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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
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......
Invariant based quartet puzzling
Springer Science and Business Media LLC - Tập 7 - Trang 1-9 - 2012
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......
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Springer Science and Business Media LLC - Tập 4 - Trang 1-10 - 2009
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......
On an enhancement of RNA probing data using information theory
Springer Science and Business Media LLC - Tập 15 - Trang 1-22 - 2020
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,......
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
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......
Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
Springer Science and Business Media LLC - Tập 9 - Trang 1-13 - 2014
The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unkno......
The feasibility of genome-scale biological network inference using Graphics Processing Units
Springer Science and Business Media LLC - Tập 12 - Trang 1-13 - 2017
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......
A robust approach based on Weibull distribution for clustering gene expression data
Springer Science and Business Media LLC - Tập 6 - Trang 1-9 - 2011
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......
Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors
Springer Science and Business Media LLC - Tập 14 - Trang 1-14 - 2019
Tumors exhibit extensive intra-tumor heterogeneity, the presence of groups of cellular populations with distinct sets of somatic mutations. This heterogeneity is the result of an evolutionary process, described by a phylogenetic tree. In addition to enabling clinicians to devise patient-specific treatment plans, phylogenetic trees of tumors enable researchers to decipher the mechanisms of tumorige......
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem
Springer Science and Business Media LLC - Tập 15 - Trang 1-15 - 2020
Transcriptomic structural variants (TSVs)—large-scale transcriptome sequence change due to structural variation - are common in cancer. TSV detection from high-throughput sequencing data is a computationally challenging problem. Among all the confounding factors, sample heterogeneity, where each sample contains multiple distinct alleles, poses a critical obstacle to accurate TSV prediction. To imp......
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