Ezgi TAŞKAN (Mezuniyet Yılı: 2015)

 1.Preclinical Studies on Convalescent Human Immune Plasma-Derived Exosome: Omics and Antiviral Properties to SARS-CoV-2

Taşlı, N. P., Gönen, Z. B., Kırbaş, O. K., Gökdemir, N. S., Bozkurt, B. T., Bayrakcı, B., … & Cetin, M. (2022). Preclinical studies on convalescent human immune plasma-derived exosome: Omics and antiviral properties to SARS-CoV-2. Frontiers in immunology, 13, 904.

2.Investigating the neuroprotective effects of nicotinamide adenine dinucleotide precursors

İşlek, Z., Taşkan, E., Yılmaz, E. N., Şahin, F., & Üçışık, M. H. (2019). Neuroprotective effects of CurcuEmulsomes on Leishmania-infected astrocytes. Anatomy: International Journal of Experimental & Clinical Anatomy, 13.

3.Functional Characterization of c.487insTGC and c.2555A>G vWF Gene Variants Identified in the Type 2 vWD Patient Population in Turkey

Berber, E., Taşkan, E., Forghieri, G., Çolakoğlu, S., Baltacı, O., Koç, B., & Oymak, Y. (2016). Functional characterization of c. 4876instgc and c2555a> g VWF gene variants identified Type 2 VWD patient population in Turkey. Journal of Thrombosis And Haemostasis.

4.Role of exosomes in malignant transformation of astrocytes.

Taskan, E., Kırbaş, O. K., Bozkurt, B. T., Şahin, F., & Kasapoğlu, B. (2020). Role of exosomes in malignant transformation of astrocytes. Anatomy: International Journal of Experimental & Clinical Anatomy, 14.

Tuğçe DALLI (Mezuniyet Yılı: 2014)

1.Thymoquinone administration ameliorates Alzheimer’s disease-like phenotype by promoting cell survival in the hippocampus of amyloid beta1-42 infused rat model

Elibol, B., Beker, M., Terzioglu-Usak, S., Dalli, T., & Kilic, U. (2020). Thymoquinone administration ameliorates Alzheimer’s disease-like phenotype by promoting cell survival in the hippocampus of amyloid beta1–42 infused rat model. Phytomedicine, 79, 153324.

2.Effect of Restraint Stress on Plasma PTH Concentration and Its Molecular Targets Expressions in Wistar Rats

Terzioglu-Usak, S., Elibol, B., Dalli, T., Guler, C., & Aysan, E. (2018). Effect of restraint stress on plasma PTH concentration and its molecular targets expressions in wistar rats. International Journal of Endocrinology and Metabolism, 16(4).

3.Thymoquinone activates MAPK pathway in hippocampus of streptozotocin-treated rat model

Dalli, T., Beker, M., Terzioglu-Usak, S., Akbas, F., & Elibol, B. (2018). Thymoquinone activates MAPK pathway in hippocampus of streptozotocin-treated rat model. Biomedicine & Pharmacotherapy, 99, 391-401.

4.Thymoquinone Can Improve Neuronal Survival and Promote Neurogenesis in Rat Hippocampal Neurons

Beker, M., Dallı, T., & Elibol, B. (2018). Thymoquinone can improve neuronal survival and promote neurogenesis in rat hippocampal neurons. Molecular Nutrition & Food Research, 62(5), 1700768

Bedri Burak DURAKSOY (Mezuniyet Yılı: 2014)

1.High-level heterologous expression of active Chaetomium thermophilum FDH in Pichia pastoris

Duman, Z. E., Duraksoy, B. B., Aktaş, F., Woodley, J. M., & Binay, B. (2020). High-level heterologous expression of active Chaetomium thermophilum FDH in Pichia pastoris. Enzyme and Microbial Technology, 137, 109552.

Mehmet Mervan ÇAKAR (Mezuniyet Yılı: 2014)

1.Enzyme Reaction Engineering as a Tool to Investigate the Potential Application of Enzyme Reaction Systems

Milčić, N., Ćevid, I., Çakar, M. M., Sudar, M., & Blažević, Z. F. (2022). Enzyme Reaction Engineering as a Tool to Investigate the Potential Application of Enzyme Reaction Systems. Hungarian Journal of Industry and Chemistry, 50(1), 45-55.

2.From Secretion in Pichia pastoris to Application in Apple Juice Processing: Exo-Polygalacturonase from Sporothrix schenckii 1099-18

Karataş, E., Tülek, A., Çakar, M. M., Tamtürk, F., Aktaş, F., & Binay, B. (2021). From Secretion in Pichia pastoris to Application in Apple Juice Processing: Exo-Polygalacturonase from Sporothrix schenckii 1099-18. Protein and Peptide Letters, 28(7), 817-830.

3.Optimisation of the Production and Bleaching Process for a New Laccase from Madurella mycetomatis, Expressed in Pichia pastoris: from Secretion to Yielding Prominent

Tülek, A., Karataş, E., Çakar, M. M., Aydın, D., Yılmazcan, Ö., & Binay, B. (2021). Optimisation of the production and bleaching process for a new Laccase from Madurella mycetomatis, expressed in Pichia pastoris: From secretion to yielding prominent. Molecular biotechnology, 63, 24-39.

4.Correction to: Optimisation of the Production and Bleaching Process for a New Laccase from Madurella mycetomatis, Expressed in Pichia pastoris: from Secretion to Yielding Prominent

Ahmet, T., Ersin, K., Çakar, M. M., Derya, A., Özlem, Y., & Barış, B. (2021). Correction to: Optimisation of the Production and Bleaching Process for a New Laccase from Madurella mycetomatis, Expressed in Pichia pastoris: from Secretion to Yielding Prominent. Molecular Biotechnology, 63(1), 91-91.

5.Investigation new positions for catalytic activity of Chaetomium thermophilum and Ceriporiopsis subvermispora formate dehydrogenases

Koçdemir, K., Şen, F., Wedajo, Y. A., Bilgici, M. Ç., Bayram, M., Selçuk, İ., … & Binay, B. (2021). Investigation new positions for catalytic activity of Chaetomium thermophilum and Ceriporiopsis subvermispora formate dehydrogenases. Biocatalysis and Biotransformation, 39(4), 302-312.

6.Engineered formate dehydrogenase from Chaetomium thermophilum, a promising enzymatic solution for biotechnical CO2 fixation

Çakar, M. M., Ruupunen, J., Mangas-Sanchez, J., Birmingham, W. R., Yildirim, D., Turunen, O., … & Binay, B. (2020). Engineered formate dehydrogenase from Chaetomium thermophilum, a promising enzymatic solution for biotechnical CO 2 fixation. Biotechnology Letters, 42, 2251-2262.

7.Tailoring of recombinant FDH: effect of histidine tag location on solubility and catalytic properties of Chaetomium thermophilum formate dehydrogenase (CtFDH)

Esen, H., Alpdağtaş, S., Mervan Çakar, M., & Binay, B. (2019). Tailoring of recombinant FDH: effect of histidine tag location on solubility and catalytic properties of Chaetomium thermophilum formate dehydrogenase (CtFDH). Preparative Biochemistry & Biotechnology, 49(5), 529-534.

8.Enhanced production of recombinant Staphylococcus simulans lysostaphin using medium engineering

Duman, Z. E., Ünlü, A., Çakar, M. M., Ünal, H., & Binay, B. (2019). Enhanced production of recombinant Staphylococcus simulans lysostaphin using medium engineering. Preparative Biochemistry & Biotechnology, 49(5), 521-528.

9.Discovery of a New Metal and NAD+-Dependent Formate Dehydrogenase from Clostridium ljungdahlii

Çakar, M. M., Mangas-Sanchez, J., Birmingham, W. R., Turner, N. J., & Binay, B. (2018). Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii. Preparative Biochemistry and Biotechnology, 48(4), 327-334.

