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We present a new formulation of phylogenetic reconstruction named maximum similarity. We describe basic algorithms based on the maximum similarity objective for computing distances between subtrees and for combining two subtrees. We present distance methods for constructing an initial tree and...
Protein structure prediction is one major task in computational biology, and various methods have been proposed for secondary structure prediction. In particular, it is a challenge to predict Î² -sheet structures since they range over several discontinuous regions in an amino acid sequence. In...
In order to handle and interpret the vast amounts of data produced by microarray experiments, the analysis of sets of genes with a common biological functionality has been shown to be advantageous compared to single gene analyses. Some statistical methods have been proposed to analyse the...
Random Threshold Networks (RTNs) are an idealized model of diluted, non-symmetric spin glasses, neural networks or gene regulatory networks. RTNs also serve as an interesting general example of any coordinated causal system. Here we study the conditions for maximal information transfer and...
The p53 gene is crucial for effective tumor suppression in humans as supported by its universal inactivation in cancer cells either through mutations affecting the p53 locus directly or through aberration of its normal regulation. The p53 tumor repressor is regulated through a negative feedback...
Classification methods are commonly divided into two categories: unsupervised and supervised. Unsupervised methods have the ability to discover new classes by grouping data into clusters or tree structures without using the class labels, but they carry the risk of producing noninterpretable...
In recent years, a flurry of new DNA sequencing technologies have altered the landscape of genomics, providing a vast amount of sequence information at a fraction of the costs that were previously feasible. The task of assembling these sequences into a genome has, however, still remained an...
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