ÖZGEÇMİŞ
1. Adı Soyadı: Osman Uğur Sezerman
2. Unvanı: Profesör
3. Öğrenim Durumu:
Derece
Alan
Üniversite
Lisans
Elektrik Mühendisliği
Boğaziçi Üniversitesi
Yüksek Lisans
Biyomedikal Mühendisliği
Boğaziçi Üniversitesi
Doktora
Biyomedikal Mühendisliği
Boston Universitesi
Yıl
4. Akademik Ünvanlar
03.2015 –
Öğretim Üyesi, Biyoistatistik ve Tıp Bilişimi Ana Bilim Dalı,
Acıbadem Üniversitesi
09.1999 – 03.2015 Öğretim Üyesi, Biyoloji Bilimleri ve Biyomühendislik, Sabancı
Üniversitesi
08.1998–09.1999 Öğretim Üyesi (Yarı Zamanlı), Bilgisayar Mühendisliği, Boğaziçi
Üniversitesi
01.1993–05.1997 Doktora Sonrası Araştırma Görevlisi, Biyomedikal Mühendisliği
Bölümü, Boston Üniversitesi
02.1990–01.1993 Araştırma Görevlisi, Biyomedikal Mühendisliği, Boston Üniversitesi
09.1987–05.1989 Eğitim Asistanı, Biyomedikal Mühendisliği, Boston Üniversitesi
01.1985–01.1987 Araştırma Görevlisi, Biyomedikal Mühendisliği, Boston Üniversitesi
01.1983–01.1985 Eğitim Asistanı, Matematik, Boğaziçi Üniversitesi
6. Yönetilen Yüksek Lisans ve Doktora Tezleri
6.1 Yüksek Lisans Tezleri
1. Baran Canpolat, “Covalent Modification of Cellulases for Textile Biofinishing”,
Sabancı Üniversitesi, 2015.
2. Serkan Sırlı, “Investigations on the N-linked glycosylation of Aspergillus niger Lipase
in Pichia pastoris.”, Sabancı Üniversitesi, 2014.
3. Hazal Yılmaz, “Modifications on Protein Termini of Bacillus thermocatenulatus
Lipase and Their Impacts on Activity and Stability”, Sabancı Üniversitesi, 2014.
4. Batuhan Orbay Yenilmez, “Generation of novel random mutagenesis lipase libraries
via directed evolution.”, Sabancı Üniversitesi, 2013.
5. Ece Egemen, “Identification of epilepsy related pathways from methylome data”,
Sabancı Üniversitesi, 2013.
6. Ebru Şahin, “Detecting motifs for computational classification of dockerin and
cohesin sequences”, Sabancı Üniversitesi, 2013.
7. Husamaldin Tayeh, “Prediction of permissive insertion sites in proteins”, Sabancı
Üniversitesi, 2013.
8. Onur Yükselen, “Combining in silico docking and molecular dynamics simulations to
predict the impact of mutations on the substrate specificity of BTL2 lipase”, Sabancı
Üniversitesi, 2012.
9. Fatma Uzbaş, “Trichoderma reesei as an expression system for homologous
production of individual cellulases”, Sabancı Üniversitesi, 2010.
10. Aslı Çalık, “Optimization of the production of Trichoderma reesei endoglucanase I in
pichia pastoris”, Sabancı Üniversitesi, 2010.
11. Sedef Dinçer, “Aspergillus niger as an expression system for heterologous expression
of ROL and BTL2”, Sabancı Üniversitesi, 2010.
12. Ceyda Sol, “Identification of disease related significant SNPs”, Sabancı Üniversitesi,
2010. (Eş Danışman: Nilay Noyan)
13. Murat Can Çobanoğlu, “Classification of GPCRs using family specific motifs,
Sabancı Üniversitesi, 2010. (Eş Danışman: Yücel Saygın)
14. Süveyda Yeniterzi, “Structural pattern detection and domain recognition for protein
function prediction”, 2009.
15. Serdar Çakıcı, “Virtual reality based approach to protein-protein docking problem”,
Sabancı Üniversitesi, 2009. (Eş Danışman: Selim Balcısoy)
16. Lale Tunçyürek, “A new genetic algorithm for the cell formation problem in group
technology”, Sabancı Üniversitesi, 2009. (Eş Danışman: Bülent Çatay)
17. Nihan Özşamlı, “Feature subset selection problem on microarray data”, Sabancı
Üniversitesi, 2009. (Eş Danışman: Kemal Kılıç)
18. Ebru Kaymak, “Arabidopsis thaliana lipases: cloning and expression in pichia
pastoris”, Sabancı Üniversitesi, 2008.
19. Galip Gürkan Yardımcı, “Structural alignment using network properties”, Sabancı
Üniversitesi, 2007.
