2021

Gumusoglu E., Gunel T., Hosseini M. K., Seymen N., Senol T., Sezerman U., Topuz S., Aydınlı K. (2021) The importance of dysregulated miRNAs on ovarian cysts and epithelial ovarian cancer. European Journal of Gynaecological Oncology, 42(1): 66-72. doi: 10.31083/j.ejgo.2021.01.2167

Khalid R. R., Maryam A., Cinaroglu S. S., Siddiqi A. R. and Sezerman O. U. (2021). A recursive molecular docking coupled with energy-based pose-rescoring and MD simulations to identify hsGC βH-NOX allosteric modulators for cardiovascular dysfunctions. Journal of Biomolecular Structure and Dynamics. doi: 10.1080/07391102.2021.1877818

2020

Sezerman U., Bozkurt T. and Isleyen F. S. (July 15th 2020). Integrating Evolutionary Genetics to Medical Genomics: Evolutionary Approaches to Investigate Disease-Causing Variants, Methods in Molecular Medicine, Yusuf Tutar, IntechOpen, DOI: 10.5772/intechopen.92738.

Aydinlar EI, Kocak M, Soykam HO, Mat B, Dikmen PY, Sezerman OU, Elmaci I, and Pamir MN. (2020). Intraoperative Neuromonitoring of Blink Reflex During Posterior Fossa Surgeries and its Correlation with Clinical Outcome. J Clin Neurophysiol. 2020 Sep 28. doi: 10.1097/WNP.0000000000000777. Epub ahead of print PMID: 33009043.

Altinoz M. A., Ucal Y., Yilmaz M. C., Kiris I., Ozisik O., Sezerman U., Ozpinar A. and Elmaci I. (2020). Progesterone at high doses reduces the growth of U87 and A172 glioblastoma cells: Proteomic changes regarding metabolism and immunity. Cancer Medicine. doi: 10.1002/cam4.3223

Mehreen, H., Saeed, S., Gerlevik, U., Tariq, A., Sezerman, U., Noreen, Z., Zhang, X., Hassan, S. and Bokhari, H. (2020) Expression and applications of HriCFP in E. coli: a novel biosensing fluorescent protein. Journal of Microbial and Biochemical Technology, [434].

Ulgen, E., Karacan, S., Gerlevik, U., Can, O., Bilguvar, K., Oktay, Y., Akyerli, C., Yuksel, S., Ersen-Danyeli, A., Tihan, T., Sezerman, O., Yakicier, C., Pamir, M., & Ozduman, K. (2020). Mutations and copy number alterations in idh-wildtype glioblastomas are shaped by different oncogenic mechanisms. Biomedicines, 8(12), 574. doi: 10.3390/biomedicines8120574

Yenenler Y., Kurt H., and Sezerman O. U. (2020). Enhancing Enzymatic Properties of Endoglucanase I Enzyme from Trichoderma Reesei via Swapping from Cellobiohydrolase I Enzyme. Catalysts. doi: 10.3390/catal9020130

Shehata M., Unlu A., Sezerman U. and Timucin E. (2020). Lipase and Water in a Deep Eutectic Solvent: Molecular Dynamics and Experimental Studies of the Effects of Water-in-Deep Eutectic Solvent on Lipase Stability. Journal of Physical Chemistry. doi: 10.1021/acs.jpcb.0c07041

Aydinlar E. I., Kocak M., Soykam H. O., Mat B., Dikmen P. Y., Sezerman O. U., et al. (2020). Intraoperative Neuromonitoring of Blink Reflex During Posterior Fossa Surgeries and its Correlation With Clinical Outcome. Journal of Clinical Neurophysiology. doi: 10.1097/wnp.0000000000000777

Altinoz M., Ucal Y. , Yilmaz M., Kiris İ., Ozisik O., Sezerman U. , et al. (2020). Progesterone at high doses reduces the growth of U87 and A172 glioblastoma cells: Proteomic changes regarding metabolism and immunity. Cancer Medicine. doi: 10.1002/cam4.3223

Taştan C., Yurtsever B., Sir K., Dilek K., Demir S., Abanuz S., et al. (2020). SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients. Turkish Journal of Biology. Turk J Biol. doi: 10.3906/biy-2004-113

Khalid, R., Maryam, A., Sezerman, O. U. , Mylonas, E., Siddiqi, A., & Kokkinidis, M., (2020). Probing the Structural Dynamics of the Catalytic Domain of Human Soluble Guanylate Cyclase. Scientific reports , vol.10, 9488.

