Publications

2024

  • Damla Ovek, Ozlem Keskin, and Attila Gursoy, ProInterVal: Validation of Protein–Protein Interfaces through Learned Interface Representations, Journal of Chemical Information and Modeling, March 2024.
  • ME Zeylan, S Senyuz, P Picón-Pagès, A García-Elías, M Tajes, FJ Muñoz, Baldomero Oliva, Jordi Garcia-Ojalvo, Eduard Barbu, Raul Vicente, Stanley Nattel, Angel Ois, Albert Puig-Pijoan, Ozlem Keskin, Attila Gursoy, Shared Proteins and Pathways of Cardiovascular and Cognitive Diseases: Relation to Vascular Cognitive Impairment, J. Proteome Res. 2024, 23, 2, 560–573
  • K Kosoglu, Z Aydin, N Tuncbag, A Gursoy, O Keskin, Structural coverage of the human interactome, Briefings in Bioinformatics, 25 (1),
  • AZ Sayin, Z Abali, S Senyuz, F Cankara, A Gursoy, O Keskin, Conformational diversity and protein–protein interfaces in drug repurposing in Ras signaling pathway, Scientific Reports 14 (1), 1239

2023

  • E Celik, G Ozcan, C Vatansever, E Paerhati, MA Kuskucu, O Dogan, SG Cekic, O Ergonul, A Gursoy, O Keskin, F Can , Alterations in vaginal microbiota among pregnant women with COVID-19,Journal of Medical Virology 2023 95 (1), e28132.
  • Picon-Pages et al. A Genome-Wide Functional Screen Identifies Enhancer and Protective Genes for Amyloid Beta-Peptide Toxicity,  Int. J. Mol. Sci. 2023, 24, 1278.

2022

  • H Lim, CJ Tsai, O Keskin, R Nussinov, A Gursoy, HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry, Bioinformatics, 2022, 38 (21), 4962-4965.
  • E Ozkan, O Celebi, O Keskin, A Gursoy, Y Gursoy-Ozdemir, Is persistent post-COVID headache associated with protein-protein interactions between antibodies against viral spike protein and CGRP receptor?: a case report , Frontiers in Pain Research, 2022, 3, 858709.
  • H Lim, F Cankara, CJ Tsai, O Keskin, R Nussinov, A Gursoy, Artificial intelligence approaches to human-microbiome protein-protein interactions, Current Opinion in Structural Biology, 2022, 73, 102328.
  • D Ovek, A aweel, Z Abali, E Tezsezen, YE Koroglu, C Tsai, R Nussinov, O Keskin, A Gursoy,  SARS-CoV-2 interactome 3D: a web interface for 3D visualization and analysis of SARS-CoV-2 human mimicry and interactions, Bioinformatics, 2022, 38 (5), 1455-1457.
  • D Ovek, Z Abali, ME Zeylan, O Keskin, A Gursoy, N Tuncbag, Artificial intelligence based methods for hot spot prediction, Current Opinion in Structural Biology, 2022, 72, 209-218.

2021

  • Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O. Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics, J Phys Chem B. 2021 May ;125(20):5210-5221.
  • Senyuz S, Jang H, Nussinov R, Keskin O, Gursoy A. Mechanistic Differences of Activation of Rac1P29S and Rac1A159V,  J Phys Chem B. 2021 Apr;125(15):3790-3802.
  • Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir Yilmaz B, Dinler Doganay G. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation,PLoS One, 2021 Aug ;16(8):e0256640.
  • Yapici-Eser H, Koroglu Y. E, Oztop-Cakmak O, Keskin O, Gursoy A, Gursoy-Ozdemir Y, Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins’ Mimicry of Human Protein Interactions“, Frontiers in Human Neuroscience, 2021 15:126
  • Weako J, Jang H, Keskin O, Nussinov R, Gursoy A, The Structural Basis of Akt PH Domain Interaction with Calmodulin“, Biophys J. 2021 Mar 25:S0006-3495(21)00248-4.
  • Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V,  Inhibition of Nonfunctional Ras“. Cell Chem Biol. 2021 Feb 18;28(2):121-133.

2020

  • Morova T, McNeill DR, Lallous N, Gonen M, Dalal K, Wilson DM, Gursoy A, Keskin O, Lack N, Androgen receptor-binding sites are highly mutated in prostate cancer, Nat Commun. 2020;11(1):832. Published 2020 Feb 11.
  • Guven-Maiorov E, Hakouz A, Valjevac S, Keskin O, Tsai CJ, Gursoy A, Nussinov A, HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry“, J Mol Biol. 2020;432(11):3395-3403.
  • Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R, Kavakli IH, Gursoy A, Keskin O, Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling, J Mol Biol. 2020;432(4):1199-1215.
  • Yang X, Cheng H, Chen J, Wang R, Saleh A, Si H, Lee S, Guven-Mairov E, Keskin O, Gursoy A, Nussinov R, Fang J, Van Waes C, Chen Z, Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-kB Pathways“, Cancer Immunol Res. 2019;7(11):1760-1774.
  • Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N. 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients“, PLoS Comput Biol. 2019;15(9):e1006789.
  • Pooley JR, Rivers CA, Kilcooley MT, Paul SN, Cavga AD, Kershaw YM, Muratcioglu S, Gursoy A, Keskin O, Lightman SL, Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA“, PLoS One. 2020;15(1):e0227520.
  • Weako J, Uba AI, Keskin O, Gursoy A, Yelekci K.,Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies“, Comput Biol Chem. 2020;86:107244.