20. Sevim Eda Barlak, “Feature selection using genetic algorithms”, Sabancı Üniversitesi,
2007.
21. Müge Erdoğmuş, “Application of automatic mutation-gene pair extraction to
diseases”, Sabancı Üniversitesi, 2007.
22. Ayşe Özlem Sezerman, “Vicinal solvent and protein coupling modulates the protein
dynamics”, Sabancı Üniversitesi, 2007. (Eş Danışman: Canan Atılgan)
23. Mehmet Tuğrul Tekbulut, “MicroRNA target prediction by constraint programming”,
Sabancı Üniversitesi, 2006.
24. Günseli Bayram Akçapınar, “Covalent modification of enzymes for textile processes”,
Sabancı Üniversitesi, 2005. (Eş Danışman: Alpay Taralp)
25. Elanur Şireli, “A computational approach to predict contact potential and disulfide
bond of proteins”, Sabancı Üniversitesi, 2004.
26. Kıvanç Bilecen, “Cloning, characterization and expression of a novel metallothionein
gene from triticum and theoretical and experimental structure-function relationship
prediction”, Sabancı Üniversitesi, 2003. (Eş Danışman: Zehra Sayers)
27. Zerrin Işık, “Computational approaches to protein structure prediction”, Sabancı
Üniversitesi, 2003. (Eş Danışman: Berrin Yanıkoğlu)
28. Rabun Koşar, “Applying genetic algorithms to inverse protein folding problem”,
Boğaziçi Üniversitesi, 2003. (Eş Danışman: Cem Ersoy)
29. Pelin Akan, “Computational approaches to understanding the protein structure”,
Sabancı Üniversitesi, 2002.
30. Mutlu Doğruel, “Computational prediction of protein subcellular localization and
function”, Sabancı Üniversitesi, 2002.
31. Yasemin Türkeli, “Analysis of genetic network using graph matching”, Boğaziçi
Üniversitesi, 2002. (Eş Danışman: Fikret Gürgen)
32. Mert Şahin, “Structure prediction of A. thaliana G protein alpha subunit using
bioinformatics tools based on sequence alignments”, Sabancı Üniversitesi, 2002. (Eş
Danışman: Zehra Sayers)
33. Ersin Başaran, “Unsupervised clustering and its application to discovery of motifs in
protein sequences”, Boğaziçi Üniversitesi, 2001. (Eş Danışman: Ethem Alpaydın)
34. Deniz S. Tanrıseven, “Using Genetic Algorithms to Identify Protein Sequence
Motifs”, Boğaziçi Üniversitesi, 2000. (Eş Danışman: Cem Ersoy)
6.2 Doktora Tezleri
1. Cem Meydan, “Discovering Discriminative and Class-specific Sequence and
Structural Motifs in Proteins”, Sabancı Üniversitesi, 2013.
2. Yasin Bakış, “Application of feature selection method on phylogenetic tree
construction using molecular and morphological data”, Abant İzzet Baysal
Üniversitesi, 2013. (Eş Danışman: Tekin Babaç)
3. Emel Durmaz, “Protein Engineering Studies on Bacillus thermocatenulatus Lipase”,
Sabancı Üniversitesi, 2012.
4. Aylin Günel, “Modeling of TLR4 signal transduction pathway”, İstanbul Teknik
Üniversitesi, 2013. (Eş Danışman: Yavuz Ekşi)
5. Burcu Bakır Güngör, “Bioinformatics approaches to associate single nucleotide
polymorphisms with human diseases according to their pathway related context”,
Sabancı Üniversitesi, 2012.
6. Zeynep Altıntaş, “Development of nanoparticle-modified sensor platform for cancer
marker detection”, Sabancı Üniversitesi, 2012. (Eş Danışman: Yaşar Gürbüz)
7. Günseli Bayram Akçapınar, “Protein engineering and covalent modification of
Trichoderma reesei cellulases in Pichia pastoris for textile biofinishing”, Sabancı
Üniversitesi, 2011.
8. Aydın Albayrak, “Classification of proteins using sequential and structural features”,
Sabancı Üniversitesi, 2011.
9. Özgür Gül, “Protein engineering of rhizopus oryzae lipase for improved
thermostability”, Sabancı Üniversitesi, 2010.
10. Alper Küçükural, “Novel techniques for protein structure characterization using graph
representation of proteins”, Sabancı Üniversitesi, 2009.