Bozaykut, P., Ekren, R., Sezerman, O. U. , Gladyshev, V., & Ozer, N., (2020). High-throughput profiling reveals perturbation of endoplasmic reticulum stress-related genes in atherosclerosis induced by high-cholesterol diet and the protective role of vitamin E. BioFactors (Oxford, England) .

Shehata, M., Timucin, E., Venturini, A., & Sezerman, O. U. , (2020). Understanding thermal and organic solvent stability of thermoalkalophilic lipases: insights from computational predictions and experiments. Journal of molecular modeling , vol.26, 122.

Z. Khalid and O. U. SEZERMAN, “A comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A)” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS , 2020.

Akkiprik, M., Koca, S., Uğurlu, M. Ü., Ekren, R., Eyüboğlu, I. P., Alan, Ö., Sezerman, O. U., … Yumuk, P. F. (2020). Response Assessment with Molecular Characterization of Circulating Tumor Cells and Plasma Micro RNAs Profiling in Locally Advanced Breast Cancer Patients During Neoadjuvant Chemotherapy. Clinical Breast Cancer. doi: 10.1016/j.clbc.2020.02.006

Wagner, A. H. , Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., Krysiak, K., … Deu-Pons, J.(2020). A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature genetics , vol.52, 448-457.

Baykal-Köse, S., Acikgoz, E., Yavuz, A. S., Geyik, Ö. G., Ateş, H., Sezerman, O. U., … Yüce, Z. (2020). Adaptive phenotypic modulations lead to therapy resistance in chronic myeloid leukemia cells. Plos One, 15(2). doi: 10.1371/journal.pone.0229104

Keleş, I. D., Ülgen, E., Erkan, M. B., Çelik, S. E., Aydın, Y., Önem, A. N., Sezerman, O. U., … Baştu, E. (2020). Comparison of endometrial prostanoid profiles in three infertile subgroups: the missing part of receptivity? Fertility and Sterility, 113(3). doi: 10.1016/j.fertnstert.2019.10.017

Saeed, S., Mehreen, H., Gerlevik, U., Tariq, A., Manzoor, S., Noreen, Z., Sezerman, O. U., … Bokhari, H. (2020). HriGFP Novel Flourescent Protein: Expression and Applications. Molecular Biotechnology. doi: 10.1007/s12033-020-00243-1

Yenenler, A., Gerlevik, U., & Sezerman, U. (2020). Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations. Turkish Journal of Biochemistry, 0(0). doi: 10.1515/tjb-2018-0180

2019

Ulgen E., Ozisik O., Sezerman O. U. (2019) pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Frontiers in Genetics, 10, 858.

Ertuzun T., Semerci A., Cakir M. E., Ekmekcioglu A., Gok M. O., Soltys D. T., de Souza-Pinto N. C., Sezerman U., Muftuoglu M. (2019) Investigation of Base Excision Repair Gene Variants in Late-Onset Alzheimer’s Disease. Plos One, 14 (8), e0221362.

Demiray S. B., Goker E. N. T., Tavmergen E., Yilmaz O., Calimlioglu N., Soykam H. O., Oktem G., Sezerman U. (2019) Differential Gene Expression Analysis of Human Cumulus Cells. Clinical and Experimental Resproductive Medicine, 46 (2), 76-86.

Ülgen E., Can Ö., Bilguvar K., Oktay Y., Akyerli C. B., Danyeli A. E., Yakıcıer M. C., Sezerman O. U., Pamir M. N., and Özduman K. (2019) Whole exome sequencing–based analysis to identify DNA damage repair deficiency as a major contributor to gliomagenesis in adult diffuse gliomas. Journal of Neurosurgery, 1-12.

Ozdemir O., Egemen E., Iseri S. A. U., Sezerman O. U., Bebek N., Baykan B., and Ozbek U. (2019) Identification of epilepsy related pathways using genome-wide DNA methylation measures: A trio-based approach. PLOS ONE.

Yenenler A., Kurt H., and Sezerman O. U. (2019) Enhancing Enzymatic Properties of Endoglucanase I Enzyme from Trichoderma Reesei via Swapping from Cellobiohydrolase I Enzyme. Catalysts, 9(2), 130.

Kurt Ö., Mansur N., Çavuş İ., Özcan O., Batir M. B., Gündüz C., Sezerman O. U., and Özbilgin A. (2019) First Report and In Silico Analysis of Leishmania virus (LRV2) identified in an autochthonous Leishmania major isolate in Turkey. The New Microbiologica, 42(1), 64-67.

