Items where Author is "Sezerman, Uğur"

Article

Erbil, Seçil and Oral, Özlem and Mitou, Geraldine and Kığ, Cenk and Durmaz, Emel and Güven-Maiorov, Emine and Gülaçtı, Ferah and Gökçe, Gökçen and Dengjel, Jön and Sezerman, Uğur and Gözüaçık, Devrim (2016) RACK1 is an interaction partner of ATG5 and a novel regulator of autophagy. Journal of Biological Chemistry, 291 (32). pp. 16753-16765. ISSN 0021-9258 (Print) 1083-351X (Online)

Öktem-Okullu, Sinem and Tiftikçi, Arzu and Saruç, Murat and Çiçek, Bahattin and Vardareli, Eser and Tözün, Nurdan and Kocagöz, Tanıl and Sezerman, Uğur and Yavuz, Ahmet Sinan and Sayı-Yazgan, Ayça (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). ISSN 1932-6203

Yavuz, Ahmet Sinan and Sezerman, Uğur (2014) Predicting sumoylation sites using support vector machines based on various sequence features, conformational flexibility and disorder. BMC Genomics, 15 (Supple). ISSN 1471-2164 (Print) 1471-2164 (Online)

Bakır-Güngör, Burcu and Remmers, Elaine F. and Meguro, Akira and Mizuki, Nobuhisa and Kastner, Daniel L. and Gül, Ahmet and Sezerman, Uğur (2014) Reply to stoimenis et al. (Accepted)

Bakır-Güngör, Burcu and Remmers, Elaine F. and Meguro, Akira and Mizuki, Nobuhisa and Kastner, Daniel L. and Gül, Ahmet and Sezerman, Uğur (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 . ISSN 1018-4813 (Print) 1476-5438 (Online)

Bakır-Güngör, Burcu and Egemen, Ece and Sezerman, Uğur (2014) PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data. Bioinformatics, 30 (9). pp. 1287-1289. ISSN 1367-4803 (Print) 1460-2059 (Online)

Tada, Seiichi and Durmaz Timuçin, Emel and Kitajima, Takashi and Sezerman, Uğur and Ito, Yoshihiro (2014) Direct in vitro selection of titanium-binding epidermal growth factor. Biomaterials, 35 (11). pp. 3497-3503. ISSN 0142-9612 (Print) 1878-5905 (Online)

Durmaz Timuçin, Emel and Sezerman, Uğur (2013) The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases. PLoS One, 8 (12). ISSN 1932-6203

Korkmaz, Gözde and Tekirdağ, Kumsal Ayşe and Özturk, Deniz Gülfem and Koşar, Ali and Sezerman, Uğur and Gözüaçık, Devrim (2013) MIR376A is a regulator of starvation-induced autophagy. PLoS One, 8 (12). ISSN 1932-6203

Bakır-Güngör, Burcu and Baykan, B. and İşeri, S. Uğur and Tuncer, F. N. and Sezerman, Uğur (2013) Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data. Epilepsy Research, 105 (1-2). pp. 92-102. ISSN 0920-1211 (Print) 1872-6844 (Online)

Durmaz Timuçin, Emel and Kuyucak, Serdar and Sezerman, Uğur (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. ISSN 1741-0126 (Print) 1741-0134 (Online)

Bakır-Güngör, Burcu and Sezerman, Uğur (2013) The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations. PLoS One, 8 (3). ISSN 1932-6203

Hirsh, Stacey L. and McKenzie, David R. and Nosworthy, Neil J. and Denman, John A. and Sezerman, Uğur and Bilek, Marcela M. M. (2013) The Vroman effect: competitive protein exchange with dynamic multilayer protein aggregates. Colloids and Surfaces B: Biointerfaces, 103 . pp. 395-404. ISSN 0927-7765 (Print) 1873-4367 (Online)

Kautto, Liisa and Grinyer, Jasmine and Paulsen, Ian and Tetu, Sasha and Pillai, Aneesh and Pardiwalla, Swapneel and Sezerman, Uğur and Bayram Akçapınar, Günseli and Bergquist, Peter and Te'o, Junior and Nevalainen, Helena (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. ISSN 1871-6784 (Print) 1876-4347 (Online)

Meydan, Cem and Otu, Hasan H. and Sezerman, Uğur (2013) Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. BMC Bioinformatics, 14 (Supple). ISSN 1471-2105

