Rosa Aghdam

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Identifying of B-cell epitopes from antigen is a challenging task in bioinformatics and applied in vaccine design and drug development. Recently, several methods have been presented to predict epitopes. The physicochemical or structural properties are used by these methods. In this paper, we propose a more appropriate epitope prediction method, LRC, that is(More)
Inferring gene regulatory networks (GRNs) is a major issue in systems biology, which explicitly characterizes regulatory processes in the cell. The Path Consistency Algorithm based on Conditional Mutual Information (PCA-CMI) is a well-known method in this field. In this study, we introduce a new algorithm (IPCA-CMI) and apply it to a number of gene(More)
Inferring Gene Regulatory Networks (GRNs) from gene expression data is a major challenge in systems biology. The Path Consistency (PC) algorithm is one of the popular methods in this field. However, as an order dependent algorithm, PC algorithm is not robust because it achieves different network topologies if gene orders are permuted. In addition, the(More)
A Profile Hidden Markov Model (PHMM) is a standard form of a Hidden Markov Models used for modeling protein and DNA sequence families based on multiple alignment. In this paper, we implement Baum-Welch algorithm and the Bayesian Monte Carlo Markov Chain (BMCMC) method for estimating parameters of small artificial PHMM. In order to improve the prediction(More)
Gene regulatory networks explain how cells control the expression of genes, which, together with some additional regulation downstream, determines the production of proteins essential for cellular function. Bayesian networks (BNs) are practical tools which have been successfully implemented in learning gene networks based on microarray gene expression data.(More)
Regulatory sequences such as promoters not only contain cis-regulatory elements as switches of transcription, but also exhibit particular topological features. In this paper, we introduce a systematic genome scale approach to characterize the roles of structural conformation and stability profile of promoter sequence in gene expression. The average free(More)
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