Alper BULUTOĞLU (Mezuniyet Yılı: 2020)

1.Comparing the levels of CTLA‐4 dependent biological defects in patients with LRBA deficiency and CTLA‐4 insufficiency

Catak, M. C., Akcam, B., Bilgic Eltan, S., Babayeva, R., Karakus, I. S., Akgun, G., … & Baris, S. (2022). Comparing the levels of CTLA‐4‐dependent biological defects in patients with LRBA deficiency and CTLA‐4 insufficiency. Allergy, 77(10), 3108-3123.

2.Clinical and Laboratory Factors Affecting the Prognosis of Severe Combined Immunodeficiency

Ozturk, E., Catak, M. C., Kiykim, A., Baser, D., Bilgic Eltan, S., Yalcin, K., … & Baris, S. (2022). Clinical and laboratory factors affecting the prognosis of severe combined immunodeficiency. Journal of clinical immunology, 42(5), 1036-1050.

3.A boy with a novel homozygous ZAP70 mutation presenting with a dermatological phenotype and postnatal decrease in CD8+ T cells

Babayeva, R., Mongellaz, C., Karakus, I. S., Cansever, M., Eltan, S. B., Catak, M. C., … & Baris, S. (2022). A boy with a novel homozygous ZAP70 mutation presenting with a dermatological phenotype and postnatal decrease in CD8+ T cells. Pediatric Allergy and Immunology, 33(3).

Oğuzhan KAYA (Mezuniyet Yılı: 2015)

1.High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids

Cerrizuela, S., Kaya, O., Kremer, L. P., Sarvari, A., Ellinger, T., Straub, J., … & Martín-Villalba, A. (2022). High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids. Star Protocols, 3(3), 101555.

2.Cdk4 and Cdk6 Couple the Cell-Cycle Machinery to Cell Growth via mTORC1

Romero-Pozuelo, J., Figlia, G., Kaya, O., Martin-Villalba, A., & Teleman, A. A. (2020). Cdk4 and Cdk6 couple the cell-cycle machinery to cell growth via mTORC1. Cell reports, 31(2), 107504.

3.Guided tissue organization and disease modeling in a kidney tubule array

Subramanian, B., Kaya, O., Pollak, M. R., Yao, G., & Zhou, J. (2018). Guided tissue organization and disease modeling in a kidney tubule array. Biomaterials, 183, 295-305.

Hasan ÇUBUK (Mezuniyet Yılı: 2020)

 1.In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutations effects on human ACE2 binding

Çubuk, H., & Özbil, M. (2022). In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 binding. Journal of Molecular Graphics and Modelling, 116, 108260.

2.A Review of Functional Characterization of Single Amino Acid Change Mutations in HNF Transcription Factors in MODY Pathogenesis

Çubuk, H., & Yalçın Çapan, Ö. (2021). A review of functional characterization of single amino acid change mutations in HNF transcription factors in MODY pathogenesis. The Protein Journal, 40(3), 348-360.

3.Computational analysis of functional monomers used in molecular imprinting for promising COVID-19 detection

Cubuk, H., Ozbil, M., & Hatir, P. C. (2021). Computational analysis of functional monomers used in molecular imprinting for promising COVID-19 detection. Computational and Theoretical Chemistry, 1199, 113215.

4.Comparison of clinically approved molecules on SARS-CoV-2 drug target proteins: a molecular docking study

Cubuk, H., & Özbil, M. (2021). Comparison of clinically approved molecules on SARS-CoV-2 drug target proteins: a molecular docking study. Turkish journal of chemistry, 45(1), 35-41.

5.A Promising Strategy Against SARS-CoV-2 Infected Patients: Antisense Therapy

Cubuk, H. (2020). A promising strategy against SARS-CoV-2 infected patients: antisense therapy.

Elif ÖZBAY (Mezuniyet Yılı: 2017)

1.An analysis for proteomic profile of NeuroD2 related changes in N2A neuroblastoma cell line

Beker, M., Bolat, B., Aslan, F. S., Ozbay, E., & Kaya, S. B. (2023). A proteomic analysis for profiling NeuroD2 related changes in N2A neuroblastoma cell line.