Bakış, Yasin and Otu, Hasan H. and Taşçı, Nivart and Meydan, Cem and Bilgin, Neşe and Yüzbaşıoğlu, Sırrı and Sezerman, Uğur (2013) Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. BMC Bioinformatics, 14 . ISSN 1471-2105

Altıntaş, Zeynep and Kallempudi, Saravan Sreenivasa and Sezerman, Uğur and Gürbüz, Yaşar (2012) A novel magnetic particle-modified electrochemical sensor for immunosensor applications. Sensors and Actuators B: Chemical, 174 . pp. 187-194. ISSN 0925-4005

Albayrak, Aydın and Sezerman, Uğur (2012) Discrimination of thermophilic and mesophilic proteins using reduced amino acid alphabets with n-grams. Current Bioinformatics, 7 (2). pp. 152-158. ISSN 1574-8936

Bayram Akçapınar, Günseli and Gül, Özgür and Sezerman, Uğur (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. ISSN 0168-1656 (print) ; 1873-4863 (online)

Anbar, Michael and Gül, Özgür and Lamed, Raphael and Sezerman, Uğur and Bayer, Edward A. (2012) Improved thermostability of clostridium thermocellum endoglucanase Cel8A by using consensus-guided mutagenesis. Applied and Environmental Microbiology, 78 (9). pp. 3458-3464. ISSN 0099-2240 (print) ; 1098-5336 (online)

Uzbaş, Fatma and Sezerman, Uğur and Hartl, Lukas and Kubicek, Christian P. and Seiboth, Bernhard (2012) A homologous production system for Trichoderma reesei secreted proteins in a cellulase-free background. Applied Microbiology and Biotechnology, 93 (4). pp. 1601-1608. ISSN 0175-7598 (print) ; 1432-0614 (online)

Çobanoğlu, Murat Can and Saygın, Yücel and Sezerman, Uğur (2011) Classification of GPCRs using family specific motifs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (6). pp. 1495-1508. ISSN 1545-5963

Bakır-Güngör, Burcu and Sezerman, Uğur (2011) A new methodology to associate SNPs with human diseases according to their pathway related context. PLoS One, 6 (10). ISSN 1932-6203

Bayram Akçapınar, Günseli and Gül, Özgür and Sezerman, Uğur (2011) Effect of codon optimization on the expression of trichoderma reesei endoglucanase 1 in pichia pastoris. Biotechnology Progress, 27 (5). pp. 1257-1263. ISSN 8756-7938

Seidl-Seiboth, Verena and Gruber, Sabine and Sezerman, Uğur and Schwecke, Torsten and Albayrak, Aydın and Neuhof, Torsten and von Doehren, Hans and Baker, Scott E. and Kubicek, Christian 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. ISSN 0022-2844

Tiber, Pınar and Orun, Oya and Nacar, Cevdet and Sezerman, Uğur and Severcan, Feride and Severcan, Mete and Matagne, André and Kan, Beki (2011) Structural characterization of recombinant bovine Go alpha by spectroscopy and homology modeling. Spectroscopy, 26 (4-5). pp. 213-229. ISSN 0712-4813

Albayrak, Aydın and Otu, Hasan Hüseyin and Sezerman, Uğur (2010) Clustering of protein families into functional subtypes using relative complexity measure with reduced amino acid alphabets. BMC Bioinformatics, 11 . ISSN 1471-2105

Meydan, Cem and Sezerman, Uğur (2010) Biomarker discovery for toxicity. Neurocomputing (Sp. Iss. SI), 73 (13-15). pp. 2384-2393. ISSN 0925-2312

Özdemir Özgentürk, Nehir and Oruç, Fatma and Sezerman, Uğur and Küçükural, Alper and Vural Korkut, Şenay and Toksöz, Feriha and Un, Cemal (2010) Generation and analysis of expressed sequence tags from olea europaea L. Comparative and Functional Genomics . ISSN 1531-6912

Solda, Giulia and Makunin, Igor V. and Sezerman, Uğur and Corradin, Alberto and Corti, Giorgio and Guffanti, Alessandro (2009) An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Briefings in Bioinformatics, 10 (5). pp. 475-489. ISSN 1467-5463

