Sharif Digital Repository

Nowadays, genetic disorders, like cancer and birth defects, are a great threat to human life. Since the first noticing of these types of diseases, many efforts have been made and researches performed in order to recognize them and find a cure for them. These disorders affect genes and they appear as abnormal traits in a genetic organism. In order to recognize abnormal genes, we need to predict splice sites in a DNA signal; then, we can process the genetic codes between two continuous splice sites and analyze the trait that it represents. In addition to abnormal genes and their consequent disorders, we can also identify other normal human traits like physical and mental features. So the... 

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the... 

In the problems of Genome-Wide Association Study (GWAS), the objective is to associate subsequences of individual's genomes to the observable characteristics called phenotypes. The genome containing the biological information of an individual can be represented by a sequence of length G. Many observable characteristics of the individuals can be related to a subsequence of a given length L, called causal subsequence. The environmental affects make the relation between the causal subsequence and the observable characteristics a stochastic function. Our objective in this paper is to detect the causal subsequence of a specific phenotype using a dataset of N individuals and their observed... 

Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we introduce the problem of private DNA sequencing, where the goal is to keep the DNA sequence private to the sequencer. We propose an architecture, where the task of reading fragments of DNA and the task of DNA assembly are separated, the former is done at the sequencer(s), and the later is completed at a local trusted data collector. To satisfy the privacy constraint at the sequencer and reconstruction condition at the data collector, we create an... 

DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation of privacy. To address this challenge, we propose a solution, which is based on separating the process of reading the fragments of sequences, which is done at a sequencing machine, and assembling the reads, which is done at a trusted local data collector. To confuse the sequencer, in a pooled sequencing scenario, in which multiple sequences are going to be sequenced simultaneously, for each target individual, we add fragments of one non-target individual,... 

Genome-Wide Association Study (GWAS) addresses the problem of associating subsequences of individuals' genomes to the observable characteristics called phenotypes. In a genome of length G, it is observed that each characteristic is only related to a specific subsequence of it with length L, called the causal subsequence. The objective is to recover the causal subsequence, using a dataset of N individuals' genomes and their observed characteristics. Recently, the problem has been investigated from an information theoretic point of view in [1]. It has been shown that there is a threshold effect for reliable learning of the causal subsequence at Gh ( N L/G ) by characterizing the capacity of... 

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... 

In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted. Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species. Furthermore, by applying a cylindrical lens, a new technique is proposed to map two-dimensional (2D) association information to a one-dimensional (1D) column of pixels, where... 

The aim of this study was to quantify the DNA damage induced in a clinical megavoltage photon beam at various depths in and out of the field. MCNPX was used to simulate 10 × 10 and 20 × 20 cm2 10-MV photon beams from a clinical linear accelerator. Photon and electron spectra were collected in a water phantom at depths of 2.5, 12.5 and 22.5 cm on the central axis and at off-axis points out to 10 cm. These spectra were used as an input to a validated microdosimetric Monte Carlo code, MCDS, to calculate the RBE of induced DSB in DNA at points in and out of the primary radiation field at three depths. There was an observable difference in the energy spectra for photons and electrons for points...