Attila Gürsoy Oct 2015 Koç University Computer Engineering

Attila Gürsoy
Oct 2015
Koç University
Computer Engineering Department
Sarıyer, Istanbul 34450
Phone: (212) 338 1720
[email protected]
http://home.ku.edu.tr/~agursoy
Academic/Research Positions Held
• Associate Dean
Engineering Faculty,
Koç University, Istanbul, Sep 2013 - present
• Professor
Computer Engineering Dept., Koç University, Istanbul, Feb 2010 - present
• Visiting Professor - Sabbatical visit
Universitad Pompeu Fabra, Barcelona, Spain, 2011-2012
• Assoc. Professor
Computer Engineering Dept., Koç University, Istanbul, Feb 2006 - Feb 2010
• Asst. Professor
Computer Engineering Dept., Koç University, Istanbul, Sep 2002 - Feb 2006
• Asst. Professor
Computer Engineering Dept., Bilkent University, Ankara, Sep 1996 - Sep 2002
• Postdoctoral Research Associate
Theoretical Biophysics Group, Beckman Institute,
University of Illinois at Urbana-Champaign, March 1994 - Aug 1996
Education/ Titles
• Higher Education Council, Associate Professor
YÖK Doçentlik Ünvanı, 2000
• Ph.D. Computer Science, May 1994,
University of Illinois at Urbana-Champaign.
Ph.D. thesis: Simplified expression of message-driven programs and quantification of their
impact on performance
• M.Sc. Computer and Information Sciences, July 1988,
Bilkent University, Ankara, Turkey.
• B.Sc. Computer Engineering, June 1986,
Middle East Technical University, Ankara, Turkey.
Honors and Awards
Science Academy, Turkey, Member, 2014
Werner-von-Siemens Excellence Award for Science and Innovation, 2005.
NATO Science Scholarship for Ph.D (TÜBİTAK, Turkey), 1988-1991.
Research Interests
Computational Biology and Bioinformatics, Parallel Programming and Algorithms,
High Performance Computing.
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Grants
TÜBİTAK Research Grant, 2014-2017, Computational and Experimental investigation of RAS homodimer ve heterodimer complexes and interactions, co-investigator.
TÜBİTAK Research Grant, 2013-2015, Relating genotypes to phenotypes in breast cancer metastasis using three dimensional protein-protein interaction networks.
TÜBİTAK Research Grant, 2014-2017, Computational and Experimental investigation of RAS homodimer ve heterodimer complexes and interactions, co-investigator.
TÜBİTAK Research Grant, 2010-2012, A new model for representing protein-protein interaction
networks.
TÜBİTAK Research Grant, 2010-2013, Extracting structural protein-protein interaction networks
to analyze cancer-related proteins and their signaling pathways, co-investigator.
ISTKA, KUBIP, 2014-2015, Biofuel Platform Istanbul for Sustainable Energy, co-investigator
DPT, Koc University, Surface Science ad Technology Center, 2010-2013, co-investigator.
DPT, Cancer Drug Technologies, 2006-2009, co-investigator.
SEE-GRID, FP6, Gridification of Protein-Protein Interaction predictions, co-investigator.
TÜBİTAK Research Grant, 2005-2008, Protein-protein interactions, co-investigator.
TÜBİTAK-NSF Research Grant, 2004-2007, Studies on protein folding, principal investigator.
TÜBİTAK Research Grant, 1997-1999, Development of algorithms and parallel object-oriented programming techniques for SMP clusters, principal investigator.
Major Research Projects and Development
• PRISM, http://prism.ccbb.ku.edu.tr/prism, 2005- , Koc University, Protein Interactions
by Structural Matching. PRISM project consists of protein interfaces, hotspots in interfaces,
and prediction of protein-protein interaction based on interfaces. It is one of first prediction
approaches that exploits interfaces at a large scale and with high performance.
• PATIKA, 2000-2002, Bilkent University, Representation and processing of biochemical pathways
• NAMD, 1994-1996, University of Illinois at Urbana-Champaign, A key contributer in the
design and implementation of NAMD, a scalable paralel object-oriented molecular dynamics
program. It received Gordon-Bell Award at Supercomputing 2002 for its unprecedented performance.
• Charm++, 1992-1996, University of Illinois at Urbana-Champaign, A key contributer in the
design and implementation of Charm++, a multi-threaded,object-based, parallel programming
language.
Professional Activities/Services
PLos ONE Academic Editor, 2011PLos Computational Biology Guest Editor 2015
TUBITAK EEEAG Executive Board Member 2014Scientific Advisory Board member, Turkish-German Workshop on Bioinformatics: Recent Developments from Health to Nanotechnology, Ege University,2014. Technical program committe member
of many conferences including ACM-BCB, ISCIS. Reviewing for major bioinformatics journals
including Plos Comp Biol, Bioinformatics, Genome Biology, BMC Bioinformatics, Nucleic Acids
Research.
Member of Koc University, Drug Design Center
Member of Koc University Computational Biology and Bioinformatics Center.
Established High Performance Computing Lab at Koc University.
Turkish Bioinformatics Society (Biyoenformatik dernegi, co-founder and vise-president) Co-founded
Bilkent University Bioinformatics Center (2002).
Number of citations in SCI: over 3300, Google Scholar over 5400
Invited Talks :
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1. Structural Networks of Signaling Pathways on Proteome Scale: Challenges and Opportunities,
Biophysical Society, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery:
Bridging Experiments and Computations, Istanbul, September 10-14, 2014
2. Modulating Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities, 2nd
International BA U Drug Design Congress, Istanbul Turkey April17-19, 2014
3. PRISM: Genome Scale Structural Protein-Protein Interaction Networks, Embo Practical Course
Symposium, Computational Biology: From Genomes to cells and systems, 4 Oct 2013, Istanbul, Turkey
4. Network biology, IUGEN Winter School, Istanbul University, Turkey, March, 2013
5. Constructing structural interactomes: template based predictionof protein-protein interactions at large-sclae, TAGp12 Workshop on Theoretical Approaches for the Genome and Proteins, Annecy-Le-Vieuex, France, Dec 2012
6. Structural Networks of signalling pathways on the proteome scale, MBG-MOBGAM, Istanbul
Technical University, Istanbul, Nov 2012,
7. Structural Networks of signalling pathways on the proteome scale, 6th International Summer School on Emerging TEchnologies in Biomedicine, ”Bioinformatics and Systems Biology
Approaches for the Analysis of Complex Biological Networks”, Patras, Greece, July, 2012
8. Integrating protein structure information into protein-protein interaction networks and its
applications, Dept of Computer Architecture, Universitst Politecnica de Catalunya, Barcelona,
Feb 2012
9. Template Based Protein-Protein Interaction Prediction and Towards Structural Interactomes,
Barcelona Biomedical Research Park, Barcelona, Jan 2012
10. Towards Structural Protein-Protein Interaction Networks and their Role in Drug Discovery,
Workshop on Bioinformatics for Anti-cancer Drug Discovery, Bilkent University, Ankara, 1718 October, 2011.
