Book chapters
1. Korkin D, Thieu T, Joshi S, Warren S. "Mining host-pathogen interactions", In: Bioinformatics - Experimental Biology Systems.Ed: Yang NS, INTECH, 2011; in press
Journals
18. Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. "DOMMINO: A database of macromolecular interactions"; Nucleic Acids Res. , in press17. Thieu T, Joshi S, Warren S, Korkin D. "Literature Mining of Host-Pathogen Interactions: Comparing Feature-based Supervised Learning and Language-based Approaches"; submitted
16. Renecker J, Lyons E, Conant G, Pires C, Freeling M, Shyu CR, Korkin D. "Long Identical Multispecies Elements in Plant Genomes"; submitted
15. Zhao N, Pang B, Shyu CR, Korkin D. "An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches"; Proteomics, 2011 Nov;11(22):4321-30
14. Zhao N, Pang B, Shyu CR, Korkin D "Charged Residues at Protein Interaction Interfaces: Unexpected Conservation and Orchestrated Divergence"; Protein Sci, 2011, Jul 20(7):1275-84
13. Zhao N, Pang B, Shyu CR, Korkin D. "Structural similarity and classification of protein interaction interfaces"; PLOS One, 2011 May 12;6(5):e19554
12. Wang Q, Korkin D, Shang Y. "A Fast Multiple Longest Common Subsequence (MLCS) Algorithm", IEEE Transactions on Knowledge and Data Engineering, 2011; Mar; vol. 23, no. 3: 321-33
11. Wang J, Joshi S, Korkin D, Mitchum MG. " Variable domain I of nematode CLEs directs post-translational targeting of CLE peptides to the extracellular space.", Plant Signal Behav, 2010; Dec 1;5(12)
10. Shyu CR, Pang B, Chi PH, Zhao N, Korkin D, Xu D. "ProteinDBS v2.0: a web server for global and local protein structure search", Nucleic Acids Res. , 2010; Jul 1;38 Suppl:W53-8
9. Wang J, Lee C, Replogle A, Joshi S, Korkin D, Hussey R, Baum TJ, Davis EL, Wang X, Mitchum MG. "Dual roles for the variable domain in protein trafficking and host-specific recognition of Heterodera glycines CLE effector proteins", New Phytol.,2010; May 20.
8. Chi PH, Pang B, Korkin D, Shyu CR. "Efficient SCOP fold classification and retrieval using index-based protein substructure alignments (IPSA)", Bioinformatics, 2009; Oct 1; Vol. 25(19):2559-65
7. Ahuja N, Korkin D, Smith DL, Chaba R, Cezairliyan BO, Sauer RT, Kim KK, and Gross CA. "Analyzing the Interaction of RseA and RseB, the Two Negative Regulators of the SigmaE Envelope Stress Response, Using a Combined Bioinformatic and Experimental Strategy", J. Biol. Chem. 2009; Feb 20; 284(8):5403-13
6. Anderson CM, Korkin D, Smith DL, Makovets S, Seidel J, Sali A, and Blackburn EH. "Tel2 mediates activation and localization of ATM/Tel1 kinase to sites of DNA damage", Genes. Dev. 2008; Apr 1; 22(7):854-9
5. Alber F, Forster F, Korkin D, Topf M, Sali A. "Integrating Diverse Data for Structure Determination of Macromolecular Assemblies", Annu. Rev. Biochem. 2008; Jul 7; 77:443-477
4. Korkin D, Davis FP, Alber F, Lucic V, Kennedy MB, Sali A. "Structural modeling of protein interactions by analogy: Application to PSD-95", PLoS Comput. Biol. 2006; 2(11): e153
3. Korkin D, Davis FP, Sali A. "Localization of protein binding sites", Protein Sci. 2005; 14(9):2350-60
2. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. "A structural perspective on protein-protein interactions", Curr. Opin. Struct. Biol. 2004; 14(3):313-24
1. Korkin D and Goldfarb L. "Multiple genome rearrangement: a general approach via the evolutionary genome graph", Bioinformatics. 2002; 18 Suppl 1:S303-11
Conference Proceedings
5. Zhao N, Pang B, Shyu CR, Korkin D "An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches", Proceedings on IEEE International Conference on Bioinformatics and Biomedicine, 2010; BIBM, pp. 185-1894. Wang Q, Pan M, Shang Y, Korkin D " A Fast Heuristic Search Algorithm for Finding the Longest Common Subsequence of Multiple Strings ", Proceedings of the 22nd International Joint Conference on Artificial Intelligence, 2010; AAAI-10