Yeniterzi, Süveyda and Sezerman, Uğur (2009) Enzyminer: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. BMC Bioinformatics, 10 (Supple). ISSN 1471-2105

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

Kallempudi, Sreenivasa Saravan and Gül, Özgür and Başağa, Hüveyda and Sezerman, Uğur and Gürbüz, Yaşar (2008) Label-free biosensors for the detection and quantification of cardiovascular risk markers. Journal of Sensor Letters, 6 . pp. 1-5. ISSN 1546-198X (Print) 1546-1971 (Online)

Gül, Özgür and Calay, Ediz Süha and Sezerman, Uğur and Başağa, Hüveyda and Gürbüz, Yaşar (2007) Sandwich-type, antibody microarrays for the detection and quantification of cardiovascular risk markers. Sensors and actuators. B, Chemical, 125 (2). pp. 581-588. ISSN 0925-4005

Yardımcı, Galip Gürkan and Küçükural, Alper and Saygın, Yücel and Sezerman, Uğur (2006) Modified association rule mining approach for the MHC-peptide binding problem. Lecture Notes in Computer Science, 4263 . pp. 165-173. ISSN 0302-9743

Budak, Hikmet and Kasap, Zeynep and Shearman, Robert C. and Dweikat, İsmail and Sezerman, Uğur and Mahmood, Abid (2006) Molecular characterization of cDNA encoding resistance gene-like sequences in Buchloe dactyloides. Molecular biotechnology, 34 (3). pp. 293-301. ISSN 1073-6085 (Print) 1559-0305 (Online)

Ergüner, Bekir and Sezerman, Uğur and Erdoğan, Özgün (2006) Prediction and classification for GPCR sequences based on ligand specific features. Lecture Notes in Computer Science, 4263 . pp. 174-181. ISSN 0302-9743

Bakır, Burcu and Sezerman, Uğur (2006) Functional classification of G-Protein coupled receptors, based on their specific ligand coupling patterns. Applications of evolutionary computing, proceedings (Lecture notes in computer science), 3907 . pp. 1-12. ISSN 0302-9743 (Print) 1611-3349 (Online)

Bilecen, Kıvanç and Öztürk, Ümit Hasan and Duru, Adil Doğanay and Sütlü, Tolga and Petoukhov, Maxim V. and Svergun, Dimitri I. and Koch, Michel H. J. and Sezerman, Uğur and Çakmak, İsmail and Sayers, Zehra (2005) Triticum durum metallothionein: isolation of the gene and structural characterization of the protein using solution scattering and molecular modeling. Journal of Biological Chemistry, 280 (14). pp. 13701-13711. ISSN 0021-9258 (Print) 1083-351X (Online)

Işık, Zerrin and Yanıkoğlu, Berrin and Sezerman, Uğur (2004) Protein structural class determination using support vector machines. Lecture notes in computer science, 3280 . pp. 82-89. ISSN 0302-9743 (Print) 1611-3349 (Online)

Papers in Conference Proceedings

Yavuz, Ahmet Sinan and Sözer, Namık Berk and Sezerman, Uğur (2014) Amino acid preferences at neddylation sites. In: International Conference on Applied Informatics for Health and Life Sciences (AIHLS 2014), Kuşadası, Turkey

Khalid, Zoya and Sezerman, Uğur (2014) Interpreting the prevalence of regulatory SNPs in cancers and protein-coding SNPs among non-cancer diseases using GWAS association studies. In: International Conference on Applied Informatics for Health and Life Sciences (AIHLS 2014), Kuşadası, Turkey

Durmaz Timuçin, Emel and Sezerman, Uğur (2014) Zinc induces self-assembly of bacterial thermoalkalophilic lipases: a strategy for thermostability. In: 28th Annual Symposium of the Protein-Society, San Diego, CA, USA

Bakır-Güngör, Burcu and Remmers, Elaine and Kastner, Daniel L. and Meguro, Akira and Mizuki, Nobuhisa and Gül, Ahmet and Sezerman, Uğur (2012) The identification of pathway markers in Behcet's disease using genomewide association data from two different populations. In: Annual Scientific Meeting of the American-College-of-Rheumatology (ACR) and Association-of-Rheumatology-Health-Professionals (ARHP), Washington, DC

Yavuz, Ahmet Sinan and Özer, Buğra and Sezerman, Uğur (2012) Pattern recognition for subfamily level classification of GPCRs using motif distillation and distinguishing power evaluation. In: 7th IAPR International Conference (PRIB 2012), Tokyo, Japan

