Download O. Ugur Sezerman Sabanci University MDBF 34056 Orhanli

CURRICULUM VITAE
EUROPEAN FORMAT
PERSONAL INFORMATION
Name, Surname
Address
House number, street name,
postcode, city, country
Telephone
Fax
E-mail
O. Ugur Sezerman
Sabanci University MDBF 34056
Orhanli Tuzla ISTANBUL
TURKEY
+90-542 422 36 88
+90 216 483 95 50
[email protected]
Website
Nationality
Place and Date of birth
Turkish
IZMIR TURKEY
25 June 1964
WORK EXPERIENCE
9/99Faculty. Biological Sciences and Bioengineering Dept.,Sabanci University,
Istanbul,TURKEY
8/98-9/99 Part-Time Faculty, Computer Engineering Dept., Bogazici University,Istanbul,
TURKEY
1/93-5/97 Post-Doc , Biomedical Engineering, Boston University
2/90-1/93 Research Assistant, Biomedical Engineering, Boston University
9/87-5/89 Teaching Assistant, Biomedical Engineering, Boston University
1/85-1/87 Research Assistant, Biomedical Engineering, Bogazici University
1/83-1/85 Teaching Assistant, Mathematics Dept., Bogazici University,Istanbul
Name and address of employer
Type of business or sector
Occupation or position held
Main activities and responsibilities
Page 1 - Curriculum vitae
of Sezerman
Sabanci University Engineering and Natural Sciences Faculty 34956 Orhanli Tuzla ISTANBUL
Academia
Associate Professor
Head of the Computational Biology Lab, Head of the Protein Engineering Lab
EDUCATION AND TRAINING
9/87-1/93
Dates (from – to)
Ph.D. Biomedical Engineering, Boston University, Boston, MA,
USA.
Thesis: New Methods for Molecular Docking with Applications to Recognition
and Design Problems in Immunology with Prof. Charles DeLisi
9/85-8/87
M.S. Biomedical Engineering, Bogazici University, Istanbul,
TURKEY
1/85-12/87
Name and type of organisation
providing education and training
Principal subjects occupational skills
covered
Title of qualification awarded
Level in National classification
B.S. Electrical Engineering, Bogazici University,
Istanbul,TURKEY
Boston University, Boston USA
Programming, Molecular Modeling, Bioinformatics, Protein engineering
Ph. D. In Biomedical Engineering
Associate professor
RESEARCH ACTIVITIES
Research sectors
Recent Scientific Activities.
Page 2 - Curriculum vitae
of Sezerman
Bioinformatics, Protein Engineering
Established Computational Biology Lab at Sabanci University
Established Protein Engineering Lab at Sabanci University
Established Fermentation Lab at Sabanci University
Organized Protein Engineering Workshop, Structural Biology Workshop, Non Coding RNA
Workshop funded by European Science Foundation in Turkey
Books and Articles
C. DeLisi, U. Sezerman and R. Rosenfeld,”Problems and Progress on Computational
Approaches to the Molecular Basis of Cell Recognition.” 25th Jerusalem Symposium on
Biochemistry and Quantum Chemistry, Pullman and Jortner eds. Kluwer Academic
Publishers, Amsterdam
S. Vajda, M.S. Jafri, O.U. Sezerman, “Necessary Conditions for Avoiding Incorrect Polypeptide
Folds in Conformational Search by Energy Minimization”, Biopolymers, 33, 173-192 (1993).
U. Sezerman, S. Vajda, J. Cornette, C. DeLisi, “ Towards Computational Determination of
Peptide-Receptor Structure”, Protein Science, 2, 1827-1843 (1993)
G. Vasmatzis, J. Cornette, U. Sezerman, C. DeLisi, “TCR Recognition of the MHC-Peptide
Dimer: Structural Properties of a Ternary Complex”, J. Mol. Biol. 261, 72-89 (1996).
U. Sezerman, S. Vajda, C. Delisi, “Free Energy Mapping of Class I MHC molecules and
Structural Determination of Bound Peptides”, Protein Science 5, 1272-1281(1996).
Z. Isik, B. Yanikoglu, U. Sezerman “Protein Structural Class Determination Using Support Vector
Machines”, Lecture Notes in Computer Science, Oct. 2004.
Bilecen, K., Ozturk, U.H., Duru, A.D., Sutlu, T., Petoukhov, M.V., Svergun, D.I., Koch, M.H.J.,
Sezerman, U.O., Cakmak, I., and Sayers, Z.” Triticum durum metallothionein: isolation of the
gene and structural characterization of the protein using solution scattering and molecular
modeling.” J. Biol. Chem. 280:13701-113711 (2005).
