- G. Kar, O. Keskin, A. Gursoy,
N. Nussinov, Allostery and population shift in drug discovery, Current
Opinion in Pharmacology, Sep, 2010.
- 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
- S. Kalyoncu, O. Keskin, A.
Gursoy,Interaction prediction and classification of PDZ domains, BMC
Bioinformatics, 11(357), 2010.
- N. Tuncbag, FS. Salman, O.
Keskin, A. Gursoy, Analysis and network representtion of hotspots in
protein interfaces using minimum cut trees, Protein-Structure Function and
Bioin- formatics, 78(10), pp. 2283-2294, 2010.
- EB. Unal, A. Gursoy, B. Erman,VitAL:
Viterbi algorithm for de novo peptide design, PLOS One, 5(6), e10926,
2010.
- N. Tuncbag, O.Keskin, A.
Gursoy, HotPoint: hotspot prediction server for protein interfaces, Nucl.
Acids. Res. (38) Web Server Issue, W402-W406, 2010.
- E. Cukuroglu, A. Gursoy, O. Keskin,
Analysis of Hot Region Organization in Hub Proteins, Annals of Biomedical
Engineering, 38(6), pp. 2068-2078, 2010.
- G. Kar, A. Gursoy, O. Keskin, Human
cancer protein-protein interaction network: a structural perspective, PLOS
Computational Biology, 5(12) , e1000601, Dec 2009
- Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R, Towards
inferring time dimensionality in protein_protein interaction networks by
integrating structures: the p53 example, Molecular BioSystems, 2009
- Unal B, Gursoy A, Erman B, Conformational energies and entropies of
peptides, and the peptide-protein binding problem, Physical Biology 6,
2009
- Tuncbag N, Gursoy A, Keskin O, Identification of computational hot
spots in protein interfaces: combining solvent accessibility and
inter-residue potentials improves the accuracy, Bioinformatics, Volume: 25
Issue: 12 Pages: 1513-1520 , 2009
- Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R, A survey of
available tools and web servers for analysis of protein-protein interactions
and interfaces, Briefings in Bioinformatics, Volume: 10 Issue: 3
Pages: 217-232, 2009
- Gursoy A, Keskin O, Nussinov R., Topological properties of protein
interaction networks from a structural perspective, Biochemical Society
Transactions, Volume: 36 Pages: 1398-1403, 2008
- Tuncbag N, Gursoy A, Guney E, Keskin O, Nussinov R, Architectures and
functional coverage of protein-protein interfaces, Journal of Molecular
Biology, Volume: 381 Issue: 3 Pages: 785-802, 2008
- Keskin, O, Tuncbag, N, Gursoy, A, Characterization and
prediction of protein interfaces to infer protein-protein interaction
networks, Current Pharmaceutical Biotechnology, (9)2, 67-76, 2008.
- Guney, E, Tuncbag, N, Keskin, O, Gursoy, A, HotSprint: database of
computational hot spots in protein interfaces, Nucleic Acid Research, (36) D662-D666, 2008.
- O. Keskin, A. Gursoy,, B. Ma, R. Nussinov, Principles of
protein-protein interactions: What are the preferred ways for proteins to
interact?,Chemical Reviews, (108) 4, 1225-1244, 2008.
- Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple
proteins in a systems biology approach,
Current Topics in Medicinal Chemistry 7 (10): 943-951 2007
- 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.
- 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.
- 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
- 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
- O. Sonmez, A. Gursoy, ``Comparison of Fixed and Dynamic Pricing
Policies in a Computational Grid", LNCS 3911, pp. 766-773 (2006)
- O. Sonmez and A. Gursoy, "Comparison of Pricing Policies for a
Computational Grid Market", LNCS Vol. 3911 pp. 766-773, 2006 (PPAM
2005).
- 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). PRISM Web Server
- 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.
- A.K. Sinop, T. Abaci, U. Akkus, A. Gursoy, U. Gudukbay, "PHR: A
Paralllel Hierarchical Radiosity System with Dynamic Load Balancing",
Journal of Supercomputing, Vol 31, pp. 249-263, 2005
- A. Palazoglu, A. Gursoy, Y. Arkun and B. Erman, "Folding
Dynamics of Proteins from Denatured to Native State: Principal Component
Analysis", Journal of Computational Biology Dec 2004, Vol. 11, No. 6:
1149-1168.
