Search for: systems-biology
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    A system-oriented strategy to enhance electron production of Synechocystis sp. PCC6803 in bio-photovoltaic devices: experimental and modeling insights

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Firoozabadi, H ; Mardanpour, M. M ; Motamedian, E ; Sharif University of Technology
    Nature Research  2021
    Bio-photovoltaic devices (BPVs) harness photosynthetic organisms to produce bioelectricity in an eco-friendly way. However, their low energy efficiency is still a challenge. A comprehension of metabolic constraints can result in finding strategies for efficiency enhancement. This study presents a systemic approach based on metabolic modeling to design a regulatory defined medium, reducing the intracellular constraints in bioelectricity generation of Synechocystis sp. PCC6803 through the cellular metabolism alteration. The approach identified key reactions that played a critical role in improving electricity generation in Synechocystis sp. PCC6803 by comparing multiple optimal solutions of... 

    Visual acuity classification using single trial visual evoked potentials

    , Article Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2 September 2009 through 6 September 2009 ; 2009 , Pages 982-985 ; 9781424432967 (ISBN) Hajipour, S ; Shamsollahi, M. B ; Abootalebi, V ; Sharif University of Technology
    Several researches have been done to identify visual system characteristics. Some of them are based on the processing of the brain signal recordings. Visual evoked potentials (VEPs) are electrical signals which are produced in response to the visual stimuli and recorded by means of electrodes placed on the head. These signals are usually characterized by the amplitude and latency of their peaks. Different types of visual stimuli and visual system characteristics can affect the shape and hence the characteristics of VEPs. In this paper, proper visual stimuli were used and VEPs were recorded in order to classify visual acuity. To achieve this goal, visual evoked potentials were recorded and... 

    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
    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... 

    Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization

    , Article Bioinformatics ; Volume 35, Issue 20 , 2019 , Pages 4081-4088 ; 13674803 (ISSN) Fooladi, H ; Moradi, P ; Sharifi Zarchi, A ; Hosein Khalaj, B ; Berger, B ; Sharif University of Technology
    Oxford University Press  2019
    The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon. Results: Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape... 

    Dynamic Simulation and Control of Reactive Systems Involving Metabolic Pathways

    , M.Sc. Thesis Sharif University of Technology Aghaee Foroushani, Mohammad (Author) ; Bozorgmehry Bozarjomehry, Ramin (Supervisor) ; Setoodeh, Payam (Co-Supervisor)
    In this project, modeling, simulation, and control of the Saccharomyces Cerevisiae were studied. In the first section, simulation and control of a structural model of saccharomyces Cerevisiae were performed. Fuzzy Logic Controller (FLC) as a model-independent controller and Global Linearization Controller (GLC) as a model-based controller were designed. Additionally, two types of Kalman filters were designed to predict all states of the structural model: 1-Extended Kalman Filter (EKF), 2- Unscented Kalman Filter (UKF). As a concise explanation, the control action of the GLC is a function of all states of the model, and since that measuring all metabolites is not practical, the EKF and UKF... 

    A bio-inspired method for hardware Trojan detection

    , Article 2017 19th International Symposium on Computer Architecture and Digital Systems, CADS 2017 ; Volume 2018-January , 8 March , 2018 , Pages 1-2 ; 9781538643792 (ISBN) Farajipour Ghohroud, N ; Hessabi, S ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2018
    Outsourcing the ICs for manufacturing introduces potential security threats such as hardware Trojans (HTs). In this paper, we propose hardware-based artificial immune system for solving this problem. This system uses a biologically-inspired technique which makes it attractive for using in computer security systems. Using our proposed method, the probability of HT detection can reach 100 percent, and the system can be made immune against HTs. © 2017 IEEE  

    Expression of functional recombinant human tissue transglutaminase (TG2) using the bac-to-bac baculovirus expression system

    , Article Advanced Pharmaceutical Bulletin ; Volume 6, Issue 1 , 2016 , Pages 49-56 ; 22285881 (ISSN) Yazdani, Y ; Azari, S ; Kalhor, H. R ; Sharif University of Technology
    Tabriz University of Medical Sciences 
    Tissue transglutaminase (TG2) is a unique multifunctional enzyme. The enzyme possesses enzymatic activities such as transamidation/crosslinking and non-enzymatic functions such as cell migration and signal transduction. TG2 has been shown to be involved in molecular mechanisms of cancers and several neurodegenerative diseases such as Alzheimer's disease. The present study aimed at cloning and expression of full length human TG2 in Bac-to-Bac baculovirus expression system and evaluation of its activity. Methods: pFastBac HTA donor vector containing coding sequence of human TG2 was constructed. The construct was transformed to DH10Bac for generating recombinant bacmid. The verified bacmid was... 

