Web site: Korkin Lab Office address:
Informatics Institute and Department of Computer Science
207 Engineering Building West, University of Missouri Office phone:
(573) 882-4762 Fax:
Development and application of structural bioinformatics methods to study structure, function, and evolution of macromolecular assemblies; studying structural mimicry in host-pathogen interactions.
Our group (the Korkin Lab) is involved in an interdisciplinary research focusing on the areas of (i) machine learning and pattern recognition, and (ii) computational biology and structural bioinformatics. The research in these areas is inspired by two basic questions.
Q1: Can we teach a computