Publications:

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; ISBN 978-953-307-280-7

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Journals and Proceedings

38. Warren S, Phinney MA, Petakovic E, Dhroso A, Shyu CR, Korkin D*, "BacPaC: A Database of Bacterial Effectors, Predicted and Curated", Submitted

37. Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR, "An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites", IEEE/ACM Trans. Comput. Biology Bioinform., 2014; In press

36. Shin D, Arthur G, Popescu M, Korkin D, Shyu CR, "Uncovering influence links in molecular knowledge networks to streamline personalized medicine", J. of Biomedical Informatics, 2014; In press

35. Dhroso A, Korkin D, Conant G, "The yeast protein interaction network has a capacity for self-organization", FEBS J., 2014; In press

34. Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Wanamaker SA, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Horvath S, Salehi-Ashtiani K, Roth FP, Tavernier J, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM. "Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism", Nature Commun., 2014, Apr 11;5:3650

33. Chen Z, Shin D, Chen S, Kovalenko M, Hadass O, Tomlison BN, Korkin D, Shyu CR, Cui J, Anthony DC, Gu Z, "Histological Quantitation of Brain Injury Using Whole Slide Imaging: A Pilot Validation Study in Mice", PLoS One, 2014, Mar 17;9(3):e92133

32. Zhao N, Han JG, Shyu CR, Korkin D, "Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning", PLoS Comput. Biol., 2014, May 1;10(5):e1003592

31. Finch TM, Zhao N,Korkin D, Frederick KH, Eggert LS, "Evidence of Positive Selection in Mitochondrial Complexes I and V of the African Elephant", PLoS One, 2014, Apr 2;9(4):e92587

30. Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR, "PBSalign: Sequence-Independent Local Alignment of Protein Binding Sites", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2013; BIBM-2013, DOI: 10.1109/BIBM.2013.6732456

29. Warren S, Wan XF, Conant G, Korkin D. "Extreme conservation of functionally important regions in H1N1 influenza proteome", PLoS One, 2013, Nov 25;8(11):e81027

28. Moretti R, ... 28 coauthors ... , Zhao N, Korkin D, ... 33 co-authors (participating groups are ordered alphabetically by PIs), Baker D. "Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions", Proteins, 2013 Jul 10. doi: 10.1002/prot.24356

27. Liu S, Kandoth P, Warren S, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale P, Hill J, Baum T, Cianzio S, Whitham S, Korkin D, Meksem K, Mitchum M. "A Soybean Cyst Nematode Resistance Gene Points to a New Mechanism of Plant Resistance to Pathogens", Nature, 2012, Dec 13;492(7428):256-60

26. Pang B, Kuang X, Zhao N, Becchi M, Korkin D, Shyu CR "PBSword: a web server for searching similar protein-protein binding sites", Nucleic Acids Res, Nucleic Acids Res., 2012, Jul;40(Web Server issue):W428-34

25. Renecker J, Lyons E, Conant G, Pires C, Freeling M, Shyu CR, Korkin D. "Long Identical Multispecies Elements in Plant Genomes", Proc Natl Acad Sci USA, 2012, 109(19):E1183-91

24. Pang B, Zhao N, Korkin D, Shyu CR "Fast protein binding site comparisons using visual words representation", Bioinformatics, 2012, 2012 May; 28(10):1345-52

23. Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. "DOMMINO: A database of macromolecular interactions", Nucleic Acids Res., 2012 Jan; 40(Database issue):D501-6

22. Thieu T, Joshi S, Warren S, Korkin D. "Literature Mining of Host-Pathogen Interactions: Comparing Feature-based Supervised Learning and Language-based Approaches", Bioinformatics, 2012 Mar 15; 28(6):867-75

21. Pang B, Zhao N, Becchi M, Korkin D, Shyu CR "Accelerating large-scale protein structural alignments with Graphics Processing Units", BMC Research Notes, 2012, 5:116

20. 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

19. 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

18. Zhao N, Pang B, Shyu CR, Korkin D. "Structural similarity and classification of protein interaction interfaces", PLOS One, 2011 May 12;6(5):e19554

17. 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

16. 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)

15. 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

14. 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

13. 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

12. 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. 185-189

11. 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

10. 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

9. 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

8. 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

7. 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

6. 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

5. 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

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

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Conference Abstracts

Zhao N, Kuang X, He Z, Shyu CR, Xu D, Korkin D, "Predicting protein binding sites on homology models by a guided integration of sequence and structure data", The 20th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2012), Long Beach, CA, July 15-17, 2012

Kuang X, Han,J, Zhao N, Pang B, Shyu CR, Korkin D, "DOMMINO: Towards integrating DNA-, RNA-, and protein-mediated macromolecular interaction data", The 20th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2012), Long Beach, CA, July 15-17, 2012

Warren S, Conant G, Korkin D, "Predicting protein binding sites on homology models by a guided integration of sequence and structure data", The 20th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2012), Long Beach, CA, July 15-17, 2012

Zhao N, Pang B, Shyu CR, Korkin D. "Understanding protein-protein interactions: Efficient classification of physiological and non-physiological protein complexes and unexpected conservation in interaction interfaces", The 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Vienna, Austria, July 17-19, 2011

Warren S, Conant G, Korkin D. "Extreme conservation in intra-viral interactions of the influenza proteome", Great Lakes Bioinformatics Conference (GLBIO 2011), Athens, OH, USA, May 2-4, 2011

Thieu T, Joshi S, Warren S, Korkin D. "Mining host-pathogen interactions from biomedical literature", The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, July 9-13, 2010

Joshi S and Korkin D. "An accurate prediction of bacterial effectors using a feature-based supervised learning approach", The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, July 9-13, 2010

Warren S, Conant G, Korkin D. "The Pearls of Swine Flu: The structural and sequence evolution of the H1N1 proteome", The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, July 9-13, 2010

Zhao N, Pang B, Shyu CR,Korkin D. "Similarity in protein-protein interactions: Disappearing and reappearing act by key interface residues", The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, July 9-13, 2010

Pang B, Zhao N, Shyu CR, Korkin D. "Efficient Retrieval of Protein Interfaces with a Machine Learning-based Similarity Measure", The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, July 9-13, 2010

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, 2009

Korkin 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

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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, 2004

Korkin 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

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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 2003

Korkin 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

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