7. Yayınlar
7.1 Uluslararası hakemli dergilerde yayınlanan makaleler
Ozden S, Turgut Kara N, Sezerman OU, Durasi İM, Chen T, Demirel G, Alpertunga B,
Chipman JK, Mally A.(2015) ,Assessment of global and gene-specific DNA methylation
in rat liver and kidney in response to non-genotoxic carcinogen exposure. Toxicol Appl
Pharmacol. 1;289(2):203-12. doi: 10.1016/j.taap.2015.09.023. Epub 2015 Sep 30.PMID:
26431795
Timucin E, Cousido-Siah A, Mitschler A, Podjarny A, Sezerman OU.(2015) Probing the
roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5.
Proteins. 2015 Nov 17. doi: 10.1002/prot.24961. [Epub ahead of print] PMID: 26573720
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., Durası İ.M., Uygunoğlu U., Tütüncü M., Demirci N.O., Saip S., Sezerman O.U.,
Siva A., Tahir Turanlı 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.
(2015) “Reply to Stoimenis et al.”, European Journal of Human Genetics, 23(10), p.
1280.
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, advance online publication.
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.
Timucin E., Sezerman O.U. (2013) “The Conserved Lid Tryptophan, W211, Potentiates
Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases.”, PLoS
ONE, 8(12), pp. 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), pp.
e82556.
Durmaz E., Kuyucak S., Sezerman U. (2013) “Modifying the catalytic preference of
tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzymesubstrate 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), pp. 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., BayramAkçapınar 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.
Altıntaş Z., Kallempudi S.S., Sezerman U., Gürbüz Y. (2012) “A novel magnetic particlemodified 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.
Bakış Y., Otu H., Sezerman O.U., (2012) “Inferring Phylogenies from Physico-Chemical
Properties of DNA”, American Journal of Bioinformatics Research, 2(1): 1-6.
Meydan C., Sezerman U. (2012) “Representation of protein secondary structure using bondorientational 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.
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 substractive hybridization method.”, Current Opinion in Biotechnology, 22(S1). pp. S122.
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, 2010 (2010), pp. 757512.
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. 1923.
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.
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.”, In Proceedings of The 2007 International Conference
on Bioinformatics & Computational Biology, June 25-28, 2007, Las Vegas, Nevada, USA.
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.
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.
Işık Z., Yanıkoğlu B., Sezerman U. (2004) “Protein structural class determination using
support vector machines.”, Lecture Notes in Computer Science, 3280. pp. 82-89.
Vasmatzis G., Cornette J., Sezerman U., DeLisi C. (1996) “TCR Recognition of the MHCPeptide 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., and 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.
Chung W.M., Wang Q., Sezerman U. (1992) “Analysis of Aviation Turbo Fuel Composition
by Laser Raman Spectroscopy.”, Applied Spectroscopy, 45, 4279-4285.
Clarke R.H., Chung W.M., Wang Q., DeJesus D., Sezerman U. (1991) “Determination of
Aromatic Composition of Fuels by Raman Spectroscopy”, J. Raman Spectroscopy, 22, 7982.
7.2 Uluslararası bilimsel toplantılarda sunulan ve bildiri kitabında (Proceedings) basılan
bildiriler
Khalid Z., Sezerman O.U. (2014) “Interpreting the prevalence of regulatory SNPs in cancers
and protein-coding SNPs among non-cancer diseases using GWAS association studies.”,
In Proceedings of International Conference on Applied Informatics for Health and Life
Sciences (AIHLS 2014), October 19-22, 2014, Kuşadası, Turkey.
Yavuz A.S., Sözer N.B., Sezerman O.U. (2014) “Amino acid preferences at neddylation
sites.”, In Proceedings of International Conference on Applied Informatics for Health and
Life Sciences (AIHLS 2014), October 19-22, 2014, Kuşadası, Turkey.
Baykal S., Yavuz A.S., Ates H., Sezerman U., Ozsan H.G., Sercan H.O., Sercan Z. (2014)
"Prolonged exposure to tyrosine kinase inhibitors cause phenotypic plasticity in K652
cells, resulting in morphology transition, drug resistance and escape from cellular aging",
In 9th International Conference on Cell and Stem Cell Engineering, September 11-13,
2014, Aachen, Germany.
Durmaz Timuçin E., Sezerman O.U. (2014) “Zinc induces self-assembly of bacterial
thermoalkalophilic lipases: a strategy for thermostability.” In Proceedings of 28th Annual
Symposium of the Protein Society, San Diego, CA, USA.
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.
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.
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.
Meydan C., Sezerman U., Otu H.H. (2009) “Prediction of peptides binding to MHC class I
alleles by partial periodic pattern mining.” In Proceedings of International Joint
Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009 (IJCBS
’09), USA: IEEE (Institute of Electrical and Electronics Engineers), August 2009, 315318.
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
Proceedings of 11th Genetic and Evolutionary Computation Conference, GECCO 2009,
New York, NY, USA: ACM (Association for Computing Machinery), July 2009, 19671970.
