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Ensemble clustering methods have become increasingly important to ease the task of choosing the most appropriate cluster algorithm for a particular data analysis problem. The consensus clustering (CC) algorithm is a recognized ensemble clustering method that uses an artificial intelligence...
Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to “overfitting.” We cast the large-scale covariance matrix estimation problem into the Bayesian hierarchical model...
Protein structure alignment is a fundamental problem in computational and structural biology. While there has been lots of experimental/heuristic methods and empirical results, very few results are known regarding the algorithmic/complexity aspects of the problem, especially on protein local...
Analysis of biopolymer sequences and structures generally adopts one of two approaches: use of detailed biophysical theoretical models of the system with experimentally-determined parameters, or largely empirical statistical models obtained by extracting parameters from large datasets. In this...
Empirical Bayes models have been shown to be powerful tools for identifying differentially expressed genes from gene expression microarray data. An example is the WAME model, where a global covariance matrix accounts for array-to-array correlations as well as differing variances between arrays....
Phylogenetic networks are models of evolution that go beyond trees, incorporating non-tree-like biological events such as recombination (or more generally reticulation), which occur either in a single species ( meiotic recombination ) or between species (reticulation due to lateral gene transfer...
Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is...
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