Saygı C., Alanay Y., Sezerman U., Yenenler A., and Özören N. (2019) A possible founder mutation in FZD6 gene in a Turkish family with autosomal recessive nail dysplasia. BMC Medical Genetics, 20(1), 15.

Bastu E, Demiral I, Gunel T, Ulgen E, Gumusoglu E, Hosseini MK, Sezerman U, Buyru F, Yeh J. Potential Marker Pathways in the Endometrium That May Cause Recurrent Implantation Failure. Reprod Sci. 2019 Jul;26(7):879-890. doi: 10.1177/1933719118792104. Epub 2018 Aug 6. PMID: 30081718.

Tsitoura E., Kazazi D., Oz-Arslan D., Sever E. A., Khalili S., Vassilaki N., Aslanoglou E., Dérian N., Six A., Sezerman O. U., Klatzmann D., and Mavromara P. (2019) Comparison of Dendritic Cell Activation by Virus-Based Vaccine Delivery Vectors Emphasizes the Transcriptional Downregulation of the Oxidative Phosphorylation Pathway. Human Gene Therapy, 30(4), 429-445.

2018

Kulabas SS, Ipek H, Tufekci AR, Arslan S, Demirtas I, Ekren R, Sezerman U and Tumer TB. (2018). Ameliorative potential of Lavandula stoechas in metabolic syndrome via multitarget interactions. J Ethnopharmacol.2018 Sep 15;223:88-98. doi: 10.1016/j.jep.2018.04.043. Epub 2018 May 2. PMID: 29729383.

Yenenler A, Venturini A, Burduroglu HC, Sezerman OU. Investigating the structural properties of the active conformation BTL2 of a lipase from Geobacillus thermocatenulatus in toluene using molecular dynamic simulations and engineering BTL2 via in-silico mutation. J Mol Model. 2018 Aug 10;24(9):229. doi: 10.1007/s00894-018-3753-1. PMID: 30097767.

Holub P., Kohlmayer F., Prasser F., Mayrhofer M.T., Schlünder I., Martin Gillian M., Casati S., Koumakis L., Wutte A., Kozera Ł., Strapagiel D., Anton G., Zanetti G., Sezerman O.U., Mendy M., Valík D., Lavitrano M., Dagher G., Zatloukal K., van Ommen GertJan B., Litton J.E. (2018) Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. Biopreservation and Biobanking.

2017

Ozisik O., Bakir-Gungor B., Diri B., Sezerman O.U. (2017) Active SubnetworkGA: A Two Stage Genetic Algorithm Approach to Active Subnetwork Search Current Bioinformatics, 12, pp. 320-328, doi:10.2174/1574893611666160527100444.

Demiray, S. B., Yilmaz, O., Goker, E. N. T., Tavmergen, E., Calimlioglu, N., Sezerman, U., … Oktem, G. (2017) Expression of the Bone Morphogenetic Protein-2 (BMP2) in the Human Cumulus Cells as a Biomarker of Oocytes and Embryo Quality. Journal of Human Reproductive Sciences, 10(3), 194–200.

Bastu E., Gunel T., Sezerman O.U., Demiral I., Gumusoglu E., Ulgen E., Hosseini M.K., Buyru F., Yeh J. (2017) RAC1 signaling pathway is crucial for etiology of repeated implantation failure (RIF). Fertility and Sterility 108(3):e362.

Sezerman O.U., Bayram Akcapinar G. (2017) Computational Approaches for de novo Design and Re-design of Metal Binding Sites on Proteins. Bioscience Reports, BSR20160179.

Ozer B., Sezerman U. (2017) An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology. PLOS ONE, 12(2), e0171694.

Sahbaz B.D., Sezerman O.U., Torun H., Birgül Iyison N. (2017) Ligand binding pocket of a novel Allatostatin receptor type C of stick insect, Carausius morosus. Scientific Reports, 7, 41266.

Khalid Z., Sezerman O.U. (2017) Prediction of HIV Drug Resistance by combining Sequence and Structural Properties. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99.

Kandemir B., Dag U., Bakir Gungor B., Durasi İ.M., Erdogan B., Sahin E., Sezerman U., Aksan Kurnaz I. (2017) In silico analyses and global transcriptional profiling reveal novel putative targets for Pea3 transcription factor related to its function in neurons. PLOS ONE, 12(2), e0170585.

Ozer B., Sezerman U. (2017) Analysis of the interplay between methylation and expression reveals its potential role in cancer aetiology. Functional & Integrative Genomics, 17(1), pp. 53-68.

2016

MetaSUB International Consortium. (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome, 4(1), 24.

