Journal Papers

1. "AI-driven covalent drug design strategies targeting main protease (m ^pro ) against SARS-CoV-2: structural insights and molecular mechanisms"
   Mohammad Hossein Haghir Ebrahimabadi, Abdurahman Ghasemlo, Fatemeh Bayani, Yahya Sefidbakht, Massoud Vosough, Sina Mozaffari-Jovin, Vladimir N. Uversky
   JOURNAL OF BIOMOLECULAR STRUCTURE and DYNAMICS, Vol. _, pp.1-29, 2024
2. "Characterization of stability, safety and immunogenicity of the mRNA lipid nanoparticle vaccine Iribovax® against COVID-19 in nonhuman primates"
   Parvin Zamani, Mohammad Mashreghi, Mahere Rezazade Bazaz, Selma Zargari, Farzaneh Alizadeh, Mahyar Dorrigiv, Asghar Abdoli, Hossein Aminianfar, Mahdi Hatamipour, Javad Zarqi, Saeed Behboodifar, Yalda Samsami, Saeideh Khorshid Sokhangouy, Yahya Sefidbakht, Vuk Uskokovic, Seyed Mahdi Rezayat, Mahmoud Reza Jaafari, Sina Mozaffari-Jovin
   JOURNAL OF CONTROLLED RELEASE, Vol. 360, pp.316-334, 2023
3. "An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines"
   Fatemeh Bayani, Negin Safaei Hashkavaei, Sareh Arjmand, SHOKOUH REZAEI, Vuk Uskokovic, Mahdi Alijanianzadeh, Vladimir N. Uversky, Seyyed Omid Ranaee Siadat, Sina Mozaffari-Jovin, Yahya Sefidbakht
   PROGRESS IN BIOPHYSICS and MOLECULAR BIOLOGY, Vol. 178, pp.32-49, 2023
4. "In silico design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2"
   Fatemeh Bayani, Negin Safaei Hashkavaei, Mohammad Reza Karamian, Vuk Uskokovich, Yahya Sefidbakht
   JOURNAL OF BIOMOLECULAR STRUCTURE and DYNAMICS, Vol. 41, pp.1-15, 2023
5. "Exploration of potential inhibitors for SARS?CoV?2 Mpro considering its mutants via structure?based drug design, molecular docking, MD simulations, MM/PBSA, and DFT calculations"
   Abdurahman Ghasemlo, Vuk Uskokovi?, Yahya Sefidbakht
   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY, Vol. 69, pp.1-19, 2022
6. "Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant"
   Fatemeh Bayani, Negin Safaei Hashkavaei, Vladimir N. Uversky, Sina Mozaffari-Jovin, Yahya Sefidbakht
   COMPUTERS IN BIOLOGY AND MEDICINE, Vol. 147, 2022
7. "Doxorubicin-loaded, pH-sensitive Albumin Nanoparticles for Lung Cancer Cell Targeting"
   Ahmedazeezahmed Alakdha, Yahya Sefidbakht, SHOKOUH REZAEI, Hasan Kouchakzadeh, Vuk Uskokovi?
   JOURNAL OF PHARMACEUTICAL SCIENCES, Vol. ., pp.1-11, 2021
8. "Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design"
   SHOKOUH REZAEI, Yahya Sefidbakht, Vuk Uskokovi?
   BRIEFINGS IN BIOINFORMATICS, Vol. 22, pp.1-20, 2021
9. "Radioprotective Role of Vitamins C and E against the Gamma Ray-Induced Damage to the Chemical Structure of Bovine Serum Albumin"
   Hajar Zarei, Mostean Bahreinipour, Yahya Sefidbakht, SHOKOUH REZAEI, Rouhollah Gheisari, Susan Kabudanian Ardestani, Vuk Uskokovi, Hiroshi Watabe
   Antioxidants, Vol. 10, 2021
10. "Development and characterization of a thermostable GH11/GH10 xylan degrading chimeric enzyme"
    , Fataneh Fatemi, Yahya Sefidbakht, Seyed Ehsan Ranaei Siadat
    ENZYME AND MICROBIAL TECHNOLOGY, Vol. 149, 2021
11. "Hydroxyapatite as a biomaterial - a gift that keeps on giving"
    Behrad Ghiasi, Yahya Sefidbakht, Sina Mozaffari-Jovin, Behnaz Gharehcheloo, Mehrnoush Mehrarya, Arash Khodadadi, Maryam Rezaei, Seyyed Omid Ranaee Siadat, Vuk Uskokovi?