11. Large-scale prediction of computational hot spots and their use in targeting and predicting
protein-protein interactions, Sabanci University, Istanbul, 27 May, 2011
12. Large-scale computational prediction of hot spots and their use in predicting and targeting
protein interactions, International FOLDAPPI Workshop on Targeting Large Protein-Protein
Interfaces, Wurzburg, Germany, April 2011.
13. Applications of Data Mining and Integration to Study Protein Interactions,
IEEE ISCIS2007 22nd International Symposium on Computer and Information Sciences 7-9
November, 2007, METU, Ankara.
14. Prediction of protein-protein interactions, 15. Istanbul Istatiksel Fizik Gunleri,19-21 June
2008, Istanbul.
15. Protein-protein etkilesimi, TUBITAK ULAKBIM II. Ulusal Grid Calistayi, March, 2007,
Ankara.
16. Integration of protein domain, interaction, and gene expression data to infer coordinated
proteins., Euro XXII, Bioinformatics, July, 2007, Prague.
17. PRISM: Protein Interactions by Structural Matching, Sabanci University, May, 2007, Istanbul.
Publications
Publications in SCI-expanded journals:
1. Muratcioglu S, Presman DM, Pooley JR, Grntved L, Hager GL, Nussinov R, Keskin O, Gursoy A., “Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling
Complex and C/EBP”, Biophys J. 2015 Sep 15;109(6):1227-39.
2. Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R., “A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway”, Biophys J. 2015 Sep
15;109(6):1214-26.
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3. Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., “The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas”, Mol Cancer Res. 2015 Sep;13(9):1265-73.
4. Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., “The
Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway”,
Sci Rep. 2015 Aug 21;5:13128
5. Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R., “GTPDependent K-Ras Dimerization”, Structure. 2015 Jul 7;23(7):1325-35.
6. Cavga AD, Karahan N, Keskin O, Gursoy A., “Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities”, Curr Top Med Chem. 2015;15(20):2005-18.
7. Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A., “PRISM: a web server and
repository for prediction of protein-protein interactions and modeling their 3D complexes”,
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9.
8. Kuzu G, Keskin O, Nussinov R, Gursoy A., “Modeling protein assemblies in the proteome”,
Mol Cell Proteomics. 2014 Mar;13(3):887-96.
9. Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O., “The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in
Inflammation and Cancer”, PLoS Comput Biol. 2014 Feb 13;10(2).
10. Cukuroglu E, Gursoy A, Nussinov R, Keskin O., “Non-redundant unique interface structures
as templates for modeling protein interactions”, PLoS One. 2014 Jan 27;9(1).
11. Cukuroglu E, Engin HB, Gursoy A, Keskin O., “Hot spots in protein-protein interfaces: Towards drug discovery”, Prog Biophys Mol Biol. 2014 Jul 2. pii: S0079-6107(14)00045-5.
12. Guven-Maiorov E, Acuner-Ozbabacan SE, Keskin O, Gursoy A, Nussinov R., “Structural
pathways of cytokines may illuminate their roles in regulation of cancer development and
immunotherapy”, Cancers (Basel). 2014 Mar 25;6(2):663-83.
13. Engin HB, Gursoy A, Nussinov R, Keskin O., “Network-based strategies can help mono- and
poly-pharmacology drug discovery: a systems biology view”, Curr Pharm Des. 2014;20(8):12017.
14. Engin HB, Guney E, Keskin O, Oliva B, Gursoy A., “Integrating structure to protein-protein
interaction networks that drive metastasis to brain and lung in breast cancer”. PLoS One.
2013 Nov 22;8(11)
15. Kuzu G, Gursoy A, Nussinov R, Keskin O., “Exploiting conformational ensembles in modeling
protein-protein interactions on the proteome scale”, J Proteome Res. 2013 Jun 7;12(6):264153.
16. Guven Maiorov E, Keskin O, Gursoy A, Nussinov R., “The structural network of inflammation
and cancer: merits and challenges”, Semin Cancer Biol. 2013 Aug;23(4):243-51.
17. Maiorov EG, Keskin O, Ng OH, Ozbek U, Gursoy A., “Identification of interconnected markers
for T-cell acute lymphoblastic leukemia”. Biomed Res Int. 2013;2013:210253.
18. Kar G, Keksin O, Fraternali F, Gursoy A., “Emerging role of the ubiquitin-proteasome system
as drug targets, Curr Pharm Des. 2013;19(18):3175-89.
19. An O, Gursoy A, Gurgey A, Keskin O., “Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2
(FHL2) patients”, Protein Sci. 2013 Jun;22(6):823-39.
20. Engin HB, Keskin O, Nussinov R, Gursoy A., “A strategy based on protein-protein interface
motifs may help in identifying drug off-targets”, J Chem Inf Model. 2012 Aug 27;52(8):227386.
21. Kuzu G, Keskin O, Gursoy A, Nussinov R., “Constructing structural networks of signaling
pathways on the proteome scale”, Curr Opin Struct Biol. 2012 Jun;22(3):367-77
22. Kar G, Kuzu G, Keskin O, Gursoy A., “Protein-protein interfaces integrated into interaction
networks: implications on drug design”, Curr Pharm Des. 2012, 18, 4697-4705
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23. Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A., “Enriching the human apoptosis
pathway by predicting the structures of protein-protein complexes”, J Struct Biol. 2012
Sep;179(3):338-46
24. Tuncbag N, Keskin O, Nussinov R, Gursoy A. “Fast and accurate modeling of protein-protein
interactions by combining template-interface-based docking with flexible refinement”, Proteins. 2012 Apr;80(4):1239-49,
25. Kar G, Keskin O, Nussinov R, Gursoy A., “Human proteome-scale structural modeling of
E2-E3 interactions exploiting interface motifs”, J Proteome Res. 2012 Feb 3;11(2):1196-207
26. Cukuroglu E, Gursoy A, Keskin O., HotRegion: a database of predicted hot spot clusters.,
Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33
27. D. Sanli, O. Keskin, A. Gursoy, B. Erman, “Structural cooperativity in histone H3 tail modifications”, Protein Sci., 20(12), 1982-1990, Dec 2011.