2.Phosphodiesterase 10A Is a Critical Target for Neuroprotection in a Mouse Model of Ischemic Stroke

Beker, M. C., Caglayan, A. B., Altunay, S., Ozbay, E., Ates, N., Kelestemur, T., … & Kilic, E. (2022). Phosphodiesterase 10A is a critical target for neuroprotection in a mouse model of ischemic stroke. Molecular Neurobiology, 1-16.

3.Beyin hasarı sonrası Bmal1 proteininin etkilediği sinyal yolaklarının proteomik analizi/ Investigation of the role of Bmal1 following brain injury using proteomic approach

Özbay, E. (2021). BMAl1’in beyin hasarı sonrası rolününproteomik açıdan incelenmesi (Master’s thesis, İstanbul Medipol Üniversitesi Sağlık Bilimleri Enstitüsü).

Gizem Nur DURAN (Mezuniyet Yılı: 2017)

1.Antiviral activity and molecular modeling studies on 1H-indole-2,3-diones carrying a naphthalene moiety

Soylu-Eter, Ö., Duran, G. N., Özbil, M., Göktaş, F., Cihan-Üstündağ, G., & Karalı, N. (2023). Antiviral activity and molecular modeling studies on 1H-indole-2, 3-diones carrying a naphthalene moiety. Journal of Molecular Structure, 1281, 135100.

2.Structural rearrangement of Neisseria meningitidis transferrin binding protein A (TbpA) prior to human transferrin protein (hTf) binding

Duran, G. N., & Özbil, M. (2021). Structural rearrangement of Neisseria meningitidis transferrin binding protein A (TbpA) prior to human transferrin protein (hTf) binding. Turkish Journal of Chemistry, 45(4), 1146-1154.

3.Synthesis, in vitro cytotoxic and apoptotic effects, and molecular docking study of novel adamantane derivatives

Turk‐Erbul, B., Karaman, E. F., Duran, G. N., Ozbil, M., Ozden, S., & Goktas, F. (2021). Synthesis, in vitro cytotoxic and apoptotic effects, and molecular docking study of novel adamantane derivatives. Archiv der Pharmazie, 354(5), 2000256.

4.Synthesis, molecular modeling and antiviral activity of novel 5-fluoro-1H-indole-2,3-dione 3-thiosemicarbazones

Sevinçli, Z. Ş., Duran, G. N., Özbil, M., & Karalı, N. (2020). Synthesis, molecular modeling and antiviral activity of novel 5-fluoro-1H-indole-2, 3-dione 3-thiosemicarbazones. Bioorganic Chemistry, 104, 104202.

Saliha SURME (Mezuniyet Yılı: 2017)

1.Nanoengineering InP Quantum Dot-Based Photoactive Biointerfaces for Optical Control of Neurons

Karatum, O., Aria, M. M., Eren, G. O., Yildiz, E., Melikov, R., Srivastava, S. B., … & Nizamoglu, S. (2021). Nanoengineering InP quantum dot-based photoactive biointerfaces for optical control of neurons. Frontiers in Neuroscience, 15, 652608.

2.The Arg293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm

Gul, S., Aydin, C., Ozcan, O., Gurkan, B., Surme, S., Baris, I., & Kavakli, I. H. (2020). The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm. Journal of Biological Chemistry, 295(50), 17187-17199.

3.Organic Photovoltaic Pseudocapacitors for Neurostimulation

Han, M., Srivastava, S. B., Yildiz, E., Melikov, R., Surme, S., Dogru-Yuksel, I. B., … & Nizamoglu, S. (2020). Organic photovoltaic pseudocapacitors for neurostimulation. ACS applied materials & interfaces, 12(38), 42997-43008.

Berin YILMAZER (Mezuniyet Yılı: 2016)

1.Comparative structural and kinetic study for development of a novel candidate L-asparaginase based pharmaceutical

Aktar, B. Y., Georgakis, N., Labrou, N., Turunen, O., & Binay, B. (2023). Comparative structural and kinetic study for development of a novel candidate L-asparaginase based pharmaceutical. Biochemical Engineering Journal, 191, 108806.