    DRUG DEVELOPMENT AND INDUSTRIAL PHARMACY, Vol. 46, pp.1035-1062, 2020
12. "Enantioseparation of mandelic acid on vancomycincolumn: Experimental and docking study"
    Mostafa Shahnani, Yahya Sefidbakht, Shokoofe Maghari, Ahmad Mehdi, Hassan Rezadoost Chahardeh, Alireza Ghassempour
    CHIRALITY, Vol. 32, pp.1289-1298, 2020
13. "Comparative molecular dynamics study of the receptor-binding domains in SARS-CoV-2 and SARS-CoV and the effects of mutations on the binding affinity"
    SHOKOUH REZAEI, Yahya Sefidbakht, Vuk Uskokovic
    JOURNAL OF BIOMOLECULAR STRUCTURE and DYNAMICS, Vol. 38, pp.1-20, 2020
14. "Graphite/gold nanoparticles electrode for direct protein attachment: characterization and gas sensing application"
    Javad Shabani Shayeh, Yahya Sefidbakht, Meisam Omidi, Fatemeh Yazdian, Lobat Tayebi
    ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH, Vol. 27, pp.1-10, 2020
15. "Colloidal graphene oxide enhances the activity of a lipase and protects it from oxidative damage: Insights from physicochemical and molecular dynamics investigations"
    Omid Kalji Karaci, Yahya Sefidbakht, Alexey M. Nesterenko, Vuk Uskokovi, Seyyed Omid Ranaee Siadat
    JOURNAL OF COLLOID AND INTERFACE SCIENCE, Vol. 567, pp.285-299, 2020
16. "How is the Effect of Silver Nanoparticles and Lipase/Cellulase Enzymes on Each Other?"
    Behnam Eysazadehjandar, Fateme Mirzajani, Yahya Sefidbakht
    Iranian Journal of Science and Technology Transaction A-Science, Vol. 44, pp.27-35, 2020
17. "Theranostic applications of stimulus-responsivesystems based on carbon dots"
    Behrad Ghiasi, Golnaz Mehdipour, Nooshin Safari, Hamidreza Behboodi, Mohadeseh Hashemi, Meisam Omidi, Yahya Sefidbakht, Amir Yadegari, Michael R. Hamblin
    INTERNATIONAL JOURNAL OF POLYMERIC MATERIALS, Vol. 70, pp.117-130, 2019
18. "An isolate of Potato Virus X capsid protein from N. benthamiana Insights from homology modeling and molecular dynamics simulation"
    Neda Esfandiari, Yahya Sefidbakht
    INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, Vol. 116, pp.939-946, 2018
19. "The effect of non-thermal atmospheric plasma on the production and activity of recombinant phytase enzyme"
    Mahsa Farasat, Sareh Arjmand, Seyyed Omid Ranaee Siadat, Yahya Sefidbakht, Hamidreza Ghomi marzdashti
    Scientific Reports, Vol. 8, pp.1-12, 2018
20. "Effect of size and chemical composition of graphene oxide nanoparticles on optical absorption cross-section"
    Mohadeseh Hashemi, Bharadwaj Muralidharan, Meisam Omidi, Javad Mohammadi, Yahya Sefidbakht, Eun Song Kima, Hugh D.C. Smyth, Mohammad Shalbaf, Thomas E. Milner
    JOURNAL OF BIOMEDICAL OPTICS, Vol. 23, 2018
21. "Continuous fast Fourier transforms cyclic Voltammetry as a new approach for investigation of skim milk k-casein proteolysis a comparative study"
    Javad Shabani Shayeh, Yahya Sefidbakht, Seyyed Omid Ranaee Siadat, kaveh niknam
    INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, Vol. 103, pp.972-977, 2017