28. N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin, “Predicting protein-protein interactions
on a proteome scale by matching evolutionary and structural similarities at interfaces using
PRISM”, Nat Protoc, 6, 1341-1354, 2011
29. O. Ulucan, O. Keskin, B. Erman, and A. Gursoy, “A Comparative Molecular Dynamics Study
of Methylation State Specificity of JMJD2A”, PLos ONE 6(9), Sep 2011
30. N. Tuncbag, A. Gursoy, O. Keskin, “Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces”, Phys. Biol. 8(3):0035006, 2011
31. S.E.A Ozbabacan, H.B. Engin, A. Gursoy and O. Keskin, “Transient protein-protein interactions”, Protein Engineering, Design & Selection 24(9) 635648, 2011
32. M. Ozboyaci, A. Gursoy, B. Erman, O. Keskin, “Mocular recognition of H3/H4 histone tails
by the tudor domains of JMJD2A: A comparative molecular dynamics simulations study”,
PLos ONE, 6(3), e14765, 2011
33. G. Kar, O. Keskin, A. Gursoy, N. Nussinov,“Allostery and population shift in drug discovery”,
Current Opinion in Pharmacology, 10 (6) 715-722, 2010
34. S.E.A Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov, “Conformational ensembles, signal
transduction and residue hot spots: Application to drug discovery, Current Opinion in Drug
Discovery and Development, 13(5), pp. 527-537, 2010
35. S. Kalyoncu, O. Keskin, A. Gursoy,“Interaction prediction and classification of PDZ domains,
BMC Bioinformatics, 11(357), 2010.
36. N. Tuncbag, FS. Salman, O. Keskin, A. Gursoy, “Analysis and network representation of
hotspots in protein interfaces using minimum cut trees, Protein-Structure Function and Bioinformatics, 78(10), pp. 2283-2294, 2010.
37. EB. Unal, A. Gursoy, B. Erman,“VitAL: Viterbi algorithm for de novo peptide design, PLOS
One, 5(6), e10926, 2010.
38. N. Tuncbag, O.Keskin, A. Gursoy, “HotPoint: hotspot prediction server for protein interfaces,
Nucl. Acids. Res. (38) Web Server Issue, W402-W406, 2010.
39. E. Cukuroglu, A. Gursoy, O. Keskin, “Analysis of Hot Region Organization in Hub Proteins,
Annals of Biomedical Engineering, 38(6), pp. 2068-2078, 2010.
40. G. Kar, A. Gursoy, O. Keskin, “Human cancer protein-protein interaction network: a structural perspective, PLOS Computational Biology, 5(12) , e1000601, Dec 2009
41. N. Tuncbag, G. Kar, A. Gursoy, O. Keskin, R. Nussinov, “Towards inferring time dimensionality in proteinprotein interaction networks by integrating structures: the p53 example”,
Molecular BioSystems, 5(12), pp. 1770-1778, Dec 2009
42. B. Unal, A. Gursoy, B. Erman, “Conformational energies and entropies of peptides, and the
peptide-protein binding problem”, Physical Biology 6(3), 2009
43. N. Tuncbag, A. Gursoy, O. Keskin, “Identification of computational hot spots in protein
interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy”,
Bioinformatics, 25(12), 1513-1520, 2009
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44. N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, R. Nussinov, “A survey of available tools and web
servers for analysis of protein-protein interactions and interfaces”, Briefings in Bioinformatics,
10(3), 217-232, 2009
45. A. Gursoy, O. Keskin, R. Nussinov, “Topological Properties of Protein Interaction Networks
from a Structural Perspective”, Biochem. Soc. Trans., 36(Pt 6), 1398-1403, 2008.
46. N. Tuncbag, A. Gursoy, E. Guney, R. Nussinov, O. Keskin, “Architectures and functional
coverage of protein-protein interfaces”, J. Mol. Biol., 381(3), 785-802, 2008.
47. O.Keskin, A. Gursoy, B. Ma, R.Nussinov, “Principles of Protein-Protein Interactions: What
are the Preferred Ways For Proteins To Interact”, Chem. Rev. 108, 1225-1244, 2008.
48. O. Keskin, N. Tuncbag, A. Gursoy, “Characterization and Prediction of Protein Interfaces to
Infer Protein-Protein Interaction Networks”, Current Pharmaceutical Biotechnology, 9, 67-76,
2008.
49. E. Guney, N. Tuncbag, A. Gursoy, O.Keskin, “HotSprint: Database of Computational Hot
Spots in Protein Interfaces”, Nucleic Acids Research, Vol. 36, 2008, D662-6., 2008.
50. O. Keskin, A. Gursoy, B. Ma., R. Nussinov, “Towards drugs targeting multiple proteins in
a systems biology approach”, Current Topics in Medicinal Chemistry, Vol. 7(10), 943-951,
2007.
51. O. Sonmez and A. Gursoy, “A Novel Economic-based Scheduling Heuristic for Computational
Grids”, International Journal of High Performance Computing Applications, 21(1), 21-29,
2007.
52. L. Ormeci, A. Gursoy, G. Tunca, B. Erman, “Computational Basis of Knowledge-Based Conformational Probabilities Derived from Local and Long-Range Interactions in Proteins”, Proteins: Structure, Function, and Bioinformatics, 66(1):29-40 , 2007.
