Protein structure Quality Assessment (QA) is an essential component in protein structure prediction and analysis. The relationship between protein sequence and structure often serves as a basis for protein structure QA. In this work, we developed a new Hidden Markov Model (HMM) to assess the compatibility of protein sequence and structure for capturing their complex relationship. More specifically, the emission of the HMM consists of protein local structures in angular space, secondary struct...

Transcription Factors (TFs) are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases. Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations....

Brain tumor segmentation aims to separate the different tumor tissues such as active cells, necrotic core, and edema from normal brain tissues of White Matter (WM), Gray Matter (GM), and Cerebrospinal Fluid (CSF). MRI-based brain tumor segmentation studies are attracting more and more attention in recent years due to non-invasive imaging and good soft tissue contrast of Magnetic Resonance Imaging (MRI) images. With the development of almost two decades, the innovative approaches applying comp...

Genome-Wide Association Studies (GWASs) aim to identify genetic variants that are associated with disease by assaying and analyzing hundreds of thousands of Single Nucleotide Polymorphisms (SNPs). Although traditional single-locus statistical approaches have been standardized and led to many interesting findings, a substantial number of recent GWASs indicate that for most disorders, the individual SNPs explain only a small fraction of the genetic causes. Consequently, exploring multi-SNPs int...

Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized nave Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected fro...

Gene expression is a critical process in biological system that is influenced and modulated by many factors including genetic variation. Expression Quantitative Trait Loci (eQTL) analysis provides a powerful way to understand how genetic variants affect gene expression. For genome wide eQTL analysis, the number of genetic variants and that of genes are large and thus the search space is tremendous. Therefore, eQTL analysis brings about computational and statistical challenges. In this paper, ...

Protein sequence motifs extraction is an important field of bioinformatics since its relevance to the structural analysis. Two major problems are related to this field: (1) searching the motifs within the same protein family; and (2) assuming a window size for the motifs search. This work proposes the Hierarchically Clustered Hidden Markov Model (HC-HMM) approach, which represents the behavior and structure of proteins in terms of a Hidden Markov Model chain and hierarchically clusters each c...

Angiogenesis, the growth of new blood vessel from existing ones, is a pivotal stage in cancer development, and is an important target for cancer therapy. We develop a hybrid mathematical model to understand the mechanisms behind tumor-induced angiogenesis. This model describes uptake of Tumor Angiogenic Factor (TAF) at extracellular level, uses partial differential equation to describe the evolution of endothelial cell density including TAF induced proliferation, chemotaxis to TAF, and haptot...

Biological network alignment is an important research topic in the field of bioinformatics. Nowadays almost every existing alignment method is designed to solve the deterministic biological network alignment problem. However, it is worth noting that interactions in biological networks, like many other processes in the biological realm, are probabilistic events. Therefore, more accurate and better results can be obtained if biological networks are characterized by probabilistic graphs. This pr...

ID-based constant-round group key agreement protocols are efficient in both computation and communication, but previous protocols did not provide valid message authentication. An improvement based on attack analysis is proposed in this paper. The improved method takes full advantage of the data transmitted at various stages of the protocol. By guaranteeing the freshness of authentication messages, the authenticity of the generator of authentication messages, and the completeness of the authen...