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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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