53. A. Gursoy, O. Keskin, M. Turkay, B. Erman, “Relationships between Unfolded Configurations
of Proteins and Dynamics of Folding to the Native State”, Journal of Polymer Science Part
B: Polymer Physics, Vol. 44, 3667-3678, 2006
54. O. Yogurtcu, E. Erzin, and A. Gursoy, “Extracting Gene Regulation Information from Microarray Time-Series Data Using Hidden Markov Model”, LNCS Vol.:4263 , Pages:144-153 ,
2006, Springer-Verlag
55. O. Sonmez, A. Gursoy, “Comparison of Fixed and Dynamic Pricing Policies in a Computational Grid”, LNCS 3911, pp. 766-773 (2006)
56. U. Ogmen, O. Keskin, S. Aytuna, R.Nussinoiv, A.Gursoy, “PRISM: Protein interactions by
Structural Matching”, Nucleic Acids Research, Vol. 33, Web Server issue, pp. W331-W336,
(2005).
57. A.S. Aytuna, A.Gursoy, O.Keskin, “Predictions of protein-protein interactions by combining
structure and sequence conservation in protein interfaces”, Bioinformatics, Vol. 21. No. 12,
pp. 2850-2855, 2005.
58. A. Palazoglu, A Gursoy, Y. Arkun, B. Erman, “Folding Dynamics of Proteins from Denatured
to Native State: Principal Component Analysis”, Journal of Computational Biology, Vol. 11,
No. 6: pp. 1149-1168, 2004.
59. A.K. Sinop, T. Abaci, U. Akkus, A. Gursoy, U. Gudukbay, “PHR: A Parallel Hierarchical
Radiosity System with Dynamic Load Balancing” Journal of Supercomputing, Vol 31, pp.
249-263, 2005.
60. A. Gursoy, L.V. Kale, “Performance and Modularity Benefits of Message-Driven Execution”
Journal of Parallel and Distributed Computing, No 64 pp. 461-480, 2004.
61. O. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman, “Relationships between amino acid
sequence and backbone torsion angle preferences in proteins”, Proteins Structure, Function,
Bioinformatics, Vol 55 No 4, pp. 992-998, 2004.
62. E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. CetinAtalay, “An Ontology for Collaborative Construction and Analysis of Cellular Pathways”,
Bioinformatics, Vol 20 No 3 pp. 349-356 , 2004.
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63. A. Gursoy, “Data Decomposition for Parallel K-Means Clustering”, LNCS Vol 3019 pp. 241248, Springer Verlag, 2004.
64. A. Kocatas, A. Gursoy, R. Cetin-Atalay, “Application of Data Mining Techniques to ProteinProtein Interaction Prediction”, LNCS Vol 2869 pp. 316-323, Springer Verlag, 2003.
65. E.Demir, O.Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, and M. Ozturk,
“PATIKA: An integrated visual environment for collaborative construction and analysis of
cellular pathways”, Bioinformatics, Vol. 8, No. 7, pp. 996–1003, 2002.
66. A. Gürsoy and I. Cengiz, “Parallel Pruning for K-means clustering pn Shared Memory Architectures”, Europar’2001, LNCS Vol. 2150, pp. 321-325, 2001.
67. A. Gürsoy and M. Atun, “Neighbourhood Preserving Load Balancing: A Self Organizing
Approach”, Europar’2000, LNCS Vol 1900 pp. 234-241, 2000.
68. L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gürsoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. “NAMD2: Greater scalability for parallel molecular
dynamics”, Journal of Computational Physics, 151, 283-312, 1999.
69. M. Nelson, W. Humphrey, A. Gürsoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, “NAMD- A
Paralel Object-Oriented Molecular Dynamics Program”, International Journal of Supercomputing Applications, Vol. 10, No. 4, , pp. 251-268, 1996.
70. M. Nelson, W. Humphrey, A. Gürsoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, R.Kuffrin,
“MDScope - A Visual Computing Environment for Structural Biology”, Computer Physics
Communications, Volume 91, Oct 1995, pages 111-134, 1995.
Book Chapters:
1. J. Planas-Iglesias, J. Bonet, M.A. Marin-Lopez, E. Feliu, A. Gursoy, and B. Oliva, Structural
Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from
Sequence, in Protein-Protein Interactions-Computational and Experimental Tools, edited by
Weibo Cai and Hao Hong, 2012, InTech.
2. Kuzu G, Keskin O, Gursoy A, Nussinov R., Expanding the conformational selection paradigm
in protein-ligand docking., Methods Mol Biol. 2012;819:59-74.
3. O. Keskin, A. Gursoy, and R. Nussinov., Principles of protein recognition and properties of
protein-protein interfaces. (2008), in Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (Computational Biology) (ed. A. Panchenko, T.
Przytycka) Springer.
4. O. Keskin, R. Nussinov and A. Gursoy., PRISM: Protein-protein Interaction prediction by
Structural Matching. (2008), in Functional Proteomics: Methods and Protocols (Methods in
Molecular Biology) (ed. J. D. Thompson, C. Schaeffer-Reiss, M. Ueffing . Humana Press.
Edited Books:
1. U. Gudukbay, T. Dayar, A. Gursoy, and E. Gelenbe, eds., Advances in Computer and Information Sciences ’98: Proceedings of the 13th International Symposium , 1998.
Publications in refereed conference proceedings:
1. D. Demircioglu, O. Keskin, A. Gursoy, ”Modeling Structural Protein Interaction Networks
for Betweenness Analysis”, 29th International Symposium on Computer And Information
Sciences, October 27-28, 2014, Krakow, Poland.
2. S. Kalyoncu, O. Keskin, A. Gursoy, ”Interaction prediction of PDZ domains using a machine
learning approach”, 2010 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), pp. 121-124, Antalya, 2010.
3. G. Kar, A. Gursoy, O. Keskin, ”Determination of the correspondence between mobility (rigidity) and conservation of the interface residues”, 2010 5th International Symposium on Health
Informatics and Bioinformatics (HIBIT), pp. 159-161, Antalya, 2010.
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4. M. Ozboyaci, O. Keskin, B. Erman, A. Gursoy, ”Computational analysis of the binding free
energy of H3K9me3 peptide to the tandem tudor domains of JMJD2A”, 2010 5th International
Symposium on Health Informatics and Bioinformatics (HIBIT), pp. 81-87, Antalya, 2010.
5. B. Ozgur, A. Gursoy, O. Keskin, ”Relation between kinetic conversion rates and ANM mode
frequencies”, 2010 5th International Symposium on Health Informatics and Bioinformatics
(HIBIT), pp. 88-92, Antalya, 2010.