22. "Recombinant Acetylcholinesterase purification and its interaction with silver nanoparticle"
    Fateme Mirzajani, Seyed Mohammad Motavalli, Shaghayegh Jabbari, Seyyed Omid Ranaee Siadat, Yahya Sefidbakht
    PROTEIN EXPRESSION AND PURIFICATION, Vol. 136, pp.58-65, 2017
23. "Homology Modeling and Molecular Dynamics Study on Schwanniomyces Occidentalis Alpha Amylase"
    Yahya Sefidbakht, Seyyed Omid Ranaee Siadat,
    JOURNAL OF BIOMOLECULAR STRUCTURE and DYNAMICS, Vol. 35, pp.1-11, 2016
24. "Caseoperoxidase mixed -casein SDS hemin imidazole complex a nano artificial enzyme"
    Zainab Moosavi-Movahedi, Hussein Gharibi, Hamid Hadi-Alijanvand, Mohammad Akbarzadeh, Mansoore Esmaili, Maliheh S. Atri, Yahya Sefidbakht, Mousa Bohlooli, Khodadad Nazari, Sohaeila javadian, Jun Hong, Ali A. Saboury, Nader Sheibani, Ali A. Moosavi-Movahedi
    JOURNAL OF BIOMOLECULAR STRUCTURE and DYNAMICS, Vol. 33, pp.1-46, 2015
25. "Antibacterial and molecular dynamics study of the Dolabellanin B2 isolated from sea slug Peronia peronii"
    , Seyyed Omid Ranaee Siadat, Jamileh Pazooki, Yahya Sefidbakht
    BIOSCIENCES BIOTECHNOLOGY RESEARCH ASIA, Vol. 12, pp.2023-2035, 2015
26. "Chemical recycling of PET wastes with different Catalysts"
    , , Yahya Sefidbakht, خديجه شكوهي,
    International Journal of Polymer Science, Vol. 2015, pp.1-11, 2015
27. ""
    Sareh Arjmand, Yahya Sefidbakht, Seyyed Omid Ranaee Siadat
    
28. "Enhancement of thermal stability of saccharomyces cerevisiae recombinant invertase by site directed mutagenesis"
    Sareh Arjmand, Ghobadi Leila , Seyyed Omid Ranaee Siadat, Yahya Sefidbakht, Fatemeh Farzaneh
    Biotechnology Tarbiat Modares University,
29. ""
    Yahya Sefidbakht, Sheyda Zarghami,
    Vol. 13, pp.124-133, 2023
30. "the history of insulins discovery and its use in diabetes managment"
    Negin Safaei Hashkavaei, Fatemeh Bayani, Narges Parniaei, Sareh Arjmand, Yahya Sefidbakht
    Vol. 13, pp.60-69, 2023
31. ""
    Samira Abdikhni, SHOKOUH REZAEI, Yahya Sefidbakht, Sareh Arjmand
    Vol. 11, pp.189-199, 2021
32. ""
    SHOKOUH REZAEI, Yahya Sefidbakht, Maedeh Soltani, Narges Tavana
    Vol. 11, pp.59-68, 2021
33. "New Coronavirus 2019 (nCoV-2019) Origin and Pathogenicity Mechanism"
    SHOKOUH REZAEI, Abdurahman Ghasemlo, Yahya Sefidbakht
    Vol. 10, pp.130-137, 2020
34. ""
    Fatemeh Ghafouri, Nasim Kian vala, Samin Haghighi poodeh, Yahya Sefidbakht
    Vol. 10, pp.33-41, 2019
35. ""
    Samin Haghighi poodeh, Yahya Sefidbakht, Hasan Kouchakzadeh
    Vol. 9, pp.82-88, 2019
36. ""
    Ali Ghorbani, Arian Zamani dehkordi, Yahya Sefidbakht
    Vol. 8, pp.128-134, 2018
37. ""
    Yahya Sefidbakht, amir hosein haghighi, mostafa ghorbani
    Vol. 15, pp.35-47, 2016
38. ""
    Yahya Sefidbakht
    Vol. 6, pp.81-86, 2015
39. ""
    Yahya Sefidbakht
    Vol. 5, pp.71-76, 2015
40. ""
    Yahya Sefidbakht
    Vol. 5, pp.49-55, 2014

Conference Papers

1. "Integrating Experimental and Molecular Dynamics Approaches to Investigate Stem Cell Exosomes and Their Therapeutic Potential in drug delivery"
