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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) ; 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,...
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
, Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) ; Hadadian Nejad Yousefi, M ; Goudarzi, M ; Sharif University of Technology
BioMed Central Ltd
2021
Abstract
Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads...
Genetic risk variants for class switching recombination defects in ataxia-telangiectasia patients
, Article Journal of Clinical Immunology ; 2021 ; 02719142 (ISSN) ; Mehrmohamadi, M ; Ranjouri, M. R ; Akrami, M ; Rezaei, N ; Saberi, A ; Yazdani, R ; Abolhassani, H ; Aghamohammadi, A ; Sharif University of Technology
Springer
2021
Abstract
Background: Ataxia-telangiectasia (A-T) is a rare autosomal recessive disorder caused by mutations in the ataxia telangiectasia mutated (ATM) gene. A-T patients manifest considerable variability in clinical and immunological features, suggesting the presence of genetic modifying factors. A striking heterogeneity has been observed in class switching recombination (CSR) in A-T patients which cannot be explained by the severity of ATM mutations. Methods: To investigate the cause of variable CSR in A-T patients, we applied whole-exome sequencing (WES) in 20 A-T patients consisting of 10 cases with CSR defect (CSR-D) and 10 controls with normal CSR (CSR-N). Comparative analyses on modifier...
Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein
, Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
Hindawi Limited
2021
Abstract
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for...
Photoluminescent carbon quantum dot/poly-L-Lysine core-shell nanoparticles: A novel candidate for gene delivery
, Article Journal of Drug Delivery Science and Technology ; Volume 61 , 2021 ; 17732247 (ISSN) ; Mofazzal Jahromi, M. A ; Abdoli, A ; Mohammad Beigi, H ; Fatahi, Y ; Nourizadeh, H ; Zare, H ; Kiani, J ; Radmanesh, F ; Rabiee, N ; Jahani, M ; Mombeiny, R ; Karimi, M ; Sharif University of Technology
Editions de Sante
2021
Abstract
Cationic polymers such as poly-L-lysine (PLL) are able to interact electrostatically with DNA to produce polymeric systems with nanometric diameters due to the neutralization and accumulation of DNA. This study integrates the outstanding properties of carbon quantum dots (CQDs) with PLL to develop a novel gene delivery vehicle with a core-shell hybrid nanostructure. The CQD/PLL core-shell nanoparticles (NPs) were, therefore, synthesized in such a way that they had narrow size distribution and an average diameter under 10 nm, both of which were confirmed by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Fourier transform infrared (FTIR) spectroscopy exhibited that...
Analysis of DNA Methylation in Single-cell Resolution Using Algorithmic Methods and Deep Neural Networks
, M.Sc. Thesis Sharif University of Technology ; Sharifi Zarchi, Ali (Supervisor)
Abstract
DNA methylation in one of the most important epigenetic variations, which causes significant variations in gene expressions of mammalians. Our current knowledge about DNA methylation is based on measurments from samples of bulk data which cause ambiguity in intracellular differences and analysis of rare cell samples. For this reason, the ability to measure DNA methylation in single-cells has the potential to play an important role in understanding many biological processes including embryonic developement, disease progression including cancer, aging, chromosome instability, X chromosome inactivation, cell differentiation and genes regulation. Recent technological advances have enabled...
Design and Simulation of CMOS Based Magnetic Sensor for Biosensing Applications
, M.Sc. Thesis Sharif University of Technology ; Akbari, Mahmood (Supervisor) ; Fotowat-Ahmady, Ali (Supervisor)
Abstract
This paper presents a scalable and ultrasensitive magnetic biosensing scheme based on on-chip LC resonance frequency-shifting. The sensor transducer gain is demonstrated as being location-dependent on the sensing surface and proportional to the local polarization magnetic field strength |B|2 generated by the sensing inductor. To improve the gain uniformity, a periodic coil is proposed as a substitution for the standard process coil. As an implementation example, the circuit is designed in a 65nm CMOS process. The spatially uniform sensor gain of the array is verified by COMSOL simulations. Overall, the presented sensor demonstrates an improvement in the uniformity of the inductor’s magnetic...
Investigation of a protein complex network
, Article European Physical Journal B ; Volume 41, Issue 1 , 2004 , Pages 113-121 ; 14346028 (ISSN) ; Ramezanpour, A ; Karimipour, V ; Sharif University of Technology
2004
Abstract
The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal...
