37,331 research outputs found
Identifying statistical dependence in genomic sequences via mutual information estimates
Questions of understanding and quantifying the representation and amount of
information in organisms have become a central part of biological research, as
they potentially hold the key to fundamental advances. In this paper, we
demonstrate the use of information-theoretic tools for the task of identifying
segments of biomolecules (DNA or RNA) that are statistically correlated. We
develop a precise and reliable methodology, based on the notion of mutual
information, for finding and extracting statistical as well as structural
dependencies. A simple threshold function is defined, and its use in
quantifying the level of significance of dependencies between biological
segments is explored. These tools are used in two specific applications. First,
for the identification of correlations between different parts of the maize
zmSRp32 gene. There, we find significant dependencies between the 5'
untranslated region in zmSRp32 and its alternatively spliced exons. This
observation may indicate the presence of as-yet unknown alternative splicing
mechanisms or structural scaffolds. Second, using data from the FBI's Combined
DNA Index System (CODIS), we demonstrate that our approach is particularly well
suited for the problem of discovering short tandem repeats, an application of
importance in genetic profiling.Comment: Preliminary version. Final version in EURASIP Journal on
Bioinformatics and Systems Biology. See http://www.hindawi.com/journals/bsb
Modeling heterogeneity in random graphs through latent space models: a selective review
We present a selective review on probabilistic modeling of heterogeneity in
random graphs. We focus on latent space models and more particularly on
stochastic block models and their extensions that have undergone major
developments in the last five years
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