   Yahya Sefidbakht
   6th International Congress and 18th Iranian Genetics Congress, pp.1375-1376, 2024
2. "Identification of potential COVID-19 Mpro inhibitors through covalent drug docking, molecular dynamics simulation, and MMGBSA calculation"
   Mohammad Hossein Haghir Ebrahimabadi, Fatemeh Bayani, Yahya Sefidbakht
   Iran's 5th Conference on Protein and Peptide Science, 2024
3. "Nanobody interactions with SARS-CoV-2 variants: Insights from computational studies on spike protein receptor binding domain mutations"
   Yahya Sefidbakht, Fatemeh Bayani
   Iran's 5th Conference on Protein and Peptide Science, 2024
4. "Stem cell-derived exosomes in deliveringAnti-cancer drugs Doxorubicin and Cyclophosphamide,cell viability and membrane simulation studies"
   Yahya Sefidbakht, Vosugh Massoud, Farnaz Maghami
   The First International Congress of Cancer Genomics, 2023
5. "study of the receptor-binding domains in SARS-CoV-2 and SARS-CoV and the effects of mutations on the binding affinity , biophysical aspects"
   Yahya Sefidbakht
   International virtual conference on Biophysics of life on Earth and the Covid-19 pandemic (World Biophysics Week 2021), 2021
6. "lipase adsorption on graphene oxide insights from molecular dynamics investigations"
   Omid Kalji Karaci, Yahya Sefidbakht, alexey nesterenko
   the 3rd conference on protein and peptide sciences, 2018
7. "Experimental and theoretical investigation on mandelic acid (rs) enantioselective separation using vancomycin chiral column"
   Yahya Sefidbakht, Mostafa Shahnani, Hassan Rezadoost Chahardeh, Alireza Ghassempour
   the 1st International Congress on Biomedicine, 2017
8. "Lipase adsorbtion on the single layer geraphene oxide"
   Yahya Sefidbakht, Omid Kalji Karaci
   the 1st International Congress on Biomedicine, 2017
9. "The effect of cold argon plasma on lipase activity"
   Yahya Sefidbakht, Omid Kalji Karaci, Sareh Arjmand, Mahsa Farasat, Seyyed Omid Ranaee Siadat, Hamidreza Ghomi marzdashti
   the 1st International Congress on Biomedicine, 2017
10. "Graphene oxide reduce pathologies damages by Hydrogene peroxide"
    Omid Kalji Karaci, Yahya Sefidbakht
    Second Nanomedicine and Nanosafety Conference, 2017
11. "Physically adsorbed lipase on Graphene oxide as a reusable biocatalyst"
    Yahya Sefidbakht, Omid Kalji Karaci
    Second Nanomedicine and Nanosafety Conference, pp.332-332, 2017
12. ""
    Yahya Sefidbakht, Seyyed Omid Ranaee Siadat,
    , 2016
13. "Poly Ethylene Terephthalate (PET) Waste Management through chemical and biocatalysts"
    Yahya Sefidbakht, Amir Hossein Haghighi, Mohammad Khonkari, Javad Shabani Shayeh
    , 2016
14. ""
    Yahya Sefidbakht, Seyyed Omid Ranaee Siadat,
    , 2015
15. ""
    Seyyed Omid Ranaee Siadat, Yahya Sefidbakht
    , 2015
16. "molecular dynamics simulation of receptor-binding domain in wuhan and omicron(B.1.1529) varaiant of SARS-COV-2"
    Negin Safaei Hashkavaei, Fatemeh Bayani, Yahya Sefidbakht