Erbil S., Oral Ö., Mitou G., Kig C., Durmaz-Timucin E., Guven-Maiorov E., Gulacti F., Gokce G., Dengjel J., Sezerman O.U., Gozuacik D. (2016) RACK1 Is an Interaction Partner of ATG5 and a Novel Regulator of Autophagy. The Journal of Biological Chemistry, 291 (32), pp.16753-6765.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N., Özduman K. (2016) IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Scientific Reports, 6, 27569.

Yukselen O., Timucin E., Sezerman U. (2016) Predicting the impact of mutations on the specific activity of Bacillus thermocatenulatus lipase using a combined approach of docking and molecular dynamics. Journal of Molecular Recognition, 29(10), pp. 466–475.

Kalkan Z., Durasi İ.M., Sezerman U., Atasever-Arslan B. (2016) Potential of GRID2 receptor gene for preventing TNF-induced neurodegeneration in autism. Neuroscience Letters, 620, pp.62–9.

Yenenler A., Sezerman O.U. (2016) Design and characterizations of two novel cellulases through single-gene shuffling of Cel12A (EG3) gene from Trichoderma reseei. Protein Engineering, Design and Selection, 29(6), pp.219-29.

Timucin E., Cousido-Siah A., Mitschler A., Podjarny A., Sezerman O.U. (2016) Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5. Proteins, 84, pp.129-42.

Bayram Akcapinar G., Sezerman O.U. (2016) Systems Biological Applications for Fungal Gene Expression. In M. Schmoll, C. Dattenböck (Eds.), Gene Expression Systems in Fungi: Advancements and Applications (pp. 385-393). Basel, Switzerland: Springer.

Timucin E., Sezerman O.U. (2016) Molecular modelling and its applications in protein engineering. In A. Glieder, C.P Kubicek, D. Mattanovich, B. Wiltschi & M. Sauer (Eds.), Synthetic Biology (pp. 281-306). Basel, Switzerland: Springer.

2015

Ozer B., Sezerman O.U. (2015) A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology. BMC Genomics, 16(S12), S7.

Yavuz A.S., Sozer N.B., Sezerman O.U. (2015) Prediction of neddylation sites from protein sequences and sequence-derived properties. BMC Bioinformatics, 16(S18), S9.

Ozden S., Turgut Kara N., Sezerman O.U., Durasi İ.M., Chen T., Demirel G., Alpertunga B., Chipman J.K., Mally A. (2015) Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure. Toxicology and Applied Pharmacology, 289(2), pp. 203-12.

Oktem-Okullu S., Tiftikci A., Saruc M., Cicek B., Vardareli E., Tozun N., Kocagoz T., Sezerman U., Yavuz A.S., Sayi-Yazgan A. (2015) Multiplex-PCR-Based Screening and Computational Modeling of Virulence Factors and T-Cell Mediated Immunity in Helicobacter pylori Infections for Accurate Clinical Diagnosis. PLOS ONE, 10(8), e0136212.

Timucin E., Sezerman O.U. (2015) Zinc Modulates Self-Assembly of Bacillus thermocatenulatus Lipase. Biochemistry, 54(25) pp. 3901-10.

Avsar T., Durasi İ.M., Uygunoglu U., Tutuncu M., Demirci N.O., Saip S., Sezerman O.U., Siva A., Tahir Turanli E. (2015) CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes. PLOS ONE, 10(5), e0122045.

Bayram Akcapinar G., Venturini A., Martelli P.L., Casadio R., Sezerman U.O. (2015) Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches. Protein Engineering, Design and Selection, 28(5), pp. 127-35.

Bayram Akcapinar G., Kappel L., Sezerman O.U., Seidl-Seiboth V. (2015) Molecular diversity of LysM carbohydrate-binding motifs in fungi. Current Genetics, 61(2), pp. 103-13.

Bakir-Gungor B., Remmers E., Meguro A., Mizuki N., Kastner D., Gul A., Sezerman O.U. Reply to Stoimenis et al. European Journal of Human Genetics, 23(10), p. 1280.

2014

Bakir-Gungor B., Remmers E., Meguro A., Mizuki N., Kastner D., Gul A., Sezerman O.U. (2014) Identification of Possible Pathogenic Pathways in Behçet’s Disease Using Genome-wide Association Study Data from Two Different Populations. European Journal of Human Genetics, 23(5), pp. 678-87. doi: 10.1038/ejhg.2014.158.

Yavuz A.S., Sezerman O.U. (2014) Predicting sumoylation sites using support vector machines based on various sequence features, conformational flexibility and disorder. BMC Genomics, 15(S9), S18.

