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    F.C.A: designing a fuzzy clustering algorithm for haplotype assembly

    , Article IEEE International Conference on Fuzzy Systems, 20 August 2009 through 24 August 2009 ; 2009 , Pages 1741-1744 ; 10987584 (ISSN) ; 9781424435975 (ISBN) Moeinzadeh, M. H ; Asgarian, E ; Noori, M. M ; Sadeghi, M ; Sharifian R., S ; Sharif University of Technology
    Abstract
    Reconstructing haplotype in MEC (Minimum Error Correction) model is an important clustering problem which focuses on inferring two haplotypes from SNP fragments (Single Nucleotide Polymorphism) containing gaps and errors. Mutated form of human genome is responsible for genetic diseases which mostly occur in SNP sites. In this paper, a fuzzy clustering approach is performed for haplotype reconstruction or haplotype assembly from a given sample Single Nucleotide Polymorphism (SNP). In the best previous approach based on reconstruction rate (Wang 2007[2]), all SNP-fragments are considered with equal values. In our proposed method the value of the fragments are based on the degree of membership... 

    Solving MEC and MEC/GI problem models, using information fusion and multiple classifiers

    , Article Innovations'07: 4th International Conference on Innovations in Information Technology, IIT, Dubai, 18 November 2007 through 20 November 2007 ; 2007 , Pages 397-401 ; 9781424418411 (ISBN) Asgarian, E ; Moeinzadeh, M. H ; Mohammadzadeht, J ; Ghazinezhad, A ; Habibi, J ; Najafi Ardabili, A ; Sharif University of Technology
    IEEE Computer Society  2007
    Abstract
    Mutations in Single Nucleotide Polymorphisms (SNPs - different variant positions (1%) from human genomes) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of recent studies in human genomics. Two sequences of mentioned SNPs in diploid human organisms are called haplotypes. In this paper, we study haplotype reconstruction from SNP-fragments with and without genotype information, problems. Designing serial and parallel classifiers was center of our research. Genetic algorithm and K-means were two components of our approaches. This combination helps us to cover the single classifier's weaknesses. ©2008 IEEE  

    A combination of PSO and K-means methods to solve haplotype reconstruction problem

    , Article 2009 International Conference on Innovations in Information Technology, IIT '09, 15 December 2009 through 17 December 2009 ; 2009 , Pages 190-194 ; 9781424456987 (ISBN) Sharifian R, S ; Baharian, A ; Asgarian, E ; Rasooli, A ; Sharif University of Technology
    Abstract
    Disease association study is of great importance among various fields of study in bioinformatics. Computational methods happen to be advantageous specifically when experimental approaches fail to obtain accurate results. Haplotypes are believed to be the most responsible biological data for genetic diseases. In this paper, the problem of reconstructing haplotypes from error-containing SNP fragments is discussed For this purpose, two new methods have been proposed by a combination of k-means clustering and particle swarm optimization algorithm. The methods and their implementation results on real biological and simulation datasets are represented which shows that they outperform the methods... 

    Designing a polymerase chain reaction device working with radiation and convection heat transfer

    , Article 2017 International Conference on Nanomaterials and Biomaterials, ICNB 2017, 11 December 2017 through 13 December 2017 ; Volume 350, Issue 1 , 2018 ; 17578981 (ISSN) Madadelahi, M ; Kalan, K ; Shamloo, A ; Sharif University of Technology
    Institute of Physics Publishing  2018
    Abstract
    Gene proliferation is vital for infectious and genetic diseases diagnosis from a blood sample, even before birth. In addition, DNA sequencing, genetic finger-print analyzing, and genetic mutation detecting can be mentioned as other procedures requiring gene reproduction. Polymerase chain reaction, briefly known as PCR, is a convenient and effective way to accomplish this task; where the DNA containing sample faces three temperature phases alternatively. These phases are known as denaturation, annealing, and elongation/extension which in this study -regarding the type of the primers and the target DNA sequence- are set to occur at 95, 58, and 72 degrees of Celsius. In this study, a PCR device... 

    Solving MEC model of haplotype reconstruction using information fusion, single greedy and parallel clustering approaches

    , Article 6th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2008, Doha, 31 March 2008 through 4 April 2008 ; 2008 , Pages 15-19 ; 9781424419685 (ISBN) Asgarian, E ; Moeinzadeh, M. H ; Sharifian-R, S ; Najafi-A, A ; Ramezani, A ; Habibi, J ; Mohammadzadeh, J ; Sharif University of Technology
    2008
    Abstract
    Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, Due to the mutated form in human genome; SNPs (Single Nucleotide Polymorphism) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of studies in human genomics. In this paper, a data fusion method based on multiple parallel classifiers for reconstruction of haplotypes from a given sample Single Nucleotide Polymorphism (SNP) is proposed. First, we design a single greedy algorithm for solving haplotype reconstructions. [2] is used as an efficient approach to be combined with first classification method. The...