En
  • دکتری (1388)

    بیوانفورماتیک

    دانشگاه تهران، ایران

  • کارشناسی‌ارشد (1379)

    زیست شناسی - بیوفیزیک

    دانشگاه تربیت مدرس،

  • کارشناسی (1375)

    علوم میکروبیولوژي

    تهران، تهران، ایران

  • بیوانفورماتیک ساختاری
  • طراحی پروتئین و پپتید
  • آزمایشگاه بیوانفورماتیک

    زمینه های پژوهشی: بیوانفورماتیک ساختاری

    کارشناس مسئول:

    هیات علمی همکار: سیدشهریار عرب

    تلفن: 82883431

    مکان: دانشگاه تربیت مدرس - دانشکده علوم زیستی

دکتر سید شهریار عرب در سال ۱۳۷۱ در دانشگاه تهران در رشته علوم میکروبیولوژی پذیرفته شد و در سال ۱۳۷۵ دوره کارشناسی خود در این رشته را به اتمام رسانید. علاقه وی به ساختار پروتئین ها باعث ادامه تحصیل در رشته بیوفیزیک در مقطع کارشناسی ارشد در دانشگاه تربیت مدرس شد. در سال ۱۳۸۰ به عنوان پژوهشگر برتر دانشگاه شناخته شد. در اولین دوره دکتری بیوانفورماتیک در دانشگاه تهران شروع به تحصیل کرد و در سال ۱۳۸۸ نیز فارغ التحصیل شد. و از سال ۱۳۹۰ به عنوان هیات علمی دانشگاه تربیت مدرس در گروه بیوفیزیک مشغول به کار میباشد. عضویت های معتبر: عضو هیئت مدیره انجمن بیوانفورماتیک ایران (1395 تا کنون) نایب رئیس انجمن بیوانفورماتیک ایران (1395 - 1398) فعالیتهای اجرایی: مدیر گروه بیوفیزیک (از سال ۱۳۹۰ تا کنون) تدوین سرفصل دوره کارشناسی ارشد بیوانفورماتیک (۱۳۹۴) تدوین سرفصل دوره دکتری بیوانفورماتیک (۱۳۹۴) راه اندازی دوره کارشناسی ارشد بیوانفورماتیک در دانشگاه تربیت مدرس (۱۳۹۶) دبیر علمی هفتمین کنفرانس بیوانفورماتیک ایران (دیماه ۱۳۹۶) بازنگری سرفصلهای دوره کارشناسی ارشد بیوانفورماتیک (۱۴۰۰)

ارتباط

رزومه

Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study

Mohammad Mahmoudi Gomari, Neda Rostami, Hossein Omidi-Ardali, Seyed Shahriar Arab
Journal PapersJournal of Biomolecular Structure and Dynamics , 2021 January 8, {Pages 09-Jan }

Abstract

Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with

In Silico Investigation of Symptom Development Model Based on Coat Protein Interactions of Two Cucumber Mosaic Virus Strains

Masoud Akbarimotlagh, Seyed Shahriar Arab, Peter Palukaitis, Masoud Shams-bakhsh
Journal Papers , 2021 February 11, {Pages }

Abstract

Accordingly, it can be deduced that probably pentameric structures of M-CMV (higher 17 pathogenicity) CP block activation of plant Fd I protein. Therefore, it can be concluded that 18 trapping Fd I in the complex of pentameric structures can lead to inhibition of the activity of plant 19 Fd I in the photosynthetic electron transport chain leading the severe symptom development seen 20 in M-CMV infected plants but not in Q-CMV infected plants. It seems likely that any factor that 21 inhibits the interaction of CMV CPs with plant Fd I can prevent this symptom development. 22 23

Prediction of Chemoresistance Trait of Cancer Cell Lines using Machine Learning Algorithms and Systems Biology Analysis

Atousa Ataei, Niloufar Seyed Majidi, Javad Zahiri, Mehrdad Rostami, Seyed Shahriar Arab, Albert A Rizvanov
Journal Papers , 2021 March 11, {Pages }

Abstract

Most of the current cancer treatment approaches are invasive along with a broad spectrum of side effects. Furthermore, cancer drug resistance known as chemoresistance is a huge obstacle during treatment. This study aims to predict the resistance of several cancer cell-lines to a drug known as Cisplatin. In this papers the NCBI GEO database was used to obtain data and then the harvested data was normalized and its batch effects were corrected by the Combat software.