    17th National and 2nd International Conference of Iranian Biophysical Chemistry 6-7 Sep, 2022 University of Guilan, 2022
17. "computational investigation of the effect of omicron mutations in the N-terminal domain of spike protein on antibody evasion"
    Fatemeh Bayani, Negin Safaei Hashkavaei, Yahya Sefidbakht
    17th National and 2nd International Conference of Iranian Biophysical Chemistry 6-7 Sep, 2022 University of Guilan, 2022
18. "investigatigating spike protein N-terminal domain mutations in antibody evasion by molecular dyanmics simulation and designing a multi-epitope-based peptide vaccine against omicron variant (BA.1) proteins"
    Fatemeh Bayani, Negin Safaei Hashkavaei, Yahya Sefidbakht
    17th National Congress of Biochemistry and 8th International Congress of Biochemistry and Molecular Biology, 2022
19. "comparison of molecular dynamics study of receptor-binding domain in wild type and omicron (B1.1529) variants of SARS-COV-2"
    Negin Safaei Hashkavaei, Fatemeh Bayani, Yahya Sefidbakht
    The 10th National Bioinformatics and first international conference of Iran, 2022
20. "Molecular dynamics simulations show structural insights into the N-terminal domain mutations of the spike protein in"
    Fatemeh Bayani, Negin Safaei Hashkavaei, Yahya Sefidbakht
    The 10th National Bioinformatics and first international conference of Iran, 2022
21. "Comparative molecular dynamics study of receptor-binding domains in wild type and Omicron (B.1.1.529) variant of SARS-CoV-2"
    Negin Safaei Hashkavaei, Fatemeh Bayani, Yahya Sefidbakht
    The 10th National Bioinformatics and first international conference of Iran, 2022
22. "molecular dynamics (md) simulation of receptor binding domain of coronaviruses"
    SHOKOUH REZAEI, Yahya Sefidbakht
    ninth iranian conference on on bioinformatics, 2020
23. "the effect of hydroxyappatite nanoparticle on the activity of thermomyces lanuginosa lipase"
    Behrad Ghiasi, Yahya Sefidbakht, Arian Zamani dehkordi, Ali Ghorbani, Seyyed Omid Ranaee Siadat
    4th internation student biotechnology congress, 2019
24. "the facile and low temperature synthesis of antibacterial silver doped hydroxyapatite by wet chemistry"
    Behrad Ghiasi, Yahya Sefidbakht
    4th internation student biotechnology congress, 2019
25. "Effect of Atmospheric pressure plasma on phytase activity"
    Mahsa Farasat, Sareh Arjmand, Seyyed Omid Ranaee Siadat, Hamidreza Ghomi marzdashti, Yahya Sefidbakht
    , 2018
26. "Geraphene oxide (GO) modulates the activity of Thermomyceslanuginosus lipase (TLL)"
    Omid Kalji Karaci, Yahya Sefidbakht
    14th conference on Biophysical chemistry, 2016
27. ""
    Fatemeh Moeinoddini, Seyyed Omid Ranaee Siadat, Yahya Sefidbakht
    International congress of Agricultural sciences food and Environment, 2016
28. "Sustainability Aspects of Iran s Milk and Dairy Industry"
    Fatemeh Moeinoddini, Seyyed Omid Ranaee Siadat, Yahya Sefidbakht
    International congress of Agricultural sciences food and Environment, 2016