Modeling Two-Dimensional Face from DNA Using the Face Embedding Approach in Deep Learning
, M.Sc. Thesis Sharif University of Technology ; Hossein Khalaj, Babak (Supervisor)
Abstract
the purpose of this research is to construct the facial image of a person from corresponding DNA. In this problem, we have a set of DNAs and facial images and we want to find the relation between the DNA and the features of facial images.using this relation we can find the facial Image of a person using the DNA. for this purpose we should first extract the features of faces that have the most variation among the population. by studying the feature extraction methods in this field, we borrow the deep neural network method that is used in face recognition fields.we found significant relations between DNA and extracted features from this network. finally using this relation we can predict the...
Design and Fabrication of Centrifugal Microfluidic Disc for Cell Lysis and DNA Extraction
,
M.Sc. Thesis
Sharif University of Technology
;
Saadatmand, Maryam
(Supervisor)
;
Garshasbi, Masoud
(Co-Supervisor)
Abstract
Centrifugal microfluidic systems due to their unique properties, including the ease of sample transfer, high controllability, the need for samples and reagents in a small volume scale, the possibility of embedding a complete laboratory and modeling a variety of processes on a disk, they have great potential to be used in the field of point of care diagnosis. Such devices can perform several different processes simultaneously and continuously by using inertial and pneumatic forces as well as a complex network of microchannels. The purpose of this research is to design and build a centrifugal microfluidic disc for lysing amniotic stem cells, followed by DNA extraction, in order to detect fetal...
Motif Finding Application Using Edit Distance Approuch
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor)
Abstract
Motif finding problem in biology is a search for repeated patterns to reveal information about gene expression, one of the most complex subsystems in genomics. ChIP-seq technology abled researchers to investigate location of protein-DNA interactions but analyzing downstream results of such experiments to find actual regulatory signals in genome is challenging. For many years, applications of motif finding had models based on limiting assumption as an exchange for lower computational complexity. Results: AKAGI program is build upon upgraded methods and new general models to investigate statistical and experimental evidences for accurately finding significant patterns among biological...
Prediction of DNA/RNA Sequence Binding Site to Protein with the Ability to Implement on GPU
, M.Sc. Thesis Sharif University of Technology ; Koohi, Sommaye (Supervisor)
Abstract
Based on the importance of DNA/RNA binding proteins in different cellular processes, finding binding sites of them play crucial role in many applications, like designing drug/vaccine, designing protein, and cancer control. Many studies target this issue and try to improve the prediction accuracy with three strategies: complex neural-network structures, various types of inputs, and ML methods to extract input features. But due to the growing volume of sequences, these methods face serious processing challenges. So, this paper presents KDeep, based on CNN-LSTM and the primary form of DNA/RNA sequences as input. As the key feature improving the prediction accuracy, we propose a new encoding...
Expression analysis of Wnt signaling pathway related lncRNAs in periodontitis: A pilot case-control study
, Article Human Gene ; Volume 33 , 2022 ; 27730441 (ISSN) ; Dashti, S ; Gholami, L ; Badrlou, E ; Sadeghpour, S ; Hussen, B. M ; Hidayat, H. J ; Nazer, N ; Shadnoush, M ; Sayad, A ; Arefian, N ; Sharif University of Technology
Elsevier B.V
2022
Abstract
LncRNAs are involved in the modulation of several signaling pathways which have a crucial effect in the differentiation of periodontal ligament cells and the induction of cementum regeneration. Autophagy and Wnt signaling are two important pathways with a wide range of interrelationships associated with periodontitis. We chose four lncRNAs based on their potential interaction with these two pathways. We examined the expression of FOXD2-AS1, NNT-AS1, GAS8-AS1, and CCAT1 lncRNAs in tissues and blood specimens of patients with periodontitis and unaffected controls using qRT-PCR. Expression amounts of FOXD2-AS1 were lower in blood of cases compared with controls (relative expression (RE) = 0.08,...
HELIOS: High-speed sequence alignment in optics
, Article PLoS Computational Biology ; Volume 18, Issue 11 , 2022 ; 1553734X (ISSN) ; 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...
CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
, Article Chemosphere ; Volume 306 , 2022 ; 00456535 (ISSN) ; Akhavan, O ; Fatahi, Y ; Ghadiri, A. M ; Kiani, M ; Makvandi, P ; Rabiee, M ; Nicknam, M. H ; Saeb, M. R ; Varma, R. S ; Ashrafizadeh, M ; Nazarzadeh Zare, E ; Sharifi, E ; Lima, E. C ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
Overexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression of ssDNA and the related antigens in the population and brisk activity in gene-editing technologies in the treatment/detection may lead to the presence of pCRISPR in the blood. Therefore, the detection and evaluation of their trace concentrations are of...
Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of...
Poly-L-lysine/hyaluronan nanocarriers as a novel nanosystem for gene delivery
, Article Journal of Microscopy ; Volume 287, Issue 1 , 2022 , Pages 32-44 ; 00222720 (ISSN) ; Bagherzadeh, M. A ; Mofazzal Jahromi, M. A ; Mohammad-Beigi, H ; Abdoli, A ; Mir, H ; Roustazadeh, A ; Pirestani, M ; Sahandi Zangabad, P ; Kiani, J ; Bakhshayesh, A ; Jahani, M ; Joghataei, M. T ; Karimi, M ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
The present research comes up with a novel DNA-loaded poly-L-lysine (PLL)/hyaluronan (HA) nanocarrier (DNA-loaded PLL/HA NCs) for gene delivery applications, as a promising candidate for gene delivery into diverse cells. A straightforward approach was employed to prepare such a nanosystem through masking DNA-loaded PLL molecules by HA. Fourier-transform infrared (FTIR) spectroscopy, dynamic light scattering (DLS), field emission-scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM) were used to analyse the interaction of the molecules as well as the physicochemical properties of the NCs. The NCs showed a negative charge of –24 ± 3 mV, with an average size of 138 ±...
Plasmon-induced near-infrared fluorescence enhancement of single-walled carbon nanotubes
, Article Carbon ; Volume 194 , 2022 , Pages 162-175 ; 00086223 (ISSN) ; Tsoulos, T. V ; Sajjadi, S. H ; Antonucci, A ; Wu, S. J ; Tagliabue, G ; Fatmehsari Haghshenas, D ; Boghossian, A. A ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
Single-walled carbon nanotubes (SWCNTs) emit near-infrared (NIR) fluorescence that is ideal for optical sensing. However, the low quantum yields diminish the sensor's signal-to-noise ratio and limits the penetration depths for in vivo measurements. In this study, we perform a systematic investigation of the plasmonic effects of Ag and Au nanoparticles of various geometries to tune and even enhance the fluorescence intensity of single-stranded DNA-wrapped SWCNTs (ssDNA-SWCNTs). We observe a chirality-dependent NIR fluorescence enhancement that varies with both nanoparticle shape and material, with Au nanorods increasing (7, 5) and (7, 6) chirality emissions by 80% and 60% and Ag nanotriangles...
Synthesis of green benzamide-decorated UiO-66-NH2 for biomedical applications
, Article Chemosphere ; Volume 299 , 2022 ; 00456535 (ISSN) ; Ghadiri, A. M ; Alinezhad, V ; Sedaghat, A ; Ahmadi, S ; Fatahi, Y ; Makvandi, P ; Saeb, M. R ; Bagherzadeh, M ; Asadnia, M ; Varma, R. S ; Lima, E. C ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
Metal-organic frameworks (MOFs) biocompatible systems can host enzymes/bacteria/viruses. Herein we synthesized a series of fatty acid amide hydrolase (FAAH)-decorated UiO-66-NH2 based on Citrus tangerine leaf extract for drug delivery and biosensor applications. Five chemically manipulated FAAH-like benzamides were localized on the UiO-66-NH2 surface with physical interactions. Comprehensive cellular and molecular analyses were conducted on HEK-293, HeLa, HepG2, PC12, MCF-7, and HT-29 cell lines (cytotoxicity assessment after 24 and 48 h). MTT results proved above 95 and 50% relative cell viability in the absence and presence of the drug, respectively. A complete targeted drug-releasing...
Cancer Detection Classification by cfDNA Methylation
, M.Sc. Thesis Sharif University of Technology ; Sharifi Zarchi, Ali (Supervisor)
Abstract
Traditional techniques use invasive histology techniques to diagnose cancer. Cancer tissue is sampled directly in this method, which is very painful for the patient. In recent years, scientists have discovered that the cell world is released into the blood plasma after cell death, obtaining useful cancer information. Since methylation changes in cancer cells are very significant and the death rate of cancer cells is high, the methylation of each tissue is different from the other. Furthermore, they were diagnosing the type of cancer.On the other hand, due to the different patterns in methylated DNA with normal DNA and the use of bisulfite treatment technique to detect the degree of...