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    Genome-Wide Association Studies: Information Theoretic Limits of Reliable Learning

    , Article 2018 IEEE International Symposium on Information Theory, ISIT 2018, 17 June 2018 through 22 June 2018 ; Volume 2018-June , 2018 , Pages 2231-2235 ; 21578095 (ISSN); 9781538647806 (ISBN) Tahmasebi, B ; Maddah Ali, M. A ; Motahari, A. S ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2018
    Abstract
    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... 

    Private shotgun and sequencing

    , Article 2019 IEEE International Symposium on Information Theory, ISIT 2019, 7 July 2019 through 12 July 2019 ; Volume 2019-July , 2019 , Pages 171-175 ; 21578095 (ISSN); 9781538692912 (ISBN) Gholami, A ; Maddah Ali, M. A ; Abolfazl Motahari, S ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    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... 

    Private shotgun DNA sequencing: A structured approach

    , Article 2019 Iran Workshop on Communication and Information Theory, IWCIT 2019, 24 April 2019 through 25 April 2019 ; 2019 ; 9781728105840 (ISBN) Gholami, A ; Maddah Ali, M. A ; Motahari, S. A ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    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,... 

    Information theory of mixed population genome-wide association studies

    , Article 2018 IEEE Information Theory Workshop, ITW 2018, 25 November 2018 through 29 November 2018 ; 2019 ; 9781538635995 (ISBN) Tahmasebi, B ; Maddah Ali, M. A ; Motahari, S. A ; Sun Yat-Sen University ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    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... 

    Speeding up DNA sequence alignment by optical correlator

    , Article Optics and Laser Technology ; Volume 108 , 2018 , Pages 124-135 ; 00303992 (ISSN) Mozafari, F ; Babashah, H ; Koohi, S ; Kavehvash, Z ; Sharif University of Technology
    Elsevier Ltd  2018
    Abstract
    In electronic computers, extensive amount of computations required for searching biological sequences in big databases leads to vast amount of energy consumption for electrical processing and cooling. On the other hand, optical processing is much faster than electrical counterpart, due to its parallel processing capability, at a fraction of energy consumption level and cost. In this regard, this paper proposes a correlation-based optical algorithm using metamaterial, taking advantages of optical parallel processing, to efficiently locate the edits as a means of DNA sequence comparison. Specifically, the proposed algorithm partitions the read DNA sequence into multiple overlapping intervals,... 

    Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

    , Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) Akbari Rokn Abadi, S ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
    NLM (Medline)  2021
    Abstract
    In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

    Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

    , Article PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN) Akbari Rokn Abadi, S ; Hashemi Dijujin, N ; Koohi, S ; Sharif University of Technology
    NLM (Medline)  2021
    Abstract
    In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

    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... 

    Design and Analysis of DNA Sequencing Methods

    , Ph.D. Dissertation Sharif University of Technology Nashtaali, Damoun (Author) ; Hossein Khalaj, Babak (Supervisor) ; Abolfazl, Motahhari (Co-Advisor)
    Abstract
    A DNA sequence is the information source of living kinds. Information of this sequence is at its constructing bases which has four different kinds. Sequencing DNA is necessary to resolve this information. At 1977, Sanger reported the first sequence of a DNA string. Recently, a human DNA string can be sequenced with 1000 in ~2 hours. Knowing DNA sequence helps to find function of each organism, predict and cure diseases (especially in cancer). Next Generation Sequencing (NGS) methods are based on shot-gun sequencing which fragmentize DNA strings and sequence each fragment. After sequencing, processing information of DNA is performed by the processing machine in two different types: alignment... 

    Recovery from random samples in a big data set

    , Article IEEE Communications Letters ; Volume 19, Issue 11 , September , 2015 , Pages 1929-1932 ; 10897798 (ISSN) Molavipour, S ; Gohari, A ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2015
    Abstract
    Consider a collection of files, each of which is a sequence of letters. One of these files is randomly chosen and a random subsequence of the file is revealed. This random subsequence can be the result of a random sampling of the file. The goal is to recover the identity of the file, assuming a simple greedy matching algorithm to search the file collection. We study the fundamental limits on the maximum size of the file collection for reliable recovery in terms of the length of the random subsequence. The sequence of each file is assumed to follow a hidden Markov model (HMM), which is a common model for many data structures such as voice or DNA sequences. The connection between this problem... 

    Noble metal nanoparticles in biosensors: Recent studies and applications

    , Article Nanotechnology Reviews ; Volume 6, Issue 3 , 2017 , Pages 301-329 ; 21919089 (ISSN) Malekzad, H ; Sahandi Zangabad, P ; Mirshekari, H ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Walter de Gruyter GmbH  2017
    Abstract
    The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers... 

    Mining DNA sequences based on spatially coded technique using spatial light modulator

    , Article IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN) Fazelian, M ; Abdollahramezani, S ; Bahrani, S ; Chizari, A ; Jamali, M. V ; Khorramshahi, P ; Tashakori, A ; Shahsavari, S ; Salehi, J. A ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2016
    Abstract
    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... 

    OptCAM: An ultra-fast all-optical architecture for DNA variant discovery

    , Article Journal of Biophotonics ; Volume 13, Issue 1 , August , 2020 Maleki, E ; Koohi, S ; Kavehvash, Z ; Mashaghi, A ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both... 

    HELIOS: High-speed sequence alignment in optics

    , Article PLoS Computational Biology ; Volume 18, Issue 11 , 2022 ; 1553734X (ISSN) Maleki, E ; Akbari Rokn Abadi, S ; Koohi, S ; Sharif University of Technology
    Public Library of Science  2022
    Abstract
    In response to the imperfections of current sequence alignment methods, originated from the inherent serialism within their corresponding electrical systems, a few optical approaches for biological data comparison have been proposed recently. However, due to their low performance, raised from their inefficient coding scheme, this paper presents a novel all-optical high-throughput method for aligning DNA, RNA, and protein sequences, named HELIOS. The HELIOS method employs highly sophisticated operations to locate character matches, single or multiple mutations, and single or multiple indels within various biological sequences. On the other hand, the HELIOS optical architecture exploits... 

    Design & Analysis of a DNA String Matching System Based on Optical Parallel Processing

    , M.Sc. Thesis Sharif University of Technology Babashah, Hossein (Author) ; Kavehvash, Zahra (Supervisor) ; Koohi, Somaie (Co-Advisor) ; Khavasi, Amin (Co-Advisor)
    Abstract
    In recent years, the biological evolution of molecular detection capabilities based on gene analysis has provided a reliable performance in the diagnosis of a disease before a symptom emerges. Human gene storage requires a large amount of computer memory (about 1.5 GB for each DNA) and the search for a specific pattern within it with electronic computers is time and power consuming. Optical computing uses light parallel processing capabilities to find the pattern in a digital field, which can be used to process large volumes of data in short time and low power consumption, while electronic computers process data in series with high power dissipation. According to the Optalysys report, the... 

    Investigating optimum procedures needed to maintain a model satellite's CG stable about design point, under subsystem configuration changes

    , Article ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis, ESDA2010, 12 July 2010 through 14 July 2010, Istanbul ; Volume 4 , 2010 , Pages 585-588 ; 9780791849187 (ISBN) Dastoom Laatleyli, H ; Abedian, A ; Teimouri, H ; Sharif University of Technology
    2010
    Abstract
    During design, microsatellites are subject to different changes like the changes in weight, location and dimension of parts and elements of subsystems and the payload. These changes should be accumulated by the structure subsystem in a way that some key structural parameters like the center of gravity (CG) and inertia moments remain unchanged. This subject is also important regarding the design of a modular structure of a satellite. In the present study it is tried to accommodate any changes in weight and location of any part(s) and element(s) of a microsatellite by optimum (minimum) rearrangement of other parts on their plane of rest in order to keep the CG and inertia moments unchanged.... 

    All-optical DNA variant discovery utilizing extended DV-curve-based wavelength modulation

    , Article Journal of the Optical Society of America A: Optics and Image Science, and Vision ; Volume 35, Issue 11 , 2018 , Pages 1929-1940 ; 10847529 (ISSN) Maleki, E ; Babashah, H ; Koohi, S ; Kavehvash, Z ; Sharif University of Technology
    OSA - The Optical Society  2018
    Abstract
    This paper presents a novel optical processing approach for exploring genome sequences built upon an optical correlator for global alignment and the extended dual-vector-curve-curve (DV-curve) method for local alignment. To overcome the problem of the traditional DV-curve method for presenting an accurate and simplified output, we propose the hybrid amplitude wavelength polarization optical DV-curve (HAWPOD) method, built upon the DV-curve method, to analyze genome sequences in three steps: DNA coding, alignment, and post-Analysis. For this purpose, a tunable graphene-based color filter is designed for wavelength modulation of optical signals. Moreover, all-optical implementation of the... 

    Enhanced electrochemical activity of a hollow carbon sphere/polyaniline-based electrochemical biosensor for HBV DNA marker detection

    , Article ACS Biomaterials Science and Engineering ; Volume 5, Issue 5 , 2019 , Pages 2587-2594 ; 23739878 (ISSN) Salimian, R ; Shahrokhian, S ; Panahi, S ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    Herein, we present a novel, simple, and ultrasensitive electrochemical DNA (E-DNA) sensor based on hollow carbon spheres (HCS) decorated with polyaniline (PANI). A thiolated 21-mer oligonucleotide, characteristic of HBV DNA, is immobilized via electrodeposited gold nanoparticles on HCS-PANI. Cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS) are used to characterize the electrochemical properties of the prepared nanocomposite. Scanning electron microscopy is employed to investigate the morphological texture of the fabricated modifier. An enhanced intrinsic signal of PANI is probed to evaluate the biosensing ability of the prepared... 

    An ultrasensitive label free human papilloma virus DNA biosensor using gold nanotubes based on nanoporous polycarbonate in electrical alignment

    , Article Analytica Chimica Acta ; Volume 1048 , 2019 , Pages 31-41 ; 00032670 (ISSN) Shariati, M ; Ghorbani, M ; Sasanpour, P ; Karimizefreh, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The... 

    Design and Implementation of DNA Pattern Recognition Algorithm Utilizing Optical Coding Method

    , M.Sc. Thesis Sharif University of Technology Maleki, Ehsan (Author) ; Koohi, Somayyeh (Supervisor) ; Kavehvash, Zahra (Supervisor)
    Abstract
    In this research, two novel optical methods have been proposed for DNA local sequence alignment. The proposed methods benefit from algorithms and methods in computer field and ability of parallelism in optical wave to achieve a low-cost process and propose an easy understanding output in DNA local sequence alignment procedure. The first method is built upon moiré matching technique which is extended by proposed HAPPOC scheme using amplitude, phase, and polarization of optical wave. For analyzing the extended moiré output, a novel 3D Artificial Neural Network is designed and developed by optical structure. The second structure, as named HAWPOD method, is based on DV-Curve method. The HAWPOD...