Tadaa S., Timucin E., Kitajimaa T., Sezerman O.U., Ito Y. (2014) Direct in vitro selection of titanium-binding epidermal growth factor. Biomaterials, 35(11), pp. 3497-3503

Bakir-Gungor B., Egemen E., Sezerman O.U. (2014) PANOGA: a web-server for identification of SNP targeted pathways from genome-wide association study data. Bioinformatics, 30(9), pp. 1287-1289.

2013

Timucin E., Sezerman O.U. (2013) The Conserved Lid Tryptophan, W211, Potentiates Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases. PLOS ONE, 8(12), e85186.

Korkmaz G., Tekirdag K.A., Ozturk D.G., Kosar A., Sezerman O.U., Gozuacik D. (2013) MIR376A Is a Regulator of Starvation-Induced Autophagy. PLOS ONE, 8(12), e82556.

Durmaz E., Kuyucak S., Sezerman U. (2013) Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein Engineering Design and Selection, 26 (5), pp. 325-333.

Bakır-Güngör B., Sezerman U. (2013) The Identification of Pathway Markers in Intracranial Aneurysm Using Genome-wide Association Data from Two Different Populations. PLOS ONE, 8(3), e57022.

Bakır-Güngör B., Baykan B., Iseri U.S., Tuncer N.F., Sezerman U. (2013) Identifying SNP Targeted Pathways in Partial Epilepsies with Genome-wide Association Study Data. Epilepsy Research, 105 (1-2), pp. 92-102.

Hirsh S.L., McKenzie D.R., Nosworthy N.J., Denman J.A., Sezerman U., Bilek M.M.M. (2013) The Vroman effect: competitive protein exchange with dynamic multilayer protein aggregates. Colloids and Surfaces B: Biointerfaces, 103, pp. 395-404.

Bakış B., Otu H.H., Taşçı N., Meydan C., Bilgin N., Yüzbaşıoğlu S., Sezerman U. (2013) Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure. BMC Bioinformatics, 14:20.

Meydan C., Otu H.H., Sezerman U. (2013) Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. BMC Bioinformatics, 14:13.

Kautto L., Grinyer J., Paulsen I., Tetu S., Pillai A., Pardiwalla S., Sezerman U., Bayram-Akçapınar G., Bergquist P., Te’o J., Nevalainen, H. (2013) Stress effects caused by the expression of a mutant cellobiohydrolase I and proteasome inhibition in trichoderma reesei rut-C30. New Biotechnology, 30 (2). pp. 183-191.

Demirezer L.O., Sezerman O.U., Ozenver N., Bodur M., Yukselen O., Kuruuzum-Uz A. (2013) In silico docking researches of some human proteins with anthranoids. Planta Medica, 79, pp. PG4.

2012

Altıntaş Z., Kallempudi S.S., Sezerman U., Gürbüz Y. (2012) A novel magnetic particle-modified electrochemical sensor for immunosensor applications. Sensors and Actuators B: Chemical, 174, pp. 187-194.

Albayrak A., Sezerman, U. (2012) Discrimination of thermophilic and mesophilic proteins using reduced amino acid alphabets with n-grams. Current Bioinformatics, 7 (2). pp. 152-158.

Bayram-Akçapınar G., Gül Ö., Sezerman U. (2012) From in silico to in vitro: modelling and production of trichoderma reesei endoglucanase 1 and its mutant in pichia pastoris. Journal of Biotechnology, 159 (1-2). pp. 61-68.

Anbar M., Gül Ö., Lamed R., Sezerman U., Bayer E.A. (2012) Improved thermostability of clostridium thermocellum endoglucanase Cel8A by using consensus-guided mutagenesis. Applied and Environmental Microbiology, 78 (9). pp. 3458-3464.

Uzbaş F., Sezerman U., Hartl L., Kubicek C.P., Seiboth B. (2012) A homologous production system for Trichoderma reesei secreted proteins in a cellulase-free background. Applied Microbiology and Biotechnology, 93 (4). pp. 1601-1608.

Meydan C., Sezerman U. (2012) Representation of protein secondary structure using bond-orientational order parameters. Lecture Notes in Computer Science, 7632, pp. 188-197.

Yavuz A.S., Özer B., Sezerman U. (2012) Pattern recognition for subfamily level classification of GPCRs using motif distillation and distinguishing power evaluation. Lecture Notes in Computer Science, 7632, pp. 267-276.