    The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency

    , Article Cell and Bioscience ; Volume 9, Issue 1 , 2019 ; 20453701 (ISSN) Yousefi, M ; Marashi, S. A ; Sharifi Zarchi, A ; Taleahmad, S ; Sharif University of Technology
    BioMed Central Ltd  2019
    Background: Pluripotency is proposed to exist in two different stages: Naive and Primed. Conventional human pluripotent cells are essentially in the primed stage. In recent years, several protocols have claimed to generate naive human embryonic stem cells (hESCs). To the best of our knowledge, none of these protocols is currently recognized as the gold standard method. Furthermore, the consistency of the resulting cells from these diverse protocols at the molecular level is yet to be shown. Additionally, little is known about the principles that govern the metabolic differences between naive and primed pluripotency. In this work, using a computational approach, we tried to shed light on... 

    A multi-scale model for determining the effects of pathophysiology and metabolic disorders on tumor growth

    , Article Scientific Reports ; Volume 10, Issue 1 , 20 February , 2020 Nikmaneshi, M. R ; Firoozabadi, B ; Mozafari, A ; Munn, L. L ; Sharif University of Technology
    Nature Research  2020
    The search for efficient chemotherapy drugs and other anti-cancer treatments would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. Because in vivo experimental methods are unable to isolate or control individual factors of the TME and in vitro models often do not include all the contributing factors, some questions are best addressed with systems biology mathematical models. In this work, we present a new fully-coupled, agent-based, multi-scale mathematical model of tumor growth, angiogenesis and metabolism that includes important aspects of the TME spanning subcellular-, cellular- and tissue-level scales. The mathematical model is... 

    Inferring causal molecular networks: Empirical assessment through a community-based effort