Yörükoğlu D., Bakış Y., Sezerman U. (2009) “An entropy based heuristic model for
predicting functional sub-type divisions of protein families.”, In Proceedings of 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.
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.
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.
Gül, Ö., İncetürkmen, E., Kütük, Ö., Başağa, H., Sezerman, U., Gürbüz, Y. (2005)
“Biosensor implementation for cardiovascular risk marker analysis.”, In Proceedings of
IEEE Sensors 2005, Oct 31-Nov 3, 2005, Irvine, California, USA.
Türkeli Y., Erçil A., Sezerman U. (2003) “Effect of Feature Extraction and Feature Selection
on Expression Data from Epithelial Ovarian Cancer.”, In 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.”, In Proceedings of the 23rd Annual EMBS
International Conference, October 25-28, Istanbul, Turkey.
7.3 Yazılan uluslararası kitaplar veya kitaplarda bölümler
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.
7.4 Ulusal hakemli dergilerde yayınlanan makaleler
7.5 Ulusal bilimsel toplantılarda sunulan ve bildiri kitabında basılan bildiriler
Akalın A., Kasap Z., Kavak E., Sezerman U. (2004) “Classification of GPCRs according to
their ligand specifity using SVMs.”, Biyomedikal Mühendisliği Ulusal Toplantısı,
BİYOMUT 2004, 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.”, BİYOENERJİ 2004 Sempozyumu, 20-22 Ekim 2004, İzmir,
Turkey.
8. Projeler
Proje No
Projede
ki
Görevi
Proje Adı
Başlama
-Bitiş
Destek
Miktarı
(TL)
104S380
105M103
107E014
108E229
109T315
109S219
266422
111T846
1302.STZ
.2012-1
112T901
Eş
Lactabacillus bakteriyel genlerinin
Yürütücü karakterizasyonu (TÜBİTAK)
“Peptide-Protein Docking and Binding
Yürütücü Free Energy Calculation” Boston
Üniversitesi ile Birlikte NSF projesi
Araştırm Özgün Protein Mikroçip Tasarımı:
acı/Uzm Moleküler Tanı Amaçlı Biyoteknoloji
an
Uygulaması (TÜBİTAK)
Eş
Development of BioMEMS for
Yürütücü Cardiovascular Risk Assessment (DPT)
İşlevsel Değişim Yapılmış Selülazların
Yürütücü
Pilot Ölçekte Üretimi (TÜBİTAK)
Viskona Özel Selülazların Endüstriyel
Yürütücü
Ölçekte Üretimi (DPT)
Araştırm
Tümleşik RF Verici - Tabanlı Biyosensör
acı/Uzm
Geliştirilmesi (TÜBİTAK)
an
İlaç Keşfi İçin Biyomedikal Ontolojilerin
Danışma
Entegrasyonu Ve Otomatik Akıl Yürütme
n
(TÜBİTAK)
Bağışıklık Sisteminde Önemli Il-7r Sitokin
Danışma
Almac Geninin Kontrol Mekanizmasının
n
Araştırılması (TÜBİTAK)
Araştırm
İdyopatik Jeneralize Epilepsilerde Tüm
acı/Uzm
Genom Metilom Analizi (TÜBİTAK)
an
Yürütücü JADE (Avrupa Komisyonu, FP7 RoK)
Selülazların Isı Dayanıklılığının
Endüstriyel Uygulamalar İçin Protein
Yürütücü
Mühendisliği Yöntemleriyle Arttırılması
(TÜBİTAK)
Tekstil Sanayiine Yönelik Katma Değerli
Yürütücü
Selülaz Enzimi Üretimi (SANTEZ)
DNA karma yöntemi ile endüstriyel
uygulamalar için farklı lipaz ve selülaz
Yürütücü
veritabanı ve kütüphanesinin oluşturulması
(TÜBİTAK)
19992001
19992001
05.200505.2008
156.780
20062008
05.200605.2008
20062009
245.500
07.200707.2010
360.000
06.200912.2011
99.172
02.201002.2013
348.259
07.201007.2013
230.000
20112014
€141.800
03.201203.2014
199.092
20122015
289.500
05.201311.2015
330.000
645693
Advanced bioinformatics for genome and
metagenome analyses and discovery of
novel biocatalists from extremophiles: 12.2014Yürütücü
implications for improving industrial 12.2018
bioprocesses (Horizon 2020 – Marie CurieSklodowska RISE)
114E637
Kolon Kanseri Etiyolojisindeki Epigenetik
Ve Diğer Faktörler ile Bu Faktörlerin 2015 Yürütücü
Hedeflediği
Önemli
Yolakların 2018
Belirlenmesi (TÜBİTAK)
694.000
€144.000