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Genome-wide association study for complex diseases will generate massive amount of single nucleotide polymorphisms (SNPs) data. Univariate statistical test (i.e. Fisher exact test) was used to single out non-associated SNPs. However, the disease-susceptible SNPs may have little marginal effects in population and are unlikely to retain after the univariate tests. Also, model-based methods are impractical...
We prove that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. We derive the optimal exon length distribution, which minimizes the probability of error in the genome...
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship...
The objective of this study was to evaluate the gene expression of four bone-related adhesive proteins during the early healing of bone defect and bone-implant interface in animal experiments. T-shaped hollow pure titanium implants with dual acid-etched surfaces were placed into femurs of 17 Sprague-Dawley rats, and bone defects with the same size were made in the same site in 15 rats. Newly formed...
Tissue engineered constructs have the potential to be used as replacements for current bone graft technologies. One component necessary for bone tissue engineering is a readily available, osteogenic cell source. Human dermal fibroblasts may have the potential to differentiate along an osteoblastic lineage, making them a candidate for use in bone tissue engineering applications. The objective of this...
In breast cancer treatment for many cases intrinsic or acquired resistance against available therapeutics leads to death. According to the present biological understanding, drug resistance is caused by molecular mechanisms in the complex network of proteins that regulate cell proliferation by activation of the estrogen receptor (ER), hereby allowing the cell to bypass the classical estrogen receptor...
One of the goals of genomic expression analysis is to construct gene interaction networks from microarray data. Time course microarray data is a common place to seek causal relationships between the expression of a regulator and its effect on the expression of its targets. By proposing gene expression patterns of regulator and target genes based on biological expectation of regulatory interactions,...
An improved genetic algorithm (IGA) is proposed to achieve S-system gene network modeling of Xenopus frog egg. Via the time-courses training datasets from Michaelis-Menten model, the optimal parameters are learned. The S-system can clearly describe activative and inhibitory interaction between genes as generating and consuming process. We concern the mitotic control in cell-cycle of Xenopus frog egg...
The challenge of biomarker identification for bionanotechnology is that we need to find less than ten potential biomarkers from high throughput data so that quantum dot synthesis and imaging can be effective. Among all the extensive biomarker research, the novelty of our research is to reduce the number the biomarkers by studying the efficacy of several classifiers and error estimation methods. Specifically,...
Computational intelligent approaches is adopted to construct the S-system of eukaryotic cell cycle for further analysis of genetic regulatory networks. A highly nonlinear power-law differential equation is constructed to describe the transcriptional regulation of gene network from the time-courses dataset. Global artificial algorithm, based on hybrid differential evolution, can achieve global optimization...
Here we show how nonlinear system identification techniques, such as fast orthogonal search (FOS) and the orthogonal search method (OSM), can be used to analyze gene expression profiles and predict the class to which a profile belongs
Over the last several years there has been an explosion of microarray technology in the biosciences, medical sciences, biotechnology, and pharmaceutical industry. The technology has centered on providing a platform for determining the gene expression profiles of hundreds to tens of thousands of genes (or transcript levels of RNA species) in tissue, tumors, cells, or biological fluids in a single experiment...
M-FISH (multicolor fluorescence in situ hybridization) is a recently developed cytogenetic technique for cancer diagnosis and research on genetic disorders which uses 5 fluors to label uniquely each chromosome and a fluorescent DNA stain. In this paper, an automated method for chromosome classification in M-FISH images is presented. The chromosome image is initially decomposed into a set of primitive...
The main focus of this paper is to mathematically represent the dynamics of cancer evolution by studying patterns of chromosomal aberrations. A mathematical model for the progression and evolution of cancer in cultured fibroblast cells is proposed. Solution of the differential equations was performed for a continuous model by assuming variable genetic aberration pseudo reaction rate constants for...
This paper presents a method for model based automated tracking of multiple worm-like creatures. These methods are essential for accurate quantitative analysis into the genetic basis of behavior that involve more than one organism. An accurate worm model is designed using the geometry of planar curves and nonlinear estimation of the model's parameters are performed using a central difference Kalman...
A synthetic vector that transform from a cationic to an anionic lipid intracellularly is described. This charge-reversal lipid was synthesized and characterized, including the supramolecular complex it forms with DNA. Enhanced gene transfection was observed using this synthetic vector compared to current cationic lipids
We describe the development of a very large-scale causal, computable model of biology and its specific application in the identification of molecular cause and effect hypotheses of mechanisms underlying the effects of androgen stimulation in the LNCaP prostate carcinoma cell line. In contrast to previous LNCaP studies in which genes have been hierarchically clustered by their pattern of response to...
Single-Nucleotide Polymorphism (SNP) array is a recently introduced technology that genotypes more than 10,000 human SNPs on a single array. It has been shown that genome-wide Loss of Heterozygosity (LOH) calls can be derived by analyzing the genotypes calls measured by SNP arrays using paired tumor and normal tissue samples. The goal of this study is to evaluate the possibility of cancer classification...
Here we show how nonlinear system identification techniques, such as fast orthogonal search (FOS) and the orthogonal search method (OSM), can be used to analyze gene expression profiles and predict the class to which a profile belongs
Genome-wide association study for complex diseases will generate massive amount of single nucleotide polymorphisms (SNPs) data. Univariate statistical test (i.e. Fisher exact test) was used to single out non-associated SNPs. However, the disease-susceptible SNPs may have little marginal effects in population and are unlikely to retain after the univariate tests. Also, model-based methods are impractical...
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