Ali Masoudi-Nejad
Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics and Center of Excellence in Biomathematics, University of Tehran, Tehran, I.R. IRAN
[ 1 ] - Finding Exact and Solo LTR-Retrotransposons in Biological Sequences Using SVM
Finding repetitive subsequences in genome is a challengeable problem in bioinformatics research area. A lot of approaches have been proposed to solve the problem, which could be divided to library base and de novo methods. The library base methods use predetermined repetitive genome’s subsequences, where library-less methods attempt to discover repetitive subsequences by analytical approach...
[ 2 ] - gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences
Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...
[ 3 ] - Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM
Structural repetitive subsequences are most important portion of biological sequences, which play crucial roles on corresponding sequence’s fold and functionality. Biggest class of the repetitive subsequences is “Transposable Elements” which has its own sub-classes upon contexts’ structures. Many researches have been performed to criticality determine the structure and function of repetitiv...
[ 4 ] - Integration and Reduction of Microarray Gene Expressions Using an Information Theory Approach
The DNA microarray is an important technique that allows researchers to analyze many gene expression data in parallel. Although the data can be more significant if they come out of separate experiments, one of the most challenging phases in the microarray context is the integration of separate expression level datasets that have gathered through different techniques. In this paper, we prese...
[ 5 ] - The Importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation
Insulin hormone is an important part of the endocrine system. It contains two polypeptide chains and plays a pivotal role in regulating carbohydrate metabolism. Insulin receptors (IR) located on cell surface interacts with insulin to control the intake of glucose. Although several studies have tried to clarify the interaction between insulin and its receptor, the mechanism of this interaction r...
[ 6 ] - Sequential and Mixed Genetic Algorithm and Learning Automata (SGALA, MGALA) for Feature Selection in QSAR
Feature selection is of great importance in Quantitative Structure-Activity Relationship (QSAR) analysis. This problem has been solved using some meta-heuristic algorithms such as: GA, PSO, ACO, SA and so on. In this work two novel hybrid meta-heuristic algorithms i.e. Sequential GA and LA (SGALA) and Mixed GA and LA (MGALA), which are based on Genetic algorithm and learning automata for QSAR f...
[ 7 ] - Patterns Prediction of Chemotherapy Sensitivity in Cancer Cell lines Using FTIR Spectrum, Neural Network and Principal Components Analysis
Drug resistance enables cancer cells to break away from cytotoxic effect of anticancer drugs. Identification of resistant phenotype is very important because it can lead to effective treatment plan. There is an interest in developing classifying models of resistance phenotype based on the multivariate data. We have investigated a vibrational spectroscopic approach in order to characterize a...
[ 8 ] - Cisplatin Resistant Patterns in Ovarian Cell Line Using FTIR and Principle Component Analysis
Cisplatin is a common chemotherapeutic agent that used for treatment of many solid cancers. Rapid identification of chemotherapy resistance is very important and may lead to effective treatment plan. Spectroscopy techniques, such as infrared spectroscopy, which are sensitive to biochemical composition of samples, have shown potentials to discriminate tissues. Developing in Fourier transform inf...
[ 9 ] - Analysis of the enzyme network involved in cattle milk production using graph theory
Understanding cattle metabolism and its relationship with milk products is important in bovine breeding. A systemic view could lead to consequences that will result in a better understanding of existing concepts. Topological indices and quantitative characterizations mostly result from the application of graph theory on biological data. In the present work, the enzyme network involved in cattle...
[ 10 ] - The Importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation
Insulin hormone is an important part of the endocrine system. It contains two polypeptide chains and plays a pivotal role in regulating carbohydrate metabolism. Insulin receptors (IR) located on cell surface interacts with insulin to control the intake of glucose. Although several studies have tried to clarify the interaction between insulin and its receptor, the mechanism of this interaction r...
[ 11 ] - Sequential and Mixed Genetic Algorithm and Learning Automata (SGALA, MGALA) for Feature Selection in QSAR
Feature selection is of great importance in Quantitative Structure-Activity Relationship (QSAR) analysis. This problem has been solved using some meta-heuristic algorithms such as: GA, PSO, ACO, SA and so on. In this work two novel hybrid meta-heuristic algorithms i.e. Sequential GA and LA (SGALA) and Mixed GA and LA (MGALA), which are based on Genetic algorithm and learning automata for QSAR f...
[ 12 ] - Patterns Prediction of Chemotherapy Sensitivity in Cancer Cell lines Using FTIR Spectrum, Neural Network and Principal Components Analysis
Drug resistance enables cancer cells to break away from cytotoxic effect of anticancer drugs. Identification of resistant phenotype is very important because it can lead to effective treatment plan. There is an interest in developing classifying models of resistance phenotype based on the multivariate data. We have investigated a vibrational spectroscopic approach in order to characterize a...
[ 13 ] - Cisplatin Resistant Patterns in Ovarian Cell Line Using FTIR and Principle Component Analysis
Cisplatin is a common chemotherapeutic agent that used for treatment of many solid cancers. Rapid identification of chemotherapy resistance is very important and may lead to effective treatment plan. Spectroscopy techniques, such as infrared spectroscopy, which are sensitive to biochemical composition of samples, have shown potentials to discriminate tissues. Developing in Fourier transform inf...