Bakir B., Sezerman U. “Functional Classification of G-Protein Coupled Receptors, Based on
Their Specific Ligand Coupling Patterns” Lecture Notes in Computer Science (LNCS), Vol. 3907,
April 2006.
Yardimci G.G., Kucukural A., Saygin Y, and Sezerman U.,”Modified Association Rule Mining
Approach for the MHC-Peptide Binding Problem”, LNCS volume 4263,(2006).
Erguner B., Erdogan O., and Sezerman U.,”Prediction and Classification for GPCR Sequences
Based on Ligand Specific Features”, LNCS volume 4263,( 2006).
Budak H., Kasap Z., Shearman R. C., Dweikat I.,Sezerman U. and Mahmood A. “Molecular
Characterization of cDNA encoding resistance gene-like sequences in Buclo dactiloides”,
Molecular Biotechnology. 34:293-301 ( 2006).
Gul O., Calay E., Sezerman U., Basaga H., Gurbuz Y.,”Sandwich type antibody microarryas for
the detection and quantification of cardiovascular risk markers”, Sensors and Actuators, 125,
581-588 (2007).
Erdoğmuş M., Sezerman U., “Application of automatic mutation gene pair extraction to
diseases”,Journal of Bioinformatics and Computational Biology, Vol.5, Issue 6,:1261-1275
(2007).
Meydan C., Yörükoğlu D., Küçükural A., Sezerman U., “Discovery of biomarkers for
hexachlorobenzene toxicity using population based methods on gene expression data”, Lecture
Notes in Computer Science, Vol.5265,412-423, 2008.
Kallempudi S., Gül Ö., Başağa H., Sezerman U., Gurbuz Y.,“Label-free biosensors for the
detection and quantification of cardiovascular risk markers”, Journal of Sensor Letters, Vol.6,
Cakici S., Sumengen S., Sezerman U., Balcısoy S., “DockPro: A VR-Based Tool for ProteinProtein Docking Problem”, International Journal of Virtual Reality, 2008.
Yeniterzi S., Sezerman U. “EnzyMiner: automatic identification of protein level mutations and
their impact on target enzymes from PubMed abstracts” BMC Bioinformatics. 10(Suppl 8): S2,
2009.
Solda G., Makunin I., Sezerman U., Corti G., Guffanti A., “An Ariadne's thread to the
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identification and annotation of noncoding RNAs in eukaryotes” , Briefings in Bioinformatics
10(5):475-489 ,2009.
Albayrak A, Otu, H. H, Sezerman U.,” Clustering of protein families into functional subtypes
using Relative Complexity Measure with reduced amino acid alphabets”, BMC Bioinformatics,
11:428, 2010.
Cobanoglu M.C., Saygin Y., Sezerman U.,“Classification of GPCRs Using Family Specific
Motifs”, IEEE Transactions on Comp. Biology and Bioinformatics , ISSN: 1545-5963, 2010.
Meydan, C. and Sezerman, U., "Biomarker discovery for toxicity", Neurocomputing (Sp. Iss. SI),
Vol.73, No.13-15, 2384-2393, 2010.
Ozgenturk N.O., Oruç F.,Sezerman U., Kucukural A., Korkut S. V., Toksoz F, and Un C.,
“Generation and Analysis of Expressed Sequence Tags from Olea europaea L.," Comparative
and Functional Genomics, vol. 2010, Article ID 757512, doi:10.1155/2010/757512, 2010.
Kucukural A, Szilagyi A, Sezerman O, Zhang Y (2010):
Protein homology analysis for function prediction with parallel sub-graph isomorphism.
In: Lodhi H, Yamanishi Y (eds.): Chemoinformatics and advanced machine learning
perspectives: complex computational methods and collaborative perspectives. IGI Global, 2010,
pp. 129-144. Book Chapter
Akcapinar G.B., Gul O., Sezerman U.,” Effect of codon optimization on the expression of
Trichoderma reesei endoglucanase 1 in Pichia pastoris”, Biotechnology Progress, DOI:
10.1002/btpr.663, 2011.
Seidl-Seiboth V, Guber S, Sezerman U, Schwecke T, Albayrak A, Neuhof T, Döhren H, Baker
SE and Kubicek CP. Novel hydrophobins from Trichoderma define a new hydrophobin subclass:
protein properties, evolution, regulation, and processing J. Mol. Evol. Volume 72, Number 4,
339-351, 2011.
Albayrak A., Sezerman U., “Discrimination of thermophilic and mesophilic proteins using
reduced amino acid alphabets with n-grams” in Press Current Bioinformatics, 2011.
