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Processed pseudogenes are DNA sequences generated through reverse transcription (RT) and retrotransposition of mature mRNAs. These sequences are usually considered junk DNA, since in most cases they lack a suitable promoter and are no longer transcribed. Nonetheless, due to their origin, they...
We propose a unified theoretical scheme to calculate genotype frequencies of polymorphic populations with biological and social inheritance. This scheme is used to simulate the effects of social non-random mating on the population's evolution in the general situation of multiple biological gene...
As pathogens evolve effective schemes to overcome the effect of antibiotics, the prevalent “one drug and one drug target” approach is falling behind. We propose novel strategies for identifying potential multiple-drug targets in pathogenic protein-protein interaction (PPI) networks with the...
An important strategy to study genome evolution is to investigate the clustering of orthologous genes among multiple genomes, in which the most popular approaches require that the distance between adjacent genes in a cluster be small. We investigate a different formulation based on constraining...
In this article, we propose an effective data mining technique for multi-class protein sequence classification. The technique, which can discover discriminative motif-sets for classification, performs its tasks in two phases. In Phase 1, it makes use of a popular motif discovery algorithm called...
In this article, we consider the problem of sorting a linear/circular, multi-chromosomal genome by reversals, block-interchanges (i.e., generalized transpositions), and translocations (including fusions and fissions) where the used operations can be weighted differently, which aims to find a...
Large multidimensional data matrices are frequent in biology. However, statistical methods often have difficulties dealing with such matrices because they contain very complex data sets. Consequently variable selection and dimensionality reduction methods are often used to reduce matrix...
A high-affinity inhibitor protein called CIP , produced by small truncations of p35, was experimentally identified. P35 is a physiological activator of the cyclin-dependent kinase cdk5. P25 is derived from proteolytic truncation of p35 within “stressed” neurons, and it is associated with the...
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