Highly Pathogenic Avian Influenza (HPAI) H5N1 has attracted much attention as a potential pandemic virus in humans, which makes death inevitable in humans. Neuraminidase (NA) has an important role in viral replication. Thus, it is an attractive target when designing anti-influenza virus drug. However, evolving viruses cause some anti-viral drugs to be ineffective, as they show resistance to them. Selection of peptides as drug candidates is important for the peptide-receptor activity and good ...

Insulin secreted by pancreatic islet β-cells is the principal regulating hormone of glucose metabolism. Disruption of insulin secretion may cause glucose to accumulate in the blood, and result in diabetes mellitus. Although deterministic models of the insulin secretion pathway have been developed, the stochastic aspect of this biological pathwa...

In proteomics, many methods for the identification of proteins have been developed. However, because of limited known genome sequences, noisy data, incomplete ion sequences, and the accuracy of protein identification, it is challenging to identify peptides using tandem mass spectral data. Noise filtering and removing thus play a key role in accurate peptide identification from tandem mass spectra. In this paper, we employ a Bayesian model to identify proteins based on the prior information of...

This study modeled the spread of an influenza epidemic in the population of Oran, Algeria. We investigated the mathematical epidemic model, SEIR (Susceptible-Exposed-Infected-Removed), through extensive simulations of the effects of social network on epidemic spread in a Small World (SW) network, to understand how an influenza epidemic spreads through a human population. A combined SEIR-SW model was built, to help understand the dynamics of infectious disease in a community, and to identify t...

RNA secondary structure has become the most exploitable feature for ab initio detection of non-coding RNA (ncRNA) genes from genome sequences. Previous work has used Minimum Free Energy (MFE) based methods developed to identify ncRNAs by measuring sequence fold stability and certainty. However, these methods yielded variable performances across different ncRNA species. Designing novel reliable structural measures will help to develop effective ncRNA gene finding tools. This paper intro...

Hepatitis C virus (HCV) treatment is on the cutting edge of medicine. Due to the high rate of mutations and low fidelity of HCV replication, resistant strains quickly become dominant in a viral population under the selection pressure of a drug. In this paper, we examined the drug resistance mechanism in the NS5A region of genotype 1a HCV virus by comparing the sequence data from interferon-ribavirin treated and untreated patients. To find the drug resistance difference, we used innovative Bay...

Essential proteins are vital to the survival of a cell. There are various features related to the essentiality of proteins, such as biological and topological features. Many computational methods have been developed to identify essential proteins by using these features. However, it is still a big challenge to design an effective method that is able to select suitable features and integrate them to predict essential proteins. In this work, we first collect 26 features, and use SVM-RFE to sele...

With the continuing development and improvement of genome-wide techniques, a great number of candidate genes are discovered. How to identify the most likely disease genes among a large number of candidates becomes a fundamental challenge in human health. A common view is that genes related to a specific or similar disease tend to reside in the same neighbourhood of biomolecular networks. Recently, based on such observations, many methods have been developed to tackle this challenge. In this r...

Allele specific expression is essential for cellular programming and development and the diversity of cellular phenotypes. Traditional analysis methods utilize RNA and depend on single nucleotide polymorphisms, thus to suffer from limited amount of materials for analysis. The rapid development of next-generation sequencing technologies provides more comprehensive and powerful approaches to analyze the genomic, epigenetic, and transcriptomic data, and further to detect and measure allele speci...

Neoadjuvant chemotherapy for breast cancer patients with large tumor size is a necessary treatment. After this treatment patients who achieve a pathologic Complete Response (pCR) usually have a favorable prognosis than those without. Therefore, pCR is now considered as the best prognosticator for patients with neoadjuvant chemotherapy. However, not all patients can benefit from this treatment. As a result, we need to find a way to predict what kind of patients can induce pCR. Various gene sig...