6. B. Unal, A. Gursoy, B. Erman, ”Inhibitor peptide design for NF-B: Markov model and genetic algorithm”,2010 5th International Symposium on Health Informatics and Bioinformatics
(HIBIT), pp. 72-80, Antalya, 2010.
7. A. Palazoglu, Y. Arkun, B. Erman, A. Gursoy, Probing Protein Folding Dynamics Using
Multivariate Statistical Techniques, ADCHEM 2009
8. E. Guney, N. Tuncbag, O. Keskin, and A. Gursoy, ”Large Scale Identification of Spatial
Motifs on the Protein-Protein Interfaces”, HIBIT 2008 International Symposium on Health
Informatics and Bioinformatics, Istanbul, 8-20 May 2008,
9. A.O Abali, E. Erzin, A. Gursoy, Learning Gene Regulation from Microarray Data via Hidden
Markov Models,,IEEE SIU, June, 2007, Eskisehir.
10. A. Erdem and A. Gürsoy, “Time Domain Web Based Usage Mining”, Proc. of IASTED
Artificial and Computational Intelligence, Tokyo, Sep 2002, pp 273-279, 2002.
11. A. Gürsoy and İ. Cengiz “Mechanism for Programming SMP Clusters”, Proc. of Intl Conf.
Parallel and Distributed Processing Techniques and Applications, PDPTA’99, Ed. H.R. Arabnia, Las Vegas, June 28- July 1, 1999 , Vol IV pp. 1723-1729, 1999.
12. İ. Cengiz and A. Gürsoy “Node-level Replicated Objects in SMP Clusters” Proc. of the 14th
Intl. Symp. on Computer and Information Sciences, ISCISXIV, Ed. M Turksever et al.
October 18-20, 1999, Kusadasi - Turkey, pp. 296-303, 1999.
13. M. Atun and A. Gürsoy “A New Load Balancing Algorithm Using Self-Organizing Maps”
Proc. of the 14th Intl. Symp. on Computer and Information Sciences, ISCISXIV, Ed. M
Turksever et al. October 18-20, 1999, Kusadasi - Turkey, pp. 787-794, 1999.
14. R. Şireli and A. Gürsoy, “Parallel Hierarchical Radiosity”, Proc. of Intl Conf. Parallel and
Distributed Processing Techniques and Applications, PDPTA’99, Ed. H.R. Arabnia, Las
Vegas, June 28- July 1, 1999 , Vol III pp. 1634-1640 Las Vegas, June 28- July 1, 1999.
15. J.C. Phillips, R. Brunner, A. Shinozaki, M. Bhandarkar, N. Krawetz, A. Gürsoy, L. Kale, R.D.
Skeel, and K. Schulten, “Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD
Code”, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in
Computational Science and Engineering, Vol 4. Springer, Berlin, 1999.
16. M. Atun, İ. Cengiz, R. Şireli, and A. Gürsoy, “Implementation of Converse Interoperable
Programming Environment on Parsytec CC Multicomputers”, Advances in Computer and
Information Sciences’98, Ed. Gudukbay et al. IOS/Ohmsha 1998, pages 367-374, 1998.
17. A. Gürsoy and L.V. Kale, “Simulating Message Driven Programs”, Proc. of ICPP, Chicago,
Aug 1996, Vol. III pp. 223-230, 1996.
18. L.V. Kale, A. Gürsoy, “Modularity, reuse, and efficiency with message-driven libraries”, Proceedings of the Seventh SIAM Conference on Parallel Processing For Scientific Computing,
San Fransisco, California, Feb 15-17 1995, pages 738-743, 1995.
19. M. Nelson, W. Humphrey, A. Gürsoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, R.Kuffrin,
“MDScope - A Visual Computing Environment for Structural Biology” , Proc. of the Intl.
Conf. on Computational Engineering Science, July 30 - August 3 , 1995, Hawaii, 1995, Volume
1, pages .476-481 Editors: S.N.Atluri, G.Yagawa, T.A.Cruse, Springer-Verlag, 1995.
20. A. Gürsoy and L.V. Kale, “Dagger: combining the benefits of synchronous and asynchronous
communication styles”, Proceedings of IPPS’94, April 1994, Cancun, pages 590-596, 1994.
21. L.V. Kale, A. Sinha, A. Gürsoy, “A Portable Software Support System for Irregular Computations”, DIMACS93, 1994.
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22. A. Gürsoy, L.V. Kale, and S.P. Vanka, “Unsteady fluid flow calculations using a machine
independent parallel programming environment”, In R. B. Pelz, A. Ecer, and J.Hauser, editors,
Parallel Computational Fluid Dynamics ’92, pages 175-185. North-Holland, 1993.
23. L.V. Kale, A. Gürsoy, “Performance Benefits of Message Driven Executions”, Intel Supercomputer User’s Group, Annual North America Users’ Conference, October 3-6, 1993, pages
209-129, 1993.
24. A. Gürsoy and L.V. Kale, “Tolerating Latency with Dagger”, International Symposium on
Computer and Information Sciences, ISCIS VIII, November 1-3, 1993, Istanbul, Turkey, pages
354-361, 1993.
25. A. Gürsoy and L.V. Kale, “High-Level Support for Divide-and-Conquer Parallelism”, Proceedings of Supercomputing’91, Albuquerque, NM., November 1991, pages 283-282, 1991.
Conference presentations and posters :
Oral Presentations
1. S.E. Acuner Ozbabacan, O. Keskin, R. Nussinov, A. Gursoy., Intelligent Systems for Molecular Biolgy, July, 2012, Long Beach, California Enriching the human apoptosis pathway by
predicting the structures of protein-protein complexes (Highlight Presentation),
2. HB Engin, A. Gursoy. B. Oliva, E. Guney, O. Keskin, Systems Level Analysis of Breast
Cancer Reveals the Differences between Lung and Brain Metastasis through Protein-Protein
Interactions, ISMB, Intelligent Systems for Molecular Biology, July, 2013, Berlin
3. E. Ozbabacan, A. Gursoy, O. Keskin, Apoptoz yolaginin protein-protein etkilesim aglari ile
incelenmesi, 10. Ulusal Kimya Muhendislik Kongresi, Sep, 2012, Istanbul
4. H. B. Engin, R. Nussinov O. Keskin, A. Gursoy, A New Network Attack Strategy Mimicking
Drug Mechanism: Interface Attack, ICREA Conf on Network Medicine Approaches to Human
Disease: from Computers to the Clinics, Nov, 2011, Barcelona
5. A. Gursoy, “Large Scale Construction of Three Dimensional Protein-Protein Complex Structures”, Molecular Perspectives on Protein-Protein Interactions, ESF-EMBO Symposium, Sant
Feliu de Guixols, Spain, Nov 2010.