Bakır-Güngör, B., Remmers E., Kastner D.L., Meguro A., Mizuki N., Gül A, Sezerman U. (2012) The identification of pathway markers in Behcet’s disease using genomewide association data from two different populations. In Proceedings of the Annual Scientific Meeting of the American-College-of-Rheumatology (ACR) and Association-of-Rheumatology-Health-Professionals (ARHP), November 9-14, 2012, Washington, DC, USA.

Yurdalan G., Ünlü E., Yüce Y., Bakır-Güngör B., Sezerman U. (2012) Integration of GWAS and microarray data to understand the disease mechanism. In Proceedings of the 7th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 19-22, 2012, Nevsehir, Turkey.

2011

Çobanoğlu M.C., Saygın Y., Sezerman U. (2011) Classification of GPCRs using family specific motifs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (6). pp. 1495-1508.

Bakır-Güngör B., Sezerman U. (2011) A new methodology to associate SNPs with human diseases according to their pathway related context. PLOS ONE, 6(10), pp. e26277.

Bayram-Akçapınar G., Gül Ö., Sezerman U. (2011) Effect of codon optimization on the expression of trichoderma reesei endoglucanase 1 in pichia pastoris. Biotechnology Progress, 27 (5). pp. 1257-1263.

Seidl-Seiboth V., Gruber S., Sezerman U., Schwecke T., Albayrak A., Neuhof T., von Doehren H., Baker S.E., Kubicek C.P. (2011) Novel hydrophobins from trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing. Journal of Molecular Evolution, 72 (4). pp. 339-351.

Tiber P., Orun O., Nacar C., Sezerman U., Severcan F., Severcan M., Matagne A., Kan B. (2011) Structural characterization of recombinant bovine Go alpha by spectroscopy and homology modeling. Spectroscopy, 26 (4-5).

Vural-Korkut S., Çelik-Altınışık, B., Sezerman U., Meydan C. (2011) Cloning of hordeum spontenaum genes which are expressed upon zinc deficiency using suppressed sub-stractive hybridization method. Current Opinion in Biotechnology, 22(S1). pp. S122.

Durası İ.M., Dağ U., Bakır-Güngör B., Erdoğan B., Aksan-Kurnaz I., Sezerman U. (2011) Identification of transcription factor binding sites in promoter databases. In Proceedings of the 6th International Symposium on Health Informatics and Bioinformatics (HIBIT), May 2-5, 2011, Izmir, Turkey.

Meydan C., Sezerman U. (2011) Short-term HIV therapy response prediction using sequence information. In Proceedings of the 6th International Symposium on Health Informatics and Bioinformatics (HIBIT), May 2-5, 2011, Izmir, Turkey.

2010

Küçükural A., Szilagyi A., Sezerman U., Zhang Y. (2010) Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism In H. Lodhi & and Y. Yamanishi (Eds) Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques. IGI Global: Hershey, US.

Albayrak A., Otu H.H., Sezerman U. (2010) Clustering of protein families into functional subtypes using relative complexity measure with reduced amino acid alphabets. BMC Bioinformatics, 11:428.

Meydan C., Sezerman U. (2010) Biomarker discovery for toxicity. Neurocomputing, 73 (13-15). pp. 2384-2393.

Özdemir Özgentürk N., Oruç F., Sezerman U., Küçükural A., Vural Korkut Ş., Toksöz F., Un C. (2010) Generation and analysis of expressed sequence tags from olea europaea L. Comparative and Functional Genomics.

Yavuz A.S., Sezerman U. (2010) SUMOtr: SUMOylation Site Prediction Based on 3D Structure and Hydrophobicity. In Proceedings of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 20-22, 2010, Antalya, Turkey.

Çobanoğlu M.C., Karabulut N.P., Sezerman U. (2010) Determining the Ligand-Specific Regions of Peptide-Binding GPCR. In Proceedings of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 20-22, 2010, Antalya, Turkey.

Özer, B., Gezici G., Meydan C., Sezerman U. (2010) Multiple Sequence Alignment Based on Structural Properties. In Proceedings of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 20-22, 2010, Antalya, Turkey.

Bakış Y., Otu H.H., Sezerman U. (2010) Physico-chemical Properties of DNA in Phylogeny Construction. In Proceedings of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 20-22, 2010, Antalya, Turkey.

Türk A., Sezerman U. (2010) Predict Permissive Sites of Protein for Insertion Domain. In Proceedings of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 20-22, 2010, Antalya, Turkey.

2009

Solda G., Makunin I.V., Sezerman U., Corradin A., Corti G., Guffanti A. (2009) An Ariadne’s thread to the identification and annotation of noncoding RNAs in eukaryotes. Briefings in Bioinformatics, 10 (5). pp. 475-489.

