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Protein folding rate is one of the important properties of a protein. Protein folding rate prediction is useful for understanding protein folding process and guiding protein design. In this study, we developed a support vector machine (SVM) based method to predict protein folding kinetic types (two-state or non-two-state) and the real-value folding rate using the features calculated from the three-dimensional...
Microarray gene expression data comes as a time series, where the expression level of a gene is recorded at specific time points. Comparing the time series produced by two genes can give us information about the regulatory or inhibitory relationship between the genes. We present a Dynamic Programming (DP) method to compare gene expression data using geometric similarity. We aim to detect similarities...
This work discusses the performance of a color decomposition based active contours for segmenting cell nuclei from glioma histopathology. By combining a nuclear staining information obtained from color decomposition with fast variational active contours we obtain unsupervised segmentation of nuclei in histopathological images. Experimental results show promise when compared with different state of...
An important goal of cancer genomic research is to identify the driving pathways underlying disease mechanisms. It is well known that somatic genome alterations (SGAs) affecting the genes that encode the proteins within a common signaling pathway exhibit mutual exclusivity, in which these SGAs usually do not co-occur in a tumor. With some success, this property has been utilized as an objective function...
A small set of genes showed reduced expression in mites on A. mellifera host, including putative transcription factors and digestive tract developmental genes. The vast majority of differentially expressed genes were up-regulated in this host. This gene set showed enrichment for genes associated with mitochondrial respiratory function and apoptosis, suggesting that mites on this host may be experiencing...
The problem of deciding whether or not a concentration of messenger RNA corresponds to a gene in expressed state is crucial in the Boolean representation of gene regulatory networks. Since there is no independent mathematical description of gene expressions, the computational answers of this problem are affected by uncertainties in the model used for the design of the computer algorithms, and by the...
HIV-1 Env glycoprotein complex is the key protein that mediates binding and entry of HIV-1 into human host cells. The complex entry process involves three main steps. First, the attachment, the interaction of gp120 and CD4. Second, the coreceptor binding, where gp120 binds the chemokine receptor CCR5 or CXCR4, and finally, the fusion of viral and host cell membranes. Despite the fact that several...
The tidal volume and breath frequency had demonstrated to have respective effect on respiratory sinus arrhythmia. This study was designed to mimic the oscillatory breath pattern as periodic breathing by healthy subjects. We aimed to determine the impacts of breathing frequency and tidal volume on the respiratory modulation on heart rate. The components of heart rate variability were calculated in...
In biology there is often the need to discover the most promising genes, among a large list of candidate genes, to further investigate. While a single data source might not be effective enough, integrating several complementary genomic data sources leads to more accurate prediction.
Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite...
This work investigates the problem of feature selection in neuroimaging features from structural MRI brain images for the classification of subjects as healthy controls, suffering from Mild Cognitive Impairment or Alzheimer's Disease. A Genetic Algorithm wrapper method for feature selection is adopted in conjunction with a Support Vector Machine classifier. In very large feature sets, feature selection...
Pediatric cardiomyopathies are a heterogeneous group of disorders in which early detection and treatment can drastically alter the course of the disease. Cardiac MRIs have become an increasingly popular option in evaluating for cardiomyopathies, though they remain expensive and time-consuming compared to echocardiography. Because guidelines for the use of cardiac MRI are vague, we investigated the...
Biological networks are usually used to model interactions among biological macromolecules in a cells. For instance protein-protein interaction networks (PIN) are used to model and analyse the set of interactions among proteins. The comparison of networks may result in the identification of conserved patterns of interactions corresponding to biological relevant entities such as protein complexes and...
The objective of this paper is to provide a hybrid algorithm for non-negative matrix factorization based on a symmetric version of Kullback-Leibler divergence, known as intrinsic information. The convergence of the proposed algorithm is shown for several members of the exponential family such as the Gaussian, Poisson, gamma and inverse Gaussian models. The speed of this algorithm is examined and its...
The design and management of information systems is driven by model-oriented approaches on different levels of abstraction. For instance, enterprise models link the organizational action system and corresponding information systems. Enterprise models are generally perceived as measures to close the gap between business and IT, as it is in the healthcare domain. Clinical Pathways (CPs) represent value-added...
Trauma is one of the leading causes of death in the U.S. and is ranked third among death causes across all age groups. This paper presents a novel fuzzy rule-based classification approach based on the concept of General Type-2 Fuzzy sets to predict mortality for trauma patients. In this approach each rule in the rule-base has an IF and a THEN part and parameters of the IF part (antecedents) are automatically...
The screening of chemical libraries is an important step in identification of new leads in the drug discovery process. It is the size of the existing chemical libraries that renders laboratory screening expensive. A solution is to incorporate virtual screening into the process in order to reduce the number of molecules to be screened in the wet lab. In this paper, we explore several approaches to...
As mobile users continue to trust their devices with sensitive data, it is important to assess the applications that are responsible for securing it. Healthcare related applications are particularly unique because of their involvement with the storage of healthcare information. The healthcare data within an application is used for treatment, payment, operations (TPO). Securing mobile healthcare applications...
We present a classifier system called SRPFP that predicts the functions of un-annotated proteins. SRPFP aims at enhancing the state of the art of biological text mining. It analyzes biomedical texts in order to discover protein function information that is difficult to retrieve. It employs semantic rules for extracting proteins functions information from biomedical abstracts. It applies a novel model...
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