6. O. Sonmez, A. Gursoy, “Novel Economic-based Scheduling Heuristics for Computational
Grids”, International Conference on Computational Science and Engineering Jun 2005, Istanbul, Turkey.
Poster Presentations
7. E. Sen, F. Halakou, O. Keskin, A. Gursoy, Network analyses to identify protein-interactions
responsible for lung and brain metastasis differentiation of breast cancer, 23rd International
Conference on Intelligent Systems for Molecular Biology, ISMB 2015, Dublin.
8. E.S Ozdemir, O Keskin, A Gursoy, Analysis of SNPs on protein-protein interfaces, Basel
Computational Biology Conference, Basel, Switzerland, June 2015.
9. EG Maiorov, O. Keskin, A. Gursoy, R. Nussinov, A structural view into signaling and regulation of Toll-like receptor pathway and its implications in inflammation and cancer crosstalk,
23rd International Conference on Intelligent Systems for Molecular Biology, ISMB 2015,
Dublin.
10. TS. Chavan, BC. Freed, H Jang, L Khavrutskii MA. Dyba, SG. Tarasov, A Gursoy, O Keskin, NI. Tarasova, V Gaponenko, R Nussinov, GTP-Dependent K-Ras Dimerization, 23rd
International Conference on Intelligent Systems for Molecular Biology, ISMB 2015, Dublin.
11. S. Muratcioglu, B. Freed, H. Yang, L. Khavrutskii, M. Dyba, S. Tarasov, A. Gursoy, O. Keskin,
N. Tarasova, V. Gaponenko, T. Chavan, R. Nussinov, Identification of effector binding sites
on H-Ras explains signal propagation, ISMB, Intelligent Systems for Molecular Biology, July,
2014, Boston
12. AD Cavga, N. Karahan, G. Kar, O. Keskin, A. Gusoy, B. Ozkan, Investigating the relationship
between characteristics of protein-protein interfaces and binding affinity, ISMB, Intelligent
Systems for Molecular Biology, July, 2014, Boston
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13. HB Engin. E. Guney, B. Oliva, A. Gursoy, O. Keskin, Structure to Protein-Protein Interaction Networks that Drive Metastasis to Brain and Lung in Breast Cancer, ISMB, Intelligent
Systems for Molecular Biology, July, 2014, Boston
14. G. Kuzu, O. Keskin. R. Nussinov A. Gursoy, Modeling protein assemblies in the proteome,
ISMB, Intelligent Systems for Molecular Biology, July, 2014, Boston
15. Selin Karagulle, Ozlem Keskin, Attila Gursoy, Critical assessment of the methods and the
features used for hot spot residue prediction at protein-protein interfaces, ISMB, Intelligent
Systems for Molecular Biology, July, 2013, Berlin
16. E. Cukuroglu, A. Gursoy, O. Keskin, Database of Protein Interface Clusters, Sao Paulo School
of Advances Science, Apr, 2012, Brazil
17. G. Kuzu, A. Gursoy, O. Keskin, Different conformations in the Protein Data Bank help in the
protein-protein interaction prediction by knowledge-based methodology, Sao Paulo School of
Advances Science, Apr, 2012, Brazil
18. G. Kuzu, C. Ulubas, O. Keskin, A. Gursoy, “Assessment of protein interaction prediction from
sequence data using n-gram analysis”, ISMB-International conference on Intelligent Systems
for Molecular Biology (ISMB), Vienna, July 2011.
19. E. Guven, O. Keskin, A. Gursoy, “Identification of Interconnected Markers for T-cell Acute
Lymphoblastic Leukemia”, ISMB-International conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, July 2011.
20. S. Beldar, O. Keskin, H. Kavakli, A. Gursoy, “Structure Based Analysis of the Interactions
between PAS Domain Containing Circadian Clock Proteins”, , ISMB-International conference
on Intelligent Systems for Molecular Biology (ISMB), Vienna, July 2011.
21. G. Kar, O. Keskin, A. Gursoy, R. Nussinov,“An interface analysis of human E2-E3 complexes:
structural insights into specificity”, ISMB-International conference on Intelligent Systems for
Molecular Biology (ISMB), Vienna, July 2011.
22. B. Engin, O. Keskin, A. Gursoy, A New Network Attack Strategy Mimicking Drug Mechanism:
Interface Attack, ISMB-International conference on Intelligent Systems for Molecular Biology
(ISMB), Vienna, July 2011.
23. H. Peynirci, O. Keskin, A. Gursoy, “Bottleneck Analysis in ProteinInterfaceProtein Interaction Networks”, ISMB-International conference on Intelligent Systems for Molecular Biology
(ISMB), Vienna, July 2011.
24. E. Cukuroglu, A. Gursoy, O. Keskin,“HotRegion: A web server of cooperative hot spots”,
ISMB-International conference on Intelligent Systems for Molecular Biology (ISMB), Vienna,
July 2011.
25. E. Cukuroglu, A. Gursoy, O. Keskin, “HotRegion: A web server of cooperative hot spots,
Hotspots at protein interfaces”, E. Cukuroglu, A. Gursoy, O. Keskin, 3DSIG-ISMB, Vienna,
July 2011.
26. N. Tuncbag, R. Nussinov, A. Gursoy,O. Keskin, “PRISM, N. Tuncbag, O. Keskin, R. Nussinov”, Protein Society, 2011, Boston, USA 27. N. Tuncbag, R. Nussinov, A. Gursoy,O. KeskinPrediction of protein-protein interactions at
genome scale, N. Tuncbag, R. Nussinov, A. Gursoy,O. Keskin, 55th Biophysical Society Annual
Meeting, Baltimore, USA, 2011.