Yeniterzi S., Sezerman U. (2009) EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. BMC Bioinformatics, 10(Suppl 8):S2

Çakıcı S., Sümengen S., Sezerman U., Balcısoy S. (2009) DockPro: a vr-based tool for protein-protein docking problem. International Journal of Virtual Reality, 8 (2). pp. 19-23.

Meydan C., Sezerman U., Otu H.H. (2009) Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining. In Zhang, J. and Li, G. Z. and Yang, J. Y. (eds.), International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009 (IJCBS ’09), USA: IEEE (Institute of Electrical and Electronics Engineers), August 2009, 315-318.

Bakış Y., Sezerman U., Babaç M.T., Meydan C. (2009) Optimization of morphological data in numerical taxonomy analysis using genetic algorithms feature selection method. In 11th Genetic and Evolutionary Computation Conference, GECCO 2009, New York, NY, USA: ACM (Association for Computing Machinery), July 2009, 1967-1970.

Yörükoğlu D., Bakış Y., Sezerman U. (2009) An entropy based heuristic model for predicting functional sub-type divisions of protein families. In 11th Genetic and Evolutionary Computation Conference, GECCO 2009, New York, NY, USA: ACM (Association for Computing Machinery), July 2009, 2173-2178.

Meydan C., Otu H.H., Sezerman U. (2009) Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining. In Proceedings of the 4th International Symposium on Health Informatics and Bioinformatics (HIBIT), April 16-17, 2009, Ankara, Turkey.

2008

Kallempudi S.S., Gül Ö., Başağa H., Sezerman U., Gürbüz Y (2008) Label-free biosensors for the detection and quantification of cardiovascular risk markers. Sensor Letters, 6 . pp. 1-5.

Küçükural A., Sezerman U., Erçil A. (2008) Discrimination of Native Folds Using Network Properties of Protein Structures. In Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC 2008), January 14-17, 2008, Kyoto, Japan.

Yeniterzi S., Yeniterzi R., Küçükural A., Noyan N., Sezerman U. (2008) A new approach to measure the similarities of protein structures using network properties. In Proceedings of the 3rd International Symposium on Health Informatics and Bioinformatics (HIBIT), May 18-20, 2008, İstanbul, Turkey.

Meydan C., Küçükural A., Sezerman U. (2008) Biomarker detection for hexachlorobenzene toxicity using genetic algorithms on gene expression data. In Proceedings of the 3rd International Symposium on Health Informatics and Bioinformatics (HIBIT), May 18-20, 2008, İstanbul, Turkey.

Aksu B., Özşamlı N., Kılıç K., Sezerman U. (2008) A modified framework for feature subset selection in microarray data. In Proceedings of the 3rd International Symposium on Health Informatics and Bioinformatics (HIBIT), May 18-20, 2008, İstanbul, Turkey.

2007

Gül Ö., Calay E.S., Sezerman U., Başağa H., Gürbüz Y (2007) Sandwich-type, antibody microarrays for the detection and quantification of cardiovascular risk markers. Sensors and Actuators B: Chemical, 125 (2). pp. 581-588.

Erdoğmuş M., Sezerman U. (2007) Application of automatic mutation gene pair extraction to diseases. Journal of Bioinformatics and Computational Biology, 5(6), pp. 1261-1275.

Küçükural A., Yeniterzi R., Yeniterzi S., Sezerman U. (2007) Evolutionary selection of minimum number of features for classification of gene expression data using genetic algorithms. ACM Genetic And Evolutionary Computation Conference (GECCO 2007) July 7-11, 2007, London, United Kingdom.

Küçükural A., Sezerman U. (2007) Potential use of graph theoretical properties of protein structures in structural alignment. Proceedings of The 2007 International Conference on Bioinformatics & Computational Biology, June 25-28, 2007, Las Vegas, Nevada, USA.

Küçükural A., Sezerman U. (2007) Detecting Native Proteins in ROSETTA Dataset Using Graph Properties. In Proceedings of the 2nd International Symposium on Health Informatics and Bioinformatics (HIBIT), April 30 – May 2, 2007, Antalya, Turkey.

Yeniterzi R., Yeniterzi S., Küçükural A., Sezerman U. (2007) Feature selection with genetic algorithms on cardiac arrhytmia database. In Proceedings of the 2nd International Symposium on Health Informatics and Bioinformatics (HIBIT), April 30 – May 2, 2007, Antalya, Turkey.

