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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
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
Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments
Springer Science and Business Media LLC - Tập 7 - Trang 1-16 - 2012
Vadim Farztdinov, Fionnuala McDyer
Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and c...... hiện toàn bộ
The feasibility of genome-scale biological network inference using Graphics Processing Units
Springer Science and Business Media LLC - Tập 12 - Trang 1-13 - 2017
Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil, Daniel A. Beard
Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network interactions include statistical inference-based approaches and methods to identify dynamical systems models that are capable of fitting multivariate data. Availability of large data sets and so...... hiện toàn bộ
A robust approach based on Weibull distribution for clustering gene expression data
Springer Science and Business Media LLC - Tập 6 - Trang 1-9 - 2011
Huakun Wang, Zhenzhen Wang, Xia Li, Binsheng Gong, Lixin Feng, Ying Zhou
Clustering is a widely used technique for analysis of gene expression data. Most clustering methods group genes based on the distances, while few methods group genes according to the similarities of the distributions of the gene expression levels. Furthermore, as the biological annotation resources accumulated, an increasing number of genes have been annotated into functional categories. As a resu...... hiện toàn bộ
Alignment- and reference-free phylogenomics with colored de Bruijn graphs
Springer Science and Business Media LLC - Tập 15 Số 1 - 2020
Roland Wittler
AbstractBackgroundThe increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence a...... hiện toàn bộ
Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity
Springer Science and Business Media LLC - Tập 5 Số 1 - 2010
Binh Thanh Nguyen, Andreas Spillner, Brent C. Emerson, Vincent Moulton
Abstract We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeography, and in the conservation of biodiversity where it is a factor in nature reserve selection. Complementing current methods for measurin...... hiện toàn bộ
Unifying duplication episode clustering and gene-species mapping inference
Springer Science and Business Media LLC - Tập 19 - Trang 1-20 - 2024
Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek
We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC). This problem is particularly relevant in metagenomics, where incomplete data often poses a challenge in the accurate reconstruction of gene histories. To solve MetaEC, we propose a polynomi...... hiện toàn bộ
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
An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data
Springer Science and Business Media LLC - Tập 11 - Trang 1-10 - 2016
Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu
Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address the missing data crudely by ignoring such atoms from their structures. In this paper, we prop...... hiện toàn bộ
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