28. Billur Engin, Attila Gursoy, Ozlem Keskin, “ A New Network Attack Strategy Mimicking
Drug Mechanism: Interface Attack”, 6th Int Symp on Health Informatics and Bioinformatics,
Izmir, April 2011.
29. Emine Guven Maiorov, Gunes Gundem, Attila Gursoy, Ozlem Keskin, “Revealing Temporal and Functional Relations in Breast Cancer Expression Profile using Biclustering Based
Analysis”, 6th Int Symp on Health Informatics and Bioinformatics, Izmir, April 2011.
30. Saliha Ece Ozbabacan, Ozlem Keskin, Attila Gursoy, Ruth Nussinov, “Prediction of ProteinProtein Interactions in the Human Apoptosis Pathway”, 6th Int Symp on Health Informatics
and Bioinformatics, Izmir, April 2011.
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31. N. Tuncbag, O.Keskin, A. Gursoy, ”HotPOINT: Hot Spot Prediction Server for Protein Interfaces”, 18th Intl Conf on Intelligent Systems and Molecular Biology, Boston, 2010.
32. S.E. Ozbabacan, O. Keskin, A. Gursoy, ”Prediction of Protein-Protein Interactions in the
Apoptosis Pathway”, 18th Intl Conf on Intelligent Systems and Molecular Biology, Boston,
2010.
33. B. Engin, A. Gursoy, O. Keskin, ”Interface and Interaction Networks”, 18th Intl Conf on
Intelligent Systems and Molecular Biology, Boston, 2010.
34. G. Kar, O. Keskin, A. Gursoy, ”The human E3 ubiquitin ligase enzyme protein interaction
network”, 18th Intl Conf on Intelligent Systems and Molecular Biology, Boston, 2010.
35. N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin, ”Large scale construction of three-dimensional
protein-protein complex structures in human proteome”, 3DSIG 2010, Boston.
36. N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin, ”Large scale construction of three-dimensional
protein-protein complex structures” RECOMB 2010, Lisbon.
37. S. Kalyoncu, O. Keskin, A. Gursoy, ”A Machine Learning Approach for Prediction of PDZ
Domain Interactions”, RECOMB 2010, Lisbon.
38. N. Tuncbag, O. Keskin, A. Gursoy, ”HotPOINT: Hot Spot Prediction Server for Protein
Interfaces”, RECOMB 2010, Lisbon.
39. G. Kar, O. Keskin, Nussinov, A. Gursoy, The human E3 ubiquitin ligase enzyme protein
interaction network, 9th European Conference on Computational Biology, Ghent, Belgium,
Sep 2010.
40. S.E. Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov, Prediction of protein-protein interactions in the apoptosis pathway, 9th European Conference on Computational Biology, Ghent,
Belgium, Sep 2010.
41. E. Cukuroglu, A. Gursoy, O. Keskin, Hub protein interfaces and hot region organization, 9th
European Conference on Computational Biology, Ghent, Belgium, Sep 2010.
42. B. Engin, A. Gursoy, O. Keskin, Attacking interface and interaction networks, 9th European
Conference on Computational Biology, Ghent, Belgium, Sep 2010.
43. N. Tuncbag, A. Gursoy, O. Keskin, R. Nussinov, ”Architectures and Functional Coverage of
Protein Interfaces”, ISMB/ECCB 2009, 3DSIG, Stockholm.
44. S. Ozbabacan, A. Gursoy, O. Keskin, Identification of Protein-protein interaction domains,ISMB
2009
45. B. Engin, E. Tuzun, A. Gursoy, O. Keskin, Attacking Interface and Interaction Networks,
ISMB 2009
46. G. Kar, A. Gursoy, O. Keskin,Human Protein-protein Interaction Network: A structural
Perspective, ISMB2009
47. N. Tuncbag, A. Gursoy, O. Keskin, Identification of Computational Hot Spots in Protein
Interfaces Using Solvent Accessibility and Inter-Residue Potentials, ISMB 2009
48. E.B. Unal, B. Erman, A. Gursoy, Conformational energies and entropies of peptides. Dependence on sequence type, and relation to peptide-protein binding, ISMB 2009
49. Guney E., Tuncbag N., Gursoy A., Keskin O., Large Scale Prediction of Computational Hot
Spots in Protein Interfaces, ECCB08 European Conference on Computational Biology, Sep
2008, Cagliari, Italy.
50. Kar G., Gursoy A., Keskin O. , Characterization of Protein Interfaces in the Human Cancer Protein-Protein Interaction Network, ECCB08 European Conference on Computational
Biology, Sep 2008, Cagliari, Italy.
51. Tuncbag N, Guney E, Ulubas C, Keskin O,Gursoy A, PRISM: A Web Server for Prediction
and Visualization of Protein-Protein Interaction, ISMB-ECC, July, 2007, Vienna
52. Guney E, Tuncbag N, Gursoy A, Keskin HotSprint: Database of Computational Hot Spots
at Protein Interfaces, ISMB-ECC, July, 2007, Vienna
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53. G. Kar, O.Keskin, A.Gursoy,Determination of the corespondence between mobility (rigidity)
and conservation of the interface residues, July, 2007, Vienna
54. A.S. Aytuna, O. Keskin, A. Gursoy, “A Novel Algorithm for Automated Prediction of ProteinProtein Interactions”, Intelligent Systems for Molecular Biology, August 2004, Glasgow, Scotland, UK.
Graduate Research Thesis Advising
PhD degrees granted
1. Emine Guven Mairov, Understanding the Relation of Cancer and Inflammation by Constructing Structural Toll-like Receptor Pathway, Koc University, August, 2015
2. Engin Cukuroglu, Clustering protein interfaces and their analysis, Koc University, January
2015
3. Guray Kuzu, Modeling protein assemblies in the proteome, Koc University, October 2014.
4. Billur Engin, A Novel Structural Protein-Protein Interaction Network Model: Its Applications
on Drug Off-Target Prediction and Genotype-Phenotype Linkage, Koc University, 2013.
5. Ece Ozbabacan, Reconstruction and Structural Analysis of Human Protein-Protein Interaction Networks for Apoptosis and Inflammatory Pathways and Implications for Cancer, Koc
University, 2013.
6. Gozde Kar, Large Scale Integration of Protein Structural Data into Protein-Protein Interaction
Networks, Koc University, 2012.
