Computational Biology Research Paper

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Discovery of Non-Coding RNA (Ruzzo) Recent genomic analyses have revealed that, although less than two percent of the human genome encodes proteins, the vast majority of DNA is transcribed into RNA, and a steady stream of discoveries have identified surprising, complex, and subtle new roles for RNA in all realms of life.

This ongoing research project is developing and applying new computational tools for discovery of non-coding RNA.

If we can decipher the sequence by identifying which sequence variations affect a certain phenotype, it would make a great impact on human life.

In recent years, it has become possible to retrieve an individual's sequence information on a genome-wide scale.

Programmed molecular self-assembly will be used for the massively parallel construction of nanoscale devices.

"Smart drugs" that target drug activity to disease cells and activate in response to specific molecular clues will have minimal side effects and improve therapeutic outcomes.

An important aspect of this challenge is the identification of binding sites on the DNA for the proteins involved in such regulation.

One approach to this problem is to deduce the binding sites by considering the regulatory regions of several functionally related genes from a single genome.

However, classical approaches focusing on genotype-phenotype correlation often fail in identifying significant associations between genotype and phenotype.

Variation in the DNA sequence can perturb a complex web of interactions among a number of biological molecules, and that change of the system can lead to phenotypic variation.

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