection in complex networks using integer optimisation
Springer Science and Business Media LLC - Tập 5 - Trang 1-11 - 2010
Gang Xu, Laura Bennett, Lazaros G Papageorgiou, Sophia Tsoka
The detection of modules or community structure is widely used to reveal the underlying properties of complex networks in biology, as well as physical and social sciences. Since the adoption of modularity as a measure of network topological properties, several methodologies for the discovery of community structure based on modularity maximisation have been developed. However, satisfactory partitio...... hiện toàn bộ
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant’s approach
Springer Science and Business Media LLC - Tập 6 - Trang 1-22 - 2011
Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
RNA secondary structure prediction is a mainstream bioinformatic domain, and is key to computational analysis of functional RNA. In more than 30 years, much research has been devoted to defining different variants of RNA structure prediction problems, and to developing techniques for improving prediction quality. Nevertheless, most of the algorithms in this field follow a similar dynamic programmi...... hiện toàn bộ
Invariant based quartet puzzling
Springer Science and Business Media LLC - Tập 7 - Trang 1-9 - 2012
Joseph P Rusinko, Brian Hipp
First proposed by Cavender and Felsenstein, and Lake, invariant based algorithms for phylogenetic reconstruction were widely dismissed by practicing biologists because invariants were perceived to have limited accuracy in constructing trees based on DNA sequences of reasonable length. Recent developments by algebraic geometers have led to the construction of lists of invariants which have been dem...... hiện toàn bộ
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Springer Science and Business Media LLC - Tập 4 - Trang 1-10 - 2009
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative models, such as Hidden Markov Models (HMMs) and Stochastic Grammars, are routinely applied. We introduce Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) as an extension of Hidden Conditional Random Fields (H...... hiện toàn bộ
On an enhancement of RNA probing data using information theory
Springer Science and Business Media LLC - Tập 15 - Trang 1-22 - 2020
Thomas J. X. Li, Christian M. Reidys
Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via chemical probing data. We employ an information-theoretic approach to solve the problem, via considering a variant of the Rényi-Ulam game. Our framework is centered around the ensemble tree,...... hiện toàn bộ
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