- O. Keskin, D. Yuret, A. Gursoy, M. Turkay and B. Erman,
"Relationships between amino acid sequence and backbone torsion angle
preferences", Proteins: Structure, Function, and Bioinformatics, Vol
55 No 4 pp. 992-998, 2004.
- A, Gursoy, L.V. Kale, "Performance and Modularity Benefits of
Message-Driven Execution", Journal of Parallel and Distributed
Computing, 64(2004) 461-480
- E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G.
Nisanci and R. Cetin-Atalay, "An Ontology for Collaborative
Construction and Analysis of Cellular Pathways",
Bioinformatics, Vol 20 No 3 pp. 349-356, 2004.
- A. Gursoy, "Data Decomposition for K-Means Parallel
Clustering", LNCS Vol 3019 pp. 241-248, 2003 (PPAM
2003)
- A. Kocatas, A. Gursoy, R. Cetin-Atalay, "Application of Data
Mining Techniques to Protein-Protein Interactions", LNCS
Vol 2869 pp. 316-323, 2003 (ISCIS 2003)
- E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R.
Cetin-Atalay, M. Ozturk, "PATIKA: An Integrated Visual Environment
for Collaborative Construction and Analysis of Cellular Pathways",
Bioinformatics, Vol 18., No 7., pp. 996-1003 (2002)
- A. Erdem, A. Gursoy, "Time Domain Based Web Usage Mining",
Proceedings of the IASTED Artificial and Computational Intelligence 2002,
Pages:273-279 , Sep , 2002, Tokyo, Japan
- A. Gursoy and I. Cengiz "Parallel
Pruning For K-Means Clustering on Shared Memory Architectures",
LNCS Vol 2150 pp. 321-325
(Europar 2001)
- A. Gursoy and M. Atun "Neighbourhood
Preserving Load Balancing: A Self Organizing Approach",
LNCS Vol 1900 pp. 234-241
(Europar 2000)
- A. Gursoy and I. 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
- I. Cengiz and A. Gursoy ``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
- M. Atun and A. Gursoy ``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
- R. Sireli and A. Gursoy, ``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,
- L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, 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)
- J.C. Phillips, R. Brunner, A. Shinozaki, M. Bhandarkar, N. Krawetz, A.
Gursoy, 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 Enginering, Springer, Berlin, 1999.
- Edited Book:
U. Gudukbay, T. Dayar, A. Gursoy, and E. Gelenbe, eds., Advances in
Computer and Information Sciences '98: Proceedings of the 13th
International Symposium on Computer and Information Sciences, 26-28
October 1998, Antalya, Turkey, IOS Press/Ohmsha, 1998.
- M. Atun, I. Cengiz, R. Sireli, and A. Gursoy, ``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.
- A. Gursoy and L.V. Kale, ``Simulating
Message Driven Programs'', Proc. of ICPP, Chicago, Aug 1996, Vol. III
pp. 223-230
- M. Nelson, W. Humphrey, A. Gursoy, 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,
Winter 1996, pp. 251-268
- M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L.V. Kale, B. Skeel, K.
Schulten, R.Kuffrin, ``\mbox{MDScope} - A Visual Computing Environment for
Structural Biology'', Computer Physics Communications, Volume 91, Oct
1995, pages 111-134.
- L.V. Kale, A. Gursoy, ``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.
- M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L.V. Kale, B. Skeel, K.
Schulten, R.Kuffrin, ``\mbox{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.
- A. Gursoy and L.V. Kale, ``Dagger:
combining the benefits of synchronous and asynchronous communication
styles'', Proceedings of IPPS'94, April 1994, Cancun, pages 590-596.
- L.V. Kale, B. Ramkumar, A.B. Sinha, A. Gursoy, ``The Charm Parallel Programming
Language and System: Part I - Description of Language Features'', Technical
Report, Parallel Programming Lab., Dept. of Computer Science, University
of Illinois at Urbana-Champaign.
- A. Gursoy, 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.
- L.V. Kale, A. Gursoy, ``Performance Benefits of Message Driven
Executions'', Intel Supercomputer User's Group, Annual North America
Users' Conference, October 3-6, 1993, pages 209-129
- A. Gursoy 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
- L.V. Kale, A. Sinha, A. Gursoy, ``A Portable Software Support System
for Irregular Computations'', DIMACS93
- A. Gursoy and L.V. Kale, ``High-Level Support for Divide-and-Conquer
Parallelism'', {\em Proceedings of Supercomputing'91}, Albuquerque, NM.,
November 1991, pages 283-282.