Akcapinar G.B., Sezerman U.,” From in silico to in vitro: Modelling and production of
Trichoderma reesei endoglucanase 1 and its mutant in Pichia pastoris” Accepted with minor
revisions. J. Biotechnology
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ULTERIORI INFORMAZIONI /
ADDITIONAL INFORMATION
Refereed Conference Publications
Meydan, Cem and Sezerman, Uğur and Otu, Hasan, "Prediction of peptides binding to MHC
class I alleles by partial periodic pattern mining", 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, Yasin and Sezerman, Uğur and Babaç, M. Tekin and Meydan, Cem, "Optimization of
morphological data in numerical taxonomy analysis using genetic algorithms feature selection
method", 11th Genetic and Evolutionary Computation Conference, GECCO 2009, New York,
NY, USA: ACM (Association for Computing Machinery), July 2009, 1967-1970
Yörükoğlu, Deniz and Bakış, Yasin and Sezerman, Uğur, "An entropy based heuristic model for
predicting functional sub-type divisions of protein families", 11th Genetic and Evolutionary
Computation Conference, GECCO 2009, New York, NY, USA: ACM (Association for Computing
Machinery), July 2009, 2173-2178
Meydan, Cem and Otu, Hasan and Sezerman, Uğur, "Prediction of peptides binding to MHC
class I alleles by partial periodic pattern mining", 4th International Symposium on Health
Informatics and Bioinformatics (HIBIT 09), Ankara: ODTU (Ortadoğu Teknik Üniversitesi), April
2009
Cem Meydan, Alper Kucukural, Uğur Sezerman,”Biomarker detection for hexachlorobenzene
toxicity using genetic algorithms on gene expression data” HIBIT08, Istanbul, 2008.
Burak Aksu, Nihan Özsamli, Kemal Kılıç, Uğur Sezerman,”A Modified framework for feature
subset selection in microarray data” HIBIT08 , Istanbul, 2008.
Süveyda Yeniterzi, Reyyan Yeniterzi, Alper Küçükural, Nilay Noyan, Uğur Sezerman “A new
approach to measure the similarities of protein structures using network properties”, HIBIT08,
İstanbul,2008.
Alper Küçükural, Uğur Sezerman, Aytül Erçil, ”Discrimination of Native Folds Using Network
Properties of Protein Structures”, APBC 2008,Kyoto,2008.
Alper Küçükural, Reyyan Yeniterzi, Süveyda Yeniterzi, Uğur Sezerman, ”Evolutionary selection
of minimum number of features for classification of gene expression data using genetic
algorithms” ,ACM Genetic And Evolutionary Computation Conference (GECCO 2007),London,
2007.
Alper Küçükural, Uğur Sezerman, ”Potential use of graph theoretical properties of protein
structures in structural alignment”, BIOCOMP 2007, Las Vegas,2007.
Alper Küçükural, Uğur Sezerman, “Detecting Native Proteins in ROSETTA Dataset Using Graph
Properties” ,HIBIT2007, Antalya,2007.
Reyyan Yeniterzi, Süveyda Yeniterzi, Alper Küçükural, Uğur Sezerman, ”Feature selection with
genetic algorithms on cardiac arrhytmia database”, HIBIT ,Antalya,2007.
Ugur Sezerman, A.Akalin, Z.Kasap, E.Kavak, “Ligand-specific classification of G protein-coupled
receptors using support vector machines and reduced alphabeth”, FEBS Journal 2006 273:p1
42, Istanbul,2006.
Özgür Gül, Ercihan İncetürkmen, Hüveyda Başağa, Uğur Sezerman, Yaşar Gurbuz, ”Biosensor
implementation for cardiovascular risk marker analysis” IEEE Sensors 2005 Conference,
Korea,2005.
A.Akalın, Z.Kasap, E. Kavak, U.Sezerman “Classification of GPCRs according to their ligand
specifity using SVMs”, BIYOMUT Conference , May-27-30, 2004.Istanbul Turkey.
Y. Turkeli, A Ercil, U. Sezerman “Effect of Feature Extraction and Feature Selection on
Expression Data from Epithelial Ovarian Cancer” IEEE EMBC 2003.
Y. Turkeli, U. Sezerman, F. Gurgen, “Information excavation from Scale free genetic networks
using attributed graph matching”, ICANN 2003.
A. Akyol, U. Sezerman, “Fold Classification of Protein Sequences by GeneticAlgorithm”, ICANN
2003.
U. Sezerman, R. Islamaj, E. Alpaydin,” Three dimensional representation of Amino Acids using
Machine Learning methods” IEEE EMBC (2001).
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