Reconstruction of intercellular signaling network by cytokine-receptor interactions

Somayeh Azadian, Javad Zahiri, Seyed Shahriar Arab, Reza Hassan Sajedi
Journal PapersIranian Journal of Biotechnology , Volume 19 , Issue 1, 2021 March 1, {Pages 67-73 }

Abstract

Background: The immune system function depends on the coordination activity of the components of system and communications between them which leads to the formation of a complex communication network between immune cells. In this network, cytokines have an important role in the communication between immune cells through the interaction to their specific receptors. These molecules cause to cellular communications and normal function of a tissue. Reconstruction of such a complex network can be a way to provide a better understanding of cytokines’ function. Objective: Our main goal from reconstructing such a network was investigation of expressed cytokines and cytokines receptors in various lineage and tissues of immune cells and identifying

Topological Analysis of Regulatory Networks Reveals Functionally Key Genes and miRNAs Involved in the Differentiation of Mesenchymal Stem Cells

Atousa Ataei, Mansour Poorebrahim, Azam Rajabpour, Albert Rizvanov, Seyed Shahriar Arab
Journal PapersIranian Journal of Biotechnology , Volume 19 , Issue 1, 2021 March 1, {Pages 21-Sep }

Abstract

Background: The details of molecular mechanisms underlying the differentiation of Mesenchymal Stem Cells (MSCs) into specific lineages are not well understood. Objectives: We aimed to construct the interactome network and topology analysis of bone marrow mesenchymal stem cell of CAGE data. Applying the enrichment results, we wanted to introduce the common genes and hub-microRNA and hub genes of these giant network. Materials and Methods: In this study, we constructed gene regulatory networks for each non-mesenchymal cell lineage according to their gene expression profiles obtained from FANTOM5 database. The putative interactions of TF-gene and protein-protein were determined using TRED, STRING, HPRD and GeneMANIA servers. In parallel, a reg

Protein sequence profile prediction using ProtAlbert transformer1

A Behjati, F Zare-Mirakabad, SS Arab, A Nowzari-Dalini
Journal Papers , , {Pages }

Abstract

Filtering of the Gene Signature as the Predictors of Cisplatin-Resistance in Ovarian Cancer

A Ataei, SS Arab, J Zahiri, A Rajabpour, K Kletenkov, A Rizvanov
Journal Papers , , {Pages }

Abstract

Peptides for targeting lrp6-overexpressed cells

E Rismani, L TeimooriToolabi, M Karimipoor, SS Arab
Journal Papers , , {Pages }

Abstract

sFLT01-anti-ANG2: a Novel Potent Inhibitor as a Next-generation Anti-angiogenic Molecule

H Ahmadieh, H Latifi-navid, ZS Soheili, M Sadeghi, S Samiei, ...
Journal Papers , , {Pages }

Abstract

Exome sequencing reveals novel rare variants in Iranian familial multiple sclerosis: The importance of POLD2 in the disease pathogenesis

Z Salehi, M Keramatipour, S Talebi, SS Arab, AN Moghadasi, ...
Journal Papers , , {Pages }

Abstract

Protein sequence profile prediction using ProtAlbert transformer1

F Zare-Mirakabad, A Behjati, SS Arab, A Nowzari-Dalini
Journal Papers , , {Pages }

Abstract

In Silico Analysis of Neutralizing Antibody Epitopes on Hepatitis C Virus Surface Glycoproteins as a Distinct Peptide Library Designing

R Zareh-Khoshchehreh, T Bamdad, SS Arab, M Behdani, M Biglar
Journal Papers , , {Pages }

Abstract

Multifunctional Acidocin 4356 combats Pseudomonas aeruginosa through membrane perturbation and virulence attenuation: Experimental results confirmed molecular dynamic simulation

Sima Modiri, Rouha Kasra Kermanshahi, Mohammad Reza Soudi, Seyed Shahriar Arab, Anahita Khammari, Benoit Cousineau, Hojatollah Vali, Hossein Shahbani Zahiri, Kambiz Akbari Noghabi
Journal PapersApplied and Environmental Microbiology , 2020 March 13, {Pages }

Abstract

A longstanding awareness in generating resistance to common antimicrobial therapies by gram-negative bacteria has made them a major threat to global health. The application of antimicrobial peptides as a therapeutic agent would be a great opportunity to combat bacterial diseases. Here, we introduce a new antimicrobial peptide (∼8.5 kDa) from probiotic strain Lactobacillus acidophilus ATCC 4356, designated as Acidocin 4356 (ACD). This multifunctional peptide exerts its anti-infective ability against Pseudomonas aeruginosa through an inhibitory action on virulence factors, bacterial killing, and biofilm degradation. Reliable performance over tough physiological conditions and low hemolytic activity confirmed a new hope for the therapeutic s

Directed Blocking of TGF-β Receptor I Binding Site Using Tailored Peptide Segments to Inhibit its Signaling Pathway

