• Kar G, Gursoy A, Keskin O, Human cancer protein-protein interaction network: A structural perspective, PLOS Computational Biology, 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.