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    Modeling of Genetic Mutations Associated with Protein Pathway Common in Alzheimer, Parkinson and Macular Degeneration Diseases

    , M.Sc. Thesis Sharif University of Technology Ghahremani, Amin (Author) ; Jahed, Mehran (Supervisor) ; Hossein Khalaj, Babak (Supervisor) ; Shahpasand, Kourosh (Co-Supervisor)
    Extensive studies have been performed on the genetic variations involved in common neurodegenerative diseases such as Alzheimer's, macular degeneration, and Parkinson's. In most cases, no specific gene has been identified pointing to a distinct pathogenic pathway, therefore, this study mainly aims to find common genes among aforementioned diseases according to determination of a specific pathogenic protein pathway.In this study, we reached a deep understanding of the function of nervous system and the discovery of causative agents of the diseases by applying the sources of information from genome datasets in bioinformatics analysis. The utilized database comprises the classification of... 

    Machine Learning Approaches for the Prediction of Pathogenicity in Genome Variations

    , M.Sc. Thesis Sharif University of Technology Sahebi, Alireza (Author) ; Sharifi Zarchi, Ali (Supervisor) ; Asgari, Ehsannedin (Supervisor)
    Genome mutations whose effects are not specified pose one of the challenges in identifying genetic diseases. Utilizing wet lab tests to detect the pathogenicity of variants can be time-consuming and fiscally expensive. A rapid and cost-effective solution to this problem is the use of machine learning-based variant effect predictors, which have the ability to determine whether a mutation is pathogenic or not. The objective of this research is to predict the pathogenicity of genome variations. The proposed model exclusively utilizes the protein sequence as its input feature and does not have access to other protein features. The data used to construct the model comprises mutations with... 

    Coalescence, Recombinations and Mutations

    , Ph.D. Dissertation Sharif University of Technology Salamat, Majid (Author) ; Pardoux, Etienne (Supervisor) ; Zohori Zageneh, Bijan (Supervisor) ; Zamani, Shiva (Co-Advisor)
    This thesis is concentrated on some subjects on population genetics. In the rst part we give formulae including the expectation and variance of the height and the length of the ancestral recombination graph (ARG) and the expectation and variance of the number of recombination events and we show that the expectation of the length of the ARG is a linear combination of the expectation of the length of Kingman's coalescent and the expectation of the height of the ARG. Also we show give a relation between the expectation of the ARG and the expectation of the number of recombination events. At the end of this part we show that the ARG comes down from innity in the sense that we can dene it with X0... 

    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
    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... 

    A quantum mechanical approach towards the calculation of transition probabilities between DNA codons

    , Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) Ghasemi, F ; Shafiee, A ; Sharif University of Technology
    Elsevier Ireland Ltd  2019
    The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the...