Reza H Sajedi, Sepideh Sepehri, S Arab, Mehrdad Behmanesh
Journal PapersIranian Journal of Biotechnology , 2020 June 2, {Pages }

Abstract

Background: TGF-β isoforms play crucial roles in diverse cellular processes. Therefore, targeting and inhibiting TGF-β signaling pathway provides a potential therapeutic opportunity. TGF-β isoforms bind and bring the receptors (TβRII and TβRI) together to form a signaling complex in an ordered manner.Objectives: Herein, an antagonistic variant of TGF-β (AnTβ) has been designed and prepared to inhibit the formation of signaling complex and consequently its signaling pathway. This TGF-β homodimeric variant contains intact TβRII binding sites and blocked TβRI binding sites by substituting three peptide segments. So, AnTβ could only bind to TβRII, but prevent binding and recruitment of TβRI to form a signaling complex.Materials and

Radiosynthesis, Biological Evaluation, and Preclinical Study of a 68Ga-Labeled Cyclic RGD Peptide as an Early Diagnostic Agent for Overexpressed αvβ3 Integrin Receptors in Non?…

Nazanin Pirooznia, Khosrou Abdi, Davood Beiki, Farshad Emami, Seyed Shahriar Arab, Omid Sabzevari, Zahra Pakdin-Parizi, Parham Geramifar
Journal PapersContrast media & molecular imaging , Volume 2020 , 2020 March 31, {Pages }

Abstract

The αvβ3 integrin receptors have high expression on proliferating growing tumor cells of different origins including non-small-cell lung cancer. RGD-containing peptides target the extracellular domain of integrin receptors. This specific targeting makes these short sequences a suitable nominee for theranostic application. DOTA-E(cRGDfK)2 was radiolabeled with 68Ga efficiently. The in vivo and in vitro stability was examined in different buffer systems. Metabolic stability was assessed in mice urine. In vitro specific binding, cellular uptake, and internalization were determined. The tumor-targeting potential of [68Ga]Ga-DOTA-E(cRGDfK)2 in a lung cancer mouse model was studied. Besides, the very early diagnostic potential of the 68Ga-label

Application of a novel pH-responsive gemini surfactant for delivery of curcumin molecules

Maral Rahimzadeh, Majid Sadeghizadeh, Farhood Najafi, Seyed Shahriar Arab, Pouneh Sadat Pourhosseini
Journal PapersMaterials Research Express , Volume 7 , Issue 6, 2020 June 10, {Pages 065403 }

Abstract

During the last few decades, extensive studies have been conducted to elucidate the anti-cancer effects of curcumin. Despite promising results indicating curcumin could impede cancer cells ability thrive and proliferation, clinical applications of it have been limited. This limitation is mainly due to low solubility, poor bioavailability, rapid metabolism, and deficient absorption. To improve the physiochemical properties of curcumin, we have synthesized a novel biodegradable gemini surfactant in which curcumin molecules were entrapped. Gemini surfactant-curcumin nanocapsules were prepared using nanoprecipitation method and characterized by several techniques including, DLS, TEM, AFM, FTIR, DSC and XRD. The in vitro MTT assay, cellular upta

Multifunctional Acidocin 4356 Combats Pseudomonas aeruginosa through Membrane Perturbation and Virulence Attenuation: Experimental Results Confirm Molecular Dynamics Simulation

Sima Modiri, Rouha Kasra Kermanshahi, Mohammad Reza Soudi, Seyed Shahriar Arab, Anahita Khammari, Benoit Cousineau, Hojatollah Vali, Hossein Shahbani Zahiri, Kambiz Akbari Noghabi
Journal PapersApplied and Environmental Microbiology , Volume 86 , Issue 10, 2020 May 5, {Pages }

Abstract

A longstanding awareness in generating resistance to common antimicrobial therapies by Gram-negative bacteria has made them a major threat to global health. The application of antimicrobial peptides as a therapeutic agent would be a great opportunity to combat bacterial diseases. Here, we introduce a new antimicrobial peptide (∼8.3 kDa) from probiotic strain Lactobacillus acidophilus ATCC 4356, designated acidocin 4356 (ACD). This multifunctional peptide exerts its anti-infective ability against Pseudomonas aeruginosa through an inhibitory action on virulence factors, bacterial killing, and biofilm degradation. Reliable performance over tough physiological conditions and low hemolytic activity confirmed a new hope for the therapeutic s

The hot sites of α-synuclein in amyloid fibril formation

Anahita Khammari, Seyed Shahriar Arab, Mohammad Reza Ejtehadi
Journal PapersScientific reports , Volume 10 , Issue 1, 2020 July 22, {Pages 14-Jan }