2019

  • Ozdemir ES, Nussinov R, Gursoy A, Keskin O., Developments in integrative modeling with dynamical interfaces, Curr Opin Struct Biol. 2019 Jun;56:11-17. doi: 10.1016/j.sbi.2018.10.007. Epub 2018 Nov 12.
  • Cavga AD, Tardu M, Korkmaz T, Keskin O, Ozturk N, Gursoy A, Kavakli IH., Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level, Funct Integr Genomics. 2019 Sep;19(5):729-742. doi: 10.1007/s10142-019-00680-5. Epub 2019 May 1.
  • Uba AI, Weako J, Keskin O, Gursoy A, Yelekci K., Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation“, J Biomol Struct Dyn.2019 May 5:1-10.

2018

  • Ozdemir ES, Gursoy A, Keskin O, Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces, Bioinformatics, 34 (17), i795-i801, 2018
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R,  Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEdelta“, The Journal of Physical Chemistry B. 122 (30), 7503-7513, 2018
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R., Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2, Journal of Biological Chemistry, 2018

2017

  • Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R., PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization, J Phys Chem B. 2017 Jun 22;121(24):5917-5927.
  • Ozgur B, Ozdemir ES, Gursoy A, Keskin O.,  Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations, J Phys Chem B. 2017 Apr 20;121(15):3686-3700.
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A., Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information, Methods Mol Biol. 2017;1558:255-270.

2016

  • Kuzu G, Keskin O, Nussinov R, Gursoy A., PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.  Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1137-1148.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry., Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2646-55.
  • Tuncbag N, Gursoy A, Keskin O, Nussinov R., The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology., Expert Rev Proteomics. 2016 May;13(5):447-9.
  • Keskin O, Tuncbag N, Gursoy A., Keskin O, Tuncbag N, Gursoy A., Chem Rev. 2016 Apr 27;116(8):4884-909.
  • Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R., Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers., Biochem J. 2016 Jun 15;473(12):1719-32.
  • Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V.,  Plasma membrane regulates Ras signaling networks. Cell Logist. 2016 Feb 18;5(4):e1136374.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?,  Expert Opin Ther Targets. 2016 Jul;20(7):831-42.
  • Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J.,  Ras Conformational Ensembles, Allostery, and Signaling., Chem Rev. 2016 Jun 8;116(11):6607-65.

2015

  • Muratcioglu S, Guven-Maiorov E, Keskin O, Gursoy A., Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol. 2015 Nov 2;35:87-92.
  • 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.
  • 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.
  • 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.
  • 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
  • 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., GTP- Dependent K-Ras Dimerization, Structure. 2015 Jul 7;23(7):1325-35.
  • 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.
  • Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O., Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics. 2015 Dec;12(6):669-82

2014

  • 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.
  • 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).
  • 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).
  • Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Mol Cell Proteomics. 2014 Mar;13(3):887-96.
  • 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.
  • Acuner-Ozbabacan ES, Engin BH, Guven-Maiorov E, Kuzu G, Muratcioglu S, Baspinar A, Chen Z, Van Waes C, Gursoy A, Keskin O, Nussinov R., The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics. 2014;15 Suppl 4:S2. doi: 10.1186/1471-2164-15-S4-S2.
  • Cukuroglu E, Engin HB, Gursoy A, Keskin O., Hot spots in protein-protein interfaces: towards drug discovery. Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):165-73
  • Demircioglu D, Keskin O, Gursoy A., Modeling structural protein interaction networks for betweenness analysis. ISCIS2014 LCNS. 2014:367-76

2013

  • 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)
  • 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.
  • 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. 2013 May 22.
  • 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.
  • 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.
  • 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):2641-53.
  • Kar G, Keskin O, Fraternali F, Gursoy A. , Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 2013;19(18):3175-89.

2012

  • 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):2273-86
  • Kar G, Kuzu G, Keskin O, Gursoy A. , Protein-protein interfaces integrated into interaction networks: implications on drug design. Curr Pharm Des. 2012 May 29.
  • 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.
  • 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
  • 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.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Expanding the conformational selection paradigm in protein-ligand docking. Methods Mol Biol. 2012;819:59-74.
  • 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.

2011

  • 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, Nature Protocol, 2011 vol. 6 (9) pp. 1341-54.
  • Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33.
  • Sanli D, Keskin O, Gursoy A, Erman B. Structural cooperativity in histone H3 tail modifications. Protein Sci. 2011 Dec;20(12):1982-90. doi: 10.1002/pro.745.
  • O. Ulucan, O. Keskin, B. Erman, A. Gursoy, A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A, PLos ONE, 2011 vol. 6 (9) pp. e24664
  • S.E.A. Ozbabacan, H.B. Engin, A. Gursoy, O. Keskin, Transient protein-protein interactions, Protein Engineering Design & Selection, 2011 vol. 24 (9) pp. 635-48.
  • N. Tuncbag, A. Gursoy, O. Keskin, Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces, Phys Biol, 2011 vol. 8 (3) pp. 035006.
  • M. Ozboyaci, A. Gursoy, B. Erman, O. Keskin, Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study, PLos ONE, 2011 vol. 6 (3) pp. e14765.

2010

  • 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 representation of hotspots in protein interfaces using minimum cut trees, Protein-Structure Function and Bioinformatics, 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.

2009

  • 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

2008

  • 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.

2007

  • 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.

2006

  • 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

2005

  • 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

2004

  • 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.

2003

  • 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)

2002

  • 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

2001

2000

1999-

  • 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.
  • 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, 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, 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.
  • 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, Proceedings of Supercomputing’91, Albuquerque, NM., November 1991, pages 283-282.