2.Application of Reductive Amination by Heterologously Expressed Thermomicrobium Roseum L-Alanine Dehydrogenase to Synthesize L-Alanine Derivatives

Bulut, H., Valjakka, J., Turunen, O., Yilmazer, B., Demir, Ğ., Jänis, J., & Binay, B. Application of Reductive Amination by Heterologously Expressed Thermomicrobium Roseum L-Alanine Dehydrogenase to Synthesize L-Alanine Derivatives. Available at SSRN 4314803.

3.Enhancing recombinant Chaetomium thermophilium Formate Dehydrogenase Expression with CRISPR Technology

Ar, E., Demiroğlu, A., Yılmaz, M. S., Yılmazer, B., Aslan, E. S., & Binay, B. (2021). Enhancing recombinant Chaetomium thermophilium formate dehydrogenase expression with CRISPR technology. The Protein Journal, 40(4), 504-511.

4.Conserved Amino Acid Residues that Affect Structural Stability of Candida boidinii Formate Dehydrogenase

Bulut, H., Yuksel, B., Gul, M., Eren, M., Karatas, E., Kara, N., … & Binay, B. (2021). Conserved amino acid residues that affect structural stability of candida boidinii formate dehydrogenase. Applied Biochemistry and Biotechnology, 193, 363-376.

5.Investigation new positions for catalytic activity of Chaetomium thermophilum and Ceriporiopsis subvermispora formate dehydrogenases

Koçdemir, K., Şen, F., Wedajo, Y. A., Bilgici, M. Ç., Bayram, M., Selçuk, İ., … & Binay, B. (2021). Investigation new positions for catalytic activity of Chaetomium thermophilum and Ceriporiopsis subvermispora formate dehydrogenases. Biocatalysis and Biotransformation, 39(4), 302-312.

6.Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme

Yilmazer, B., Isupov, M. N., De Rose, S. A., Bulut, H., Benninghoff, J. C., Binay, B., & Littlechild, J. A. (2020). Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme. Journal of Structural Biology, 212(3), 107657.

7.Effect of Metal Ions on the Activity of Ten NAD-Dependent Formate Dehydrogenases

Bulut, H., Valjakka, J., Yuksel, B., Yilmazer, B., Turunen, O., & Binay, B. (2020). Effect of metal ions on the activity of ten NAD-dependent formate dehydrogenases. The Protein Journal, 39, 519-530.

8.Functional effects of active site mutations in NAD+-dependent formate dehydrogenases on transformation of hydrogen carbonate to formate

Pala, U., Yelmazer, B., Çorbacıoğlu, M., Ruupunen, J., Valjakka, J., Turunen, O., & Binay, B. (2018). Functional effects of active site mutations in NAD+-dependent formate dehydrogenases on transformation of hydrogen carbonate to formate. Protein Engineering, Design and Selection, 31(9), 327-335.

9.Problem of the Century: The Emission of Carbon Dioxide (CO2): An Ezymatic Solution

https://www.researchgate.net/publication/320518741_Problem_of_the_Century_The_Emission_of_Carbon_Dioxide_CO2_An_
Ezymatic_Solution

Kübra TELLİ (Mezuniyet Yılı: 2015)

 1.Epithelial-mesenchymal transition as a potential route for DAPT resistance in breast cancer cells

Telli, K., & Yalcin-Ozuysal, O. (2023). Epithelial-mesenchymal transition as a potential route for DAPT resistance in breast cancer cells. Turkish Journal of Biochemistry, (0).

2.HologLev: A Hybrid Magnetic Levitation Platform Integrated with Lensless Holographic Microscopy for Density-Based Cell Analysis

Delikoyun, K., Yaman, S., Yilmaz, E., Sarigil, O., Anil-Inevi, M., Telli, K., . & Tekin, H. C. (2021). HologLev: A hybrid magnetic levitation platform integrated with lensless holographic microscopy for density-based cell analysis. Acs Sensors, 6(6), 2191-2201.