Abstract

The role of alpha-synuclein (αS) amyloid fibrillation has been recognized in various neurological diseases including Parkinson’s Disease (PD). In early stages, fibrillation occurs by the structural transition from helix to extended states in monomeric αS followed by the formation of beta-sheets. This alpha-helix to beta-sheet transition (αβT) speeds up the formation of amyloid fibrils through the formation of unstable and temporary configurations of the αS. In this study, the most important regions that act as initiating nuclei and make unstable the initial configuration were identified based on sequence and structural information. In this regard, a Targeted Molecular Dynamics (TMD) simulation was employed using explicit solvent mode

177Lu-labeled cyclic RGD peptide as an imaging and targeted radionuclide therapeutic agent in non-small cell lung cancer: Biological evaluation and preclinical study

Nazanin Pirooznia, Khosrou Abdi, Davood Beiki, Farshad Emami, Seyed Shahriar Arab, Omid Sabzevari, Samira Soltani-Gooshkhaneh
Journal PapersBioorganic chemistry , Volume 102 , 2020 September 1, {Pages 104100 }

Abstract

Non-small cell lung carcinoma (NSCLC) is among the most lethal lung cancers responsible for 80–85% of death. αvβ3 integrin receptor subtype has been identified as a lung cancer biomarker since its expression correlates with tumor progression and metastasis. The extracellular domain of the receptor forms a binding site for RGD-based sequences. Therefore, specific targeting of αvβ3 integrin receptors by these short peptides can be an excellent candidate for cancer imaging and therapy. In this research, the radiolabeling of DOTA-E(cRGDfK)2 with 177Lu was efficiently implemented. The Log P value, in vivo, in vitro, metabolic stability, cellular uptake and specific binding of the radiopeptide was determined. The tumor targeting capacity an

Effects of Linker Flexibility and Conformational Changes of IP3 Receptor on Split Luciferase Complementation Assay

Maryam Moradi, Saman Hosseinkhani, Seyed Shahriar Arab, Anahita Khammari
Journal PapersIranian Journal of Biotechnology , Volume 18 , Issue 4, 2020 December 1, {Pages 106-114 }

Abstract

Background: IP3-induced Ca2+ release, mediated by IP3R, is one of the most momentous cellular signaling mechanisms that regulate in a wide variety of essential cellular functions. Involvement of disrupted IP3 signaling pathways in numerous pathophysiology conditions is implicated to find the best methods for its measurement. Hence, several different biosensors have developed to monitor temporal changes of IP3 by using the IP3-binding domain of IP3 receptors. Objectives: Based on a previous study, we developed and characterized a series of bioluminescent biosensors using the human type-II IP3 receptor ligand binding domain (residues 1–604), named LAIRE (luminescent analyzer for IP3 receptor element) to study the effect of flexible and rigi

دروس نیمسال جاری

  • دكتري
    بيوانفورماتيك پيشرفته ( واحد)
    دانشکده علوم زیستی، گروه بيو فيزيك
  • دكتري
    بيوانفورماتيك پيشرفته ( واحد)
  • كارشناسي ارشد
    بيوانفورماتيك ( واحد)
  • كارشناسي ارشد
    بيوانفورماتيك ( واحد)
  • كارشناسي ارشد
    مدلسازي و پيشگويي ساختار ماكرومولكولها ( واحد)
  • كارشناسي ارشد
    مدلسازي و پيشگويي ساختار ماكرومولكولها ( واحد)

دروس نیمسال قبل

  • دكتري
    computational and systems biology ( واحد)
    دانشکده علوم زیستی، گروه بيوتكنولوژي پزشكي
  • كارشناسي ارشد
    مباني بيوانفورماتيك ( واحد)
  • كارشناسي ارشد
    مباني بيوانفورماتيك ( واحد)
  • كارشناسي ارشد
    پايگاه داده هاي زيستي ( واحد)
  • كارشناسي ارشد
    بيوانفورماتيك ساختاري ( واحد)
  • 1397
    افخمي, الهام
    توسعه نرم‌افزار براي آناليز داده‌هاي دورنگ‌نمايي دوراني جهت تعيين محتواي ساختار دوم پروتئين‌ها
  • 1397
    حجتي, مريم
  • 1397
    دوست محمدي, عليرضا
  • 1398
    بيگدلي, علي
  • 1398
    فضلعلي, فاطمه
  • 1398
    مدني, سيده هانيه
  • 1396
    وفايي, رايحه
    آناليز ساختاري آنزيم DNA پليمراز Pfu و مطالعه مكانيسم پردازش آنزيم با استفاده از شبيه سازي ديناميك مولكولي
  • 1397
    برهاني كودهي, صديقه
  • مدیر گروه بیوفیزیک
  • مدیر گروه بیوفیزیک
    داده ای یافت نشد

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