7. Nurcan Tuncbag, Multi-Scale Analysis and Prediction of Protein-Protein Interactions, Koc
University, 2010.
8. Besray Unal, De Novo Peptide Design Strategies, 2011.
M.Sc. degrees granted
1. Alper Baspinar, PRISM 2.0: Optimizing PRISM and Designing a Web Server for Structural
Modeling of Protein ? Protein Interactions, September, 2015
2. Emel Sen Kilic, Network Analyses to Identify Candidate Proteins and Interactions Responsible
for Breast Cancer Lung and Brain Metastasis Differentiation, July 2015
3. Deniz Demircioglu, Performance and Accuracy Analysis of iMatch: A Structural Alignment
Tool Prototype for Protein Binding Site Surface Alignment, July, 2015
4. Tayfun Tumkaya, Critical Assessment of the Methods and the Features Used for Hot Spot
Prediction at Protein-Protein Interfaces , July 2014.
5. Selin Karagulle, Critical Assessment of the Methods and the Features Used for Hot Spot
Prediction at Protein-Protein Interfaces , May 2014.
6. Pelin Atici, Automation of PRISM Algorithm for Prediction of Protein-Protein Interactions,
Aug 2013.
7. Busra Topal, Interfaces of Intrinsically Disordered Proteins, March 2013, (co-advisor)
8. Tugce Yildizoglu, Computational Analysis of binding preferences of PICK1 for its PDZ partners, Oct 2012, (co-advisor)
9. Serap Beldar,Structure Based Analysis of the Interactions Between PER-ARNT-SIM (PAS)
Domain Containing Proteins in Circadian Rhythm, December 2011, (co-advisor)
10. Omer An, Structural and functional analysis of perforin mutations in association with clinical
data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients, December 2011,
(co-advisor)
11. Engin Cukuroglu, Hot Regions in ProteinProtein Interactions and Analysis of Hot Region
Distribution in Hub Proteins, August 2011, (co-advisor)
12. Emine Guven, Identification of Interconnected Markers for T-cell Acute Lymphoblastic Leukemia,
August 2011, (co-advisor)
12
13. Osman Eryurt, Identifying gene regulatory communities from microarray time-series espression profiles using HMM, August 2011
14. Beytullah Ozgur, Protein intrinsic normal modes are correlated with pre-existing conformer
populations, October 2010, (co-advisor)
15. Sibel Kalyoncu, PDZ Domains: Interaction Prediction, Classification and Peptide Library
Construction, November 2010 (co-advisor)
16. Deniz Sanli, Determination of Statistical Correlations Between Methylated Lysine Residues
of Histone H3 Tail by Molecular Dynamics Simulations, Sep 2009, (co-advisor)
17. Ozlem Ulucan, A Comparative Molecular Dynamics Study of Methylation State Specificity of
JMJD2A, August 2009, (co-advisor)
18. Musa Ozboyaci, Molecular Recognition of the Methylated Histone Peptides by the Tandem
Tudor Domains of JMJD2A, Sep 2009, (co-advisor)
19. Cengiz Ulubas, Critical Assessment of Protein-Protein Interaction Databases and Features
towards Prediction of Interactions, June 2009
20. Gozde Kar, Analysis of human protein-protein interaction network and cancer proteins using
structural information, Sep 2008, (co-advisor)
21. Emre Guney, Large Scale Characterization of Protein Interactions: Identification of Hot Spots
and Spatial Motifs in Protein-Protein Interfaces, 2007.
22. Gunes Gundem, Revealing Temporal and Functional Relations in Breast Cancer Expression
Profile Using Biclustering Based Analysis, (co-advisor) 2006
23. Utkan Ogmen, PRISM: A System for the Query, Visualiztion and Analyis of Protein Interfaces
abd Their Networks, 2006
24. Ozan Sonmez, Scheduling in a Computational Grid Economy System , Koc Univesity, 2005,
25. Meric Ovacik, Statistical Mechanics and Local Dynamics of Denaturated Proteins, Koc University, (2005) (co-advisor)
26. Alper Kocatas, Integrating gene expression, protein interaction and protein domain data to
improve gene expression clustering, Koc Univ., (2005)
27. Ali Selim Aytuna, A high-performance algorithm for automated prediction of protein-protein
interactions, Koc Univ., (2005),
28. Gurkan Nisanci, Neon: A script based software framework for querying cellular pathways,
Bilkent Univ., (2003),
29. Alpay Erdem, Time domain based web usage mining for web site improvement, Bilkent Univ.,
(2002),
30. Hayreddin Bahsi, Inferring phylogenetical tree by using hierarchical self-organizing maps,
Bilkent Univ., (2002),
31. Cenk Sen, Data decomposition techniques for parallel tree-based k-means clustering, Bilkent
Univ., (2002),
32. Erdogan Bikmaz, Balancing computation load and communication overhead with multilevel
self-organizing maps, Bilkent Univ., (2001),
33. Murat Atun, A new load balancing heuristic using self-organizing maps, Bilkent Univ., (2000),
34. Ilker Cengiz, Programming SMP clusters: Node-level object groups and their use in a framework for nbody applications, Bilkent Univ., (2000),
35. Murat Atun, A new load balancing heuristic using self-organizing maps, Bilkent Univ., (2000),
36. A. Resat Sireli, Parallelization of hierarchical radiosity algorithms on distributed systems,
Bilkent Univ., (1998),
M.Sc. thesis students supervised at present:
• Bilgesu Erdogan
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• Cemal Yamak
• Dogus Dogru
• Emre Buyuktuna
• Efe Elbeyli
• Gulden Hazal Karadag
• Mahan Rajaei Golsefidi
PhD thesis students supervised at present:
• Ayse Derya Cavga
• Nilay Karahan
• Farideh Harakou
• Serena Muratcioglu
• Emine Sila Ozdemir
Teaching - Courses taught:
Undergraduate level:
Introduction to Programming and Algorithms (JAVA)
Data Structures and Algorithms (in C++ and Java)
Programming Language Concepts
Software Engineering
Concurrent Programming
Database Systems
Distributed Systems
Computer Architecture
Graduate level:
Bioinformatics and Algorithms for Computational Biology
Parallel Programming Languages
Parallel Methods for Scientific Computations
Parallel Computing
Introduction to Computational Science
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