    , Article Nature Methods ; Volume 13, Issue 4 , 2016 , Pages 310-322 ; 15487091 (ISSN) Hill, S. M ; Heiser, L.M ; Cokelaer, T ; Linger, M ; Nesser, N. K ; Carlin, D. E ; Zhang, Y ; Sokolov, A ; Paull, E. O ; Wong, C. K ; Graim, K ; Bivol, A ; Wang, H ; Zhu, F ; Afsari, B ; Danilova, L. V ; Favorov, A. V ; Lee, W. S ; Taylor, D ; Hu, C. W ; Long, B. L ; Noren, D. P ; Bisberg, A. J ; Mills, G. B ; Gray, J. W ; Kellen, M ; Norman, T ; Friend, S ; Qutub, A. A ; Fertig, E. J ; Guan, Y ; Song, M ; Stuart, J. M ; Spellman, P. T ; Koeppl, H ; Stolovitzky, G ; Saez Rodriguez, J ; Mukherjee, S ; Afsari, B ; Al-Ouran, R ; Anton, B ; Arodz, T ; Askari Sichani, O ; Bagheri, N ; Berlow, N ; Bisberg, A. J ; Bivol, A ; Bohler, A ; Bonet, J ; Bonneau, R ; Budak, G ; Bunescu, R ; Caglar, M ; Cai, B ; Cai, C ; Carlin, D. E ; Carlon, A ; Chen, L ; Ciaccio, M. F ; Cokelaer, T ; Cooper, G ; Coort, S ; Creighton, C. J ; Daneshmand, S. M. H ; De La Fuente, A ; Di Camillo, B ; Danilova, L. V ; Dutta-Moscato, J ; Emmett, K ; Evelo, C ; Fassia, M. K. H ; Favorov, A. V ; Fertig, E. J ; Finkle, J. D ; Finotello, F ; Friend, S ; Gao, X ; Gao, J ; Garcia Garcia, J ; Ghosh, S ; Giaretta, A ; Graim, K ; Gray, J. W ; Großeholz, R ; Guan, Y ; Guinney, J ; Hafemeister, C ; Hahn, O ; Haider, S ; Hase, T ; Heiser, L. M ; Hill, S. M ; Hodgson, J ; Hoff, B ; Hsu, C. H ; Hu, C. W ; Hu, Y ; Huang, X ; Jalili, M ; Jiang, X ; Kacprowski, T ; Kaderali, L ; Kang, M ; Kannan, V ; Kellen, M ; Kikuchi, K ; Kim, D. C ; Kitano, H ; Knapp, B ; Komatsoulis, G ; Koeppl, H ; Krämer, A ; Kursa, M. B ; Kutmon, M ; Lee, W. S ; Li, Y ; Liang, X ; Liu, Z ; Liu, Y ; Long, B. L ; Lu, S ; Lu, X ; Manfrini, M ; Matos, M. R. A ; Meerzaman, D ; Mills, G. B ; Min, W ; Mukherjee, S ; Müller, C. L ; Neapolitan, R. E ; Nesser, N. K ; Noren, D. P ; Norman, T ; Oliva, B ; Opiyo, S. O ; Pal, R ; Palinkas, A ; Paull, E. O ; Planas Iglesias, J ; Poglayen, D ; Qutub, A. A ; Saez Rodriguez, J ; Sambo, F ; Sanavia, T ; Sharifi-Zarchi, A ; Slawek, J ; Sokolov, A ; Song, M ; Spellman, P. T ; Streck, A ; Stolovitzky, G ; Strunz, S ; Stuart, J. M ; Taylor, D ; Tegnér, J ; Thobe, K ; Toffolo, G. M ; Trifoglio, E ; Unger, M ; Wan, Q ; Wang, H ; Welch, L ; Wong, C. K ; Wu, J. J ; Xue, A. Y ; Yamanaka, R ; Yan, C ; Zairis, S ; Zengerling, M ; Zenil, H ; Zhang, S ; Zhang, Y ; Zhu, F ; Zi, Z ; Sharif University of Technology
    Nature Publishing Group  2016
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was... 

    Optimization of multistage biological nutrient removal reactors for removal of nitrogen and phosphorus from saline refinery wastewater

    , Article International Journal of Environmental Science and Technology ; Volume 17, Issue 12 , 2020 , Pages 4865-4878 Delashoob, A ; Borghei, S. M ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2020
    The present study aimed at investigating the biological treatment of nitrogen and phosphorus from the saline wastewater in various systems. In the end, moving bed biofilm reactor and anaerobic/anoxic/aerobic (AOA) were chosen as the best systems. In the present study, the investigations were carried out in two 24-h and 12-h retention times for three nitrogen concentrations, 200 mg/l, 300 mg/l, and 400 mg/l, two phosphorus concentrations, 14 mg/l and 20 mg/l, three Chemical oxygen demand (COD) concentrations, 800 mg/l, 1000 mg/l, and 1200 mg/l, and four salt concentrations, 10 g/l, 12 g/l, 17 g/l, and 20 g/l. The obtained results indicated that the COD removal percentage was high in a range... 

    An integrative Bayesian network approach to highlight key drivers in systemic lupus erythematosus

    , Article Arthritis Research and Therapy ; Volume 22, Issue 1 , June , 2020 Maleknia, S ; Salehi, Z ; Rezaei Tabar, V ; Sharifi Zarchi, A ; Kavousi, K ; Sharif University of Technology
    BioMed Central  2020
    Background: A comprehensive intuition of the systemic lupus erythematosus (SLE), as a complex and multifactorial disease, is a biological challenge. Dealing with this challenge needs employing sophisticated bioinformatics algorithms to discover the unknown aspects. This study aimed to underscore key molecular characteristics of SLE pathogenesis, which may serve as effective targets for therapeutic intervention. Methods: In the present study, the human peripheral blood mononuclear cell (PBMC) microarray datasets (n = 6), generated by three platforms, which included SLE patients (n = 220) and healthy control samples (n = 135) were collected. Across each platform, we integrated the datasets by...