Meydan, Cem and Sezerman, Uğur (2012) Representation of protein secondary structure using bond-orientational order parameters. In: 7th IAPR International Conference (PRIB 2012), Tokyo, Japan

Korkut, Senay Vural and Altınışık, Başak Çelik and Sezerman, Uğur and Meydan, Cem (2011) Cloning of hordeum spontenaum genes which are expressed upon zinc deficiency using suppressed sub-stractive hybridization method. In: European Biotechnology Congress, Istanbul, Turkey

Durası, İlknur Melis and Dağ, Uğur and Güngör, Burcu Bakır and Erdoğan, Burcu and Kurnaz, Işıl Aksan and Sezerman, Uğur (2011) Identification of transcription factor binding sites in promoter databases. In: 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT 2011), Izmir, Turkey

Meydan, Cem and Sezerman, Uğur (2011) Short-term HIV therapy response prediction using sequence information. In: 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT 2011), Izmir, Turkey

Meydan, Cem and Sezerman, Uğur and Otu, Hasan (2009) Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining. In: International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009 (IJCBS '09), Shangai, China

Yörükoğlu, Deniz and Bakış, Yasin and Sezerman, Uğur (2009) An entropy based heuristic model for predicting functional sub-type divisions of protein families. In: 11th Genetic and Evolutionary Computation Conference, GECCO 2009, Montreal, Québec, Canada

Bakış, Yasin and Sezerman, Uğur and Babaç, M. Tekin and Meydan, Cem (2009) Optimization of morphological data in numerical taxonomy analysis using genetic algorithms feature selection method. In: 11th Genetic and Evolutionary Computation Conference, GECCO 2009, Montreal, Québec, Canada

Meydan, Cem and Otu, Hasan and Sezerman, Uğur (2009) Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining. In: 4th International Symposium on Health Informatics and Bioinformatics (HIBIT 09), Ankara, Türkiye

Çakıcı, Serdar and Sümengen, Selçuk and Sezerman, Uğur and Balcısoy, Selim (2008) DockPro: a VR-based tool for protein-protein docking problem. In: 7th ACM SIGGRAPH International Conference on Virtual-Reality Continuum and Its Applications in Industry (VRCAI 2008), Fusionopolis , Singapore

Meydan, Cem and Küçükural, Alper and Yörükoğlu, Deniz and Sezerman, Uğur (2008) Biomarker detection for hexachlorobenzene toxicity using genetic algorithms on gene expression data. In: HIBIT08, ISTANBUL

Küçükural, Alper and Sezerman, Uğur and Erçil, Aytül (2007) DISCRIMINATION OF NATIVE FOLDS USING NETWORK PROPERTIES OF PROTEIN STRUCTURES. In: APBC 2008, Kyoto JAPAN (Accepted)

Küçükural, Alper and Yeniterzi, Reyyan and Yeniterzi, Süveyda and Sezerman, Uğur (2007) Evolutionary selection of minimum number of features for classification of gene expression data using genetic algorithms. In: 9th Annual Conference on Genetic and Evolutionary Computation (GECCO 2007), London, England

Küçükural, Alper and Sezerman, Uğur (2007) Potential use of graph theoretical properties of protein structures in structural alignment. In: BIOCOMP 2007, Las Vegas, Nevada, USA

Sezerman, Uğur (2005) Uluslararası standardlarda biyodizel üretimi. In: BİYOENERJİ 2004, İzmir, Turkey

Akalın, Altuna and Kasap, Zeynep and Kavak, Ersen and Sezerman, Uğur (2004) G proteinleri bağlayan moleküllerin ligand seçiciliklerinin SVM yöntemiyle belirlenmesi. In: Biyomedikal Mühendisliği Ulusal Toplantısı, BİYOMUT 2004, İstanbul, Turkey

Book Section / Chapter

Küçükural, Alper and Szilagyi, Andras and Sezerman, Uğur and Zhang, Yang (2011) Protein homology analysis for function prediction with parallel sub-graph isomorphism. In: Lodhi, Huma and Yamanashi, Yoshihiro, (eds.) Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques. IGI Global, Hershey, PA, USA, pp. 129-144. ISBN 9781615209118 ; 1615209115