3. Wang J, Replogle A, Joshi S, Korkin D, Hussey R, Baum TJ, Davis EL, Wang X, and Mitchum MG. "Cellular targeting and host-specific recognition of cyst nematode CLE proteins", Biology of Plant-Microbe Interactions, Vol. 7, Congress on Molecular Plant-Microbe Interactions, Quebec City, 2009
2. Wang Q, Korkin D, Shang Y. "Efficient Dominant Point Algorithms for the Multiple Longest Common Subsequence (MLCS) Problem", Proceedings of the 21st International Joint Conference on Artificial Intelligence, 2009; IJCAI’09
1. Korkin D, Wang Q, Shang Y. "An Efficient Parallel Algorithm for the Multiple Longest Common Subsequence (MLCS) Problem", 37th International Conference on Parallel Processing, 2008; ICPP, pp.354-363
Conference Abstracts
Zhao N, Pang B, Shyu CR, Korkin D. "Structural classification and retrieval of protein interfaces: Detecting homology and analogy in protein interactions", The 17th International Conference on Intelligent Systems for Molecular Biology and 8th Europeam Conference on Computational Biology (ISMB/ECCB 2009), Stockholm, Sweden, June 27-July 2, 2009Korkin D, Chiu W, Frydman J, Sali A. "Predicting configuration of homologous subunits in protein assemblies", The 16th International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, ON, Canada, July 19-23, 2008
Korkin D, Davis FP, Alber F, Sali A. "Modeling Protein Complexes Using Comparative Patch Analysis", The 2006 Computational Systems Bioinformatics Conference (CSB 2006), Stanford, CA, USA, August 14-18, 2006
Korkin D, Davis FP, Sali A. "Localization of protein binding sites within families of homologous proteins", The 13th International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, MI, USA, June 25-29, 2005
Korkin D. "On a new model for cheminformatics: Learning the classes of compounds", The 224-th National ACS Meeting, Division of Chemical Information, Boston, MA, USA, August 18-22, 2002
Korkin D and Goldfarb L. "Multiple Genome Rearrangement: A General Approach via the Evolutionary Genome Graph", The 10th International Conference on Intelligent Systems for Molecular Biology, Edmonton, AL, Canada, August 3-7, 2002
Goldfarb L, Golubitsky O, Korkin D. "Fundamentally new form of structural representation in chemistry", The 222-nd National ACS Meeting, Division of Computers in Chemistry, Chicago, IL, USA, August 26-30, 2001
Korkin D. "On a new, evolutionary, form of object representation in bioinformatics", Atlantic Bioinformatics, Fredericton, NB, Canada, June 2000
Korkin D. "Constructing secure database systems via the network pump", The International Conference On Intelligent Systems, Moscow State University, Moscow, Russia, October 1998
Technical reports
Goldfarb L, Gay D, Golubitsky O, Korkin D, "What is a structural representation? Second variation", Faculty of Computer Science, U.N.B., Technical Report, TR04-165, 2004Korkin D. "On a Novel Evolutionary Based Model for Genome Rearrangement", Faculty of Computer Science, University of New Brunswick, Technical Report, TR02-150, 2002
Korkin D. "A new dominant point-based parallel algorithm for multiple longest common subsequence problem", Faculty of Computer Science, University of New Brunswick, Technical Report, TR01-148, 2001
Goldfarb L, Golubitsky O, Korkin D. "What is a structural representation in chemistry: Towards a unified framework for CADD?" Faculty of Computer Science, University of New Brunswick, Technical Report, TR00-138, 2000
Goldfarb L, Golubitsky O, Korkin D. "What is a structural representation?", Faculty of Computer Science, U.N.B., Technical Report, TR00-137, 2000
Dissertations
Korkin D. "A new model for molecular representation and classification: A formal approach based on the ETS framework", Department of Computer Science, University of New Brunswick, Ph.D. Thesis, February 2003Korkin D. "Analysis of the covert channels via their simulation as automata with probabilistic output", Faculty of Mechanics and Mathematics, Moscow State University, M.Sc. Thesis, June 1999