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    Deep feature extraction of single-cell transcriptomes by generative adversarial network

    , Article Bioinformatics ; Volume 37, Issue 10 , 2021 , Pages 1345-1351 ; 13674803 (ISSN) Bahrami, M ; Maitra, M ; Nagy, C ; Turecki, G ; Rabiee, H. R ; Li, Y ; Sharif University of Technology
    Oxford University Press  2021
    Abstract
    Motivation: Single-cell RNA-sequencing (scRNA-seq) offers the opportunity to dissect heterogeneous cellular compositions and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition designs. Results: Here, we present a single-cell Generative Adversarial Network (scGAN) to simultaneously acquire patterns from raw data while minimizing the confounding effect driven by technical artifacts or other factors inherent to the data. Specifically, scGAN models the data likelihood of the raw scRNA-seq counts by projecting each cell onto a latent embedding.... 

    PFP-WGAN: Protein function prediction by discovering gene ontology term correlations with generative adversarial networks

    , Article PLoS ONE ; Volume 16, Issue 2 , 2021 ; 19326203 (ISSN) Seyyedsalehi, S. F ; Soleymani, M ; Rabiee, H. R ; Kaazempur Mofrad, M. R ; Sharif University of Technology
    Public Library of Science  2021
    Abstract
    Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

    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,... 

    Dependency of codon usage on protein sequence patterns: A statistical study

    , Article Theoretical Biology and Medical Modelling ; Vol. 11, issue. 1 , 2014 ; ISSN: 17424682 Foroughmand-Araabi, M. H ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Sharif University of Technology
    Abstract
    Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

    Advancement of sensor integrated organ-on-chip devices

    , Article Sensors (Switzerland) ; Volume 21, Issue 4 , 2021 , Pages 1-44 ; 14248220 (ISSN) Clarke, G.A ; Hartse, B. X ; Niaraki Asli, A. E ; Taghavimehr, M ; Hashemi, N ; Abbasi Shirsavar, M ; Montazami, R ; Alimoradi, N ; Nasirian, V ; Ouedraogo, L. J ; Hashemi, N. N ; Sharif University of Technology
    MDPI AG  2021
    Abstract
    Organ-on-chip devices have provided the pharmaceutical and tissue engineering worlds much hope since they arrived and began to grow in sophistication. However, limitations for their applicability were soon realized as they lacked real-time monitoring and sensing capabilities. The users of these devices relied solely on endpoint analysis for the results of their tests, which created a chasm in the understanding of life between the lab the natural world. However, this gap is being bridged with sensors that are integrated into organ-on-chip devices. This review goes in-depth on different sensing methods, giving examples for various research on mechanical, electrical resistance, and bead-based... 

    You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome

    , Article Computers in Biology and Medicine ; Volume 106 , 2019 , Pages 106-113 ; 00104825 (ISSN) Kashani, B ; Hasani Bidgoli, M ; Motahari, S. A ; Sedaghat, N ; Modarressi, M. H ; Sharif University of Technology
    Elsevier Ltd  2019
    Abstract
    Background: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. Methods: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally... 

    Meta-aligner: long-read alignment based on genome statistics

    , Article BMC Bioinformatics ; Volume 18, Issue 1 , 2017 ; 14712105 (ISSN) Nashta Ali, D ; Aliyari, A ; Ahmadian Moghadam, A ; Edrisi, M. A ; Motahari, S. A ; Khalaj, B. H ; Sharif University of Technology
    Abstract
    Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

    IMOS: improved meta-aligner and minimap2 on spark

    , Article BMC Bioinformatics ; Volume 20, Issue 1 , 2019 ; 14712105 (ISSN) Hadadian Nejad Yousefi, M ; Goudarzi, M ; Motahari, A ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)... 

    Fast chromium removal by Shewanella sp.: an enzymatic mechanism depending on serine protease

    , Article International Journal of Environmental Science and Technology ; Volume 17, Issue 1 , April , 2020 , Pages 143-152 Kheirabadi, M ; Mahmoodi, R ; Mollania, N ; Kheirabadi, M ; Sharif University of Technology
    Springer  2020
    Abstract
    Environmental pollutions with heavy metals pose serious health and ecological risks. Sabzevar in the northeast of Iran has natural chromic mines and then chromium-polluted soils and groundwater. In the present work, the metal-tolerant bacterial strain KR2 was identified as Shewanella sp. following 16S rDNA gene sequence analysis. Bioremediation ability of isolated bacterial from agricultural soils that irrigated by groundwater, Shewanella sp., was evaluated for uptaking of chromium with varying Cr(VI) concentrations from 50 to 500 ppm in aerobic conditions (pH 7.0, 37 °C). The Shewanella sp. strain KR2 showed an obvious heavy metal tolerant in the wide range of heavy metals including: Cr6+,... 

    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... 

    Effects of bacillus amyloliquefaciens lfb112 on growth performance, carcass traits, immune, and serum biochemical response in broiler chickens

    , Article Antibiotics ; Volume 10, Issue 11 , 2021 ; 20796382 (ISSN) Ahmat, M ; Cheng, J ; Abbas, Z ; Cheng, Q ; Fan, Z ; Ahmad, B ; Hou, M ; Osman, G ; Guo, H ; Wang, J ; Zhang, R ; Sharif University of Technology
    MDPI  2021
    Abstract
    This study aimed to investigate the effects of Bacillus amyloliquefaciens LFB112 on the growth performance, carcass traits, immune response, and serum biochemical parameters of broiler chickens. A total of 396 1 day old, mixed-sex commercial Ross 308 broilers with similar body weights were allotted into six treatment groups. The assigned groups were the CON group (basal diet with no supplement), AB (antibiotics) group (basal diet + 150 mg of aureomycin/kg), C+M group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 powder with vegetative cells + metabolites), C group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 vegetative cell powder with removed metabolites), M group... 

    SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

    , Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) Akbarinejad, S ; 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... 

    Effects of bacillus amyloliquefaciens lfb112 on growth performance, carcass traits, immune, and serum biochemical response in broiler chickens

    , Article Antibiotics ; Volume 10, Issue 11 , 2021 ; 20796382 (ISSN) Ahmat, M ; Cheng, J ; Abbas, Z ; Cheng, Q ; Fan, Z ; Ahmad, B ; Hou, M ; Osman, G ; Guo, H ; Wang, J ; Zhang, R ; Sharif University of Technology
    MDPI  2021
    Abstract
    This study aimed to investigate the effects of Bacillus amyloliquefaciens LFB112 on the growth performance, carcass traits, immune response, and serum biochemical parameters of broiler chickens. A total of 396 1 day old, mixed-sex commercial Ross 308 broilers with similar body weights were allotted into six treatment groups. The assigned groups were the CON group (basal diet with no supplement), AB (antibiotics) group (basal diet + 150 mg of aureomycin/kg), C+M group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 powder with vegetative cells + metabolites), C group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 vegetative cell powder with removed metabolites), M group... 

    SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

    , Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) Akbarinejad, S ; 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... 

    Probabilistic safety assessment of a UF 6 production process

    , Article Advances in Safety, Reliability and Risk Management - Proceedings of the European Safety and Reliability Conference, ESREL 2011 ; 2012 , Pages 1384-1389 ; 9780415683791 (ISBN) Ebrahimi, B ; Sharif University of Technology
    2012
    Abstract
    Application of Probabilistic Safety Assessment (PSA) to a Uranium hexafluoride (UF 6) production process is presented in this paper. The process is constituted from three main units: UF 4 conversion to UF 6, condensation of produced UF 6 gas and tail gas treatment. Radioactive gas is present in all parts of the process and occurrence of high pressure or high temperature in the process equipments may lead to radioactive release to workplace and environment. The work is mainly based on PSA experience in nuclear power plants. Accordingly for the process, eight group of Initiating Events (IE) that lead to UF 6 gas release have been identified using HAZOP study. For each IE, based on related... 

    Characterization of a moderate thermophilic Nocardia species able to grow on polycyclic aromatic hydrocarbons

    , Article Letters in Applied Microbiology ; Volume 45, Issue 6 , December , 2007 , Pages 622-628 ; 02668254 (ISSN) Zeinali, M ; Vossoughi, M ; Ardestani, S. K ; Sharif University of Technology
    2007
    Abstract
    Aims: Our goal was the characterization of a new moderate thermophilic polycyclic aromatic hydrocarbon (PAH)-utilizing Nocardia strain. Methods and Results: A thermophilic bacterium, strain TSH1, was isolated from a contaminated soil. The macroscopic and microscopic features fit well with the description of Nocardia species. The results of 16S rRNA gene analysis showed 100% match to the type strain of N. otitidiscaviarum DSM 43242T. Strain TSH1 showed the same mycolic acid pattern as the type strain of N. otitidiscaviarum but its fatty acid profile did not permit identification to the species level. The carbon utilization profile of strain TSH1 was different from N. otitidiscaviarum. The... 

    DNA impedance biosensor for detection of cancer, TP53 gene mutation, based on gold nanoparticles/aligned carbon nanotubes modified electrode

    , Article Analytica Chimica Acta ; Vol. 836, issue , July , 2014 , p. 34-44 ; ISSN: 00032670 Fayazfar, H ; Afshar, A ; Dolati, M ; Dolati, A ; Sharif University of Technology
    Abstract
    For the first time, a new platform based on electrochemical growth of Au nanoparticles on aligned multi-walled carbon nanotubes (A-MWCNT) was developed for sensitive lable-free DNA detection of the TP53 gene mutation, one of the most popular genes in cancer research. Electrochemical impedance spectroscopy (EIS) was used to monitor the sequence-specific DNA hybridization events related to TP53 gene. Compared to the bare Ta or MWCNT/Ta electrodes, the synergistic interactions of vertically aligned MWCNT array and gold nanoparticles at modified electrode could improve the density of the probe DNA attachment and resulting the sensitivity of the DNA sensor greatly. Using EIS, over the extended... 

    Core flooding tests to investigate the effects of IFT reduction and wettability alteration on oil recovery during MEOR process in an Iranian oil reservoir

    , Article Applied Microbiology and Biotechnology ; Volume 97, Issue 13 , July , 2013 , Pages 5979-5991 ; 01757598 (ISSN) Rabiei, A ; Sharifinik, M ; Niazi, A ; Hashemi, A ; Ayatollahi, S ; Sharif University of Technology
    2013
    Abstract
    Microbial enhanced oil recovery (MEOR) refers to the process of using bacterial activities for more oil recovery from oil reservoirs mainly by interfacial tension reduction and wettability alteration mechanisms. Investigating the impact of these two mechanisms on enhanced oil recovery during MEOR process is the main objective of this work. Different analytical methods such as oil spreading and surface activity measurements were utilized to screen the biosurfactant-producing bacteria isolated from the brine of a specific oil reservoir located in the southwest of Iran. The isolates identified by 16S rDNA and biochemical analysis as Enterobacter cloacae (Persian Type Culture Collection (PTCC)... 

    Dna-Rna hybrid (R-loop): From a unified picture of the mammalian telomere to the genome-wide profile

    , Article Cells ; Volume 10, Issue 6 , 2021 ; 20734409 (ISSN) Rassoulzadegan, M ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
    MDPI  2021
    Abstract
    Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular...