Amirhossein Manzourolajdad

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UNLABELLED RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both(More)
RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated(More)
Because of a high mutation rate, HIV exists as a viral swarm of many sequence variants evolving under various selective pressures from the human immune system. Although the Nef gene codes for the most immunogenic of HIV accessory proteins, which alone makes it of great interest to HIV research, it also encodes an RNA structure, whose contribution to HIV(More)
Stochastic context-free grammars (SCFG) have been used in RNA Secondary structure modeling. An SCFG consists of a set of grammar rules with probability for each. Given a grammar design, finding the best set of probabilities that yield optimum performance can be challenging. Although current Expectation Maximization (EM) MaximumLikelihood (ML)-based model(More)
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