2006

Budak H., Kasap Z., Shearman R.C., Dweikat İ., Sezerman U., Mahmood A. (2006) Molecular characterization of cDNA encoding resistance gene-like sequences in Buchloe dactyloides. Molecular Biotechnology, 34 (3). pp. 293-301.

Ergüner B., Erdoğan Ö., Sezerman U., (2006) Prediction and classification for GPCR sequences based on ligand specific features. Lecture Notes in Computer Science, 4263. pp. 174-181.

Yardımcı G.G., Küçükural A., Saygın Y., Sezerman U. (2006) Modified association rule mining approach for the MHC-peptide binding problem. Lecture Notes in Computer Science, 4263 . pp. 165-173.

Bakır B., Sezerman U. (2006) Functional classification of G-Protein coupled receptors, based on their specific ligand coupling patterns. Lecture Notes in Computer Science, 3907. pp. 1-12.

Sezerman U., Akalın A., Kasap Z., Kavak E. (2006) Ligand-specific classification of G protein-coupled receptors using support vector machines and reduced alphabeth. FEBS Journal, 273(s1), pp.63.

2005 and earlier

Bilecen K., Öztürk Ü.H., Duru A.D., Sütlü T., Petoukhov M.V., Svergun D.I., Koch M.H.J., Sezerman U., Çakmak İ., Sayers Z. (2005) Triticum durum metallothionein: isolation of the gene and structural characterization of the protein using solution scattering and molecular modeling. The Journal of Biological Chemistry, 280 (14). pp. 13701-13711.

Gül, Ö., İncetürkmen, E., Kütük, Ö., Başağa, H., Sezerman, U., Gürbüz, Y. (2005) Biosensor implementation for cardiovascular risk marker analysis IEEE Sensors 2005: Oct 31-Nov 3, 2005, Irvine, California, USA.

Işık Z., Yanıkoğlu B., Sezerman U. (2004) Protein structural class determination using support vector machines. Lecture Notes in Computer Science, 3280. pp. 82-89.

Akalın A., Kasap Z., Kavak E., Sezerman U. (2004) Classification of GPCRs according to their ligand specifity using SVMs. In Proceedings of BİYOMUT Conference, May 27-30, 2004, Istanbul, Turkey.

Akyarlı A., Alpaslan N., Çicek D., Diktaş E., Elmacı Y., Karagözlü C., Öztüre N., Sayın R., Sezerman U., Sındır K.O., Sipahi D., Şahin M.O. (2004) Biyodizel yakıtın uluslararası standartlarda üretimi. (in Turkish) In Proceedings of BİYOENERJİ 2004 Sempozyumu, 20-22 Ekim 2004, İzmir, Turkey.

Türkeli Y., Erçil A., Sezerman U. (2003) Effect of Feature Extraction and Feature Selection on Expression Data from Epithelial Ovarian Cancer. Proceedings of 25th Annual International Conference of IEEE EMBS, September 17-21, 2003, Cancun, Mexico.

Türkeli Y., Sezerman U., Gürgen F. (2003) Information excavation from Scale-free genetic networks using attributed graph matching. ICANN-ICONIP 2003.

Akyol A., Sezerman U. (2003) Fold Classification of Protein Sequences by Genetic Algorithm. ICANN-ICONIP 2003.

Sezerman U., Islamaj R., Alpaydin E. (2001) Three dimensional representation of amino acids using machine learning methods. Proceedings of the 23rd Annual EMBS International Conference, October 25-28, Istanbul, Turkey.

Vasmatzis G., Cornette J., Sezerman U., DeLisi C. (1996) TCR Recognition of the MHC-Peptide Dimer: Structural Properties of a Ternary Complex. Journal of Molecular Biology, 261, pp. 72-89.

Sezerman U., Vajda S., DeLisi C. (1996) Free Energy Mapping of Class I MHC molecules and Structural Determination of Bound Peptides. Protein Science, 5, pp. 1272-1281.

Vajda S., Jafri M.S., Sezerman U. (1993) Necessary Conditions for Avoiding Incorrect Polypeptide Folds in Conformational Search by Energy Minimization. Biopolymers, 33 (1), pp. 173-192.

Sezerman U., Vajda S., Cornette J., DeLisi, C. (1993) Towards Computational Determination of Peptide-Receptor Structure. Protein Science, 2, pp. 1827-1843.

DeLisi C., Sezerman U., Rosenfeld R. (1992) Problems and Progress in Computational Approaches to the Molecular Basis of Recognition. Membrane Proteins: Structures, Interactions and Models, The Jerusalem Symposia on Quantum Chemistry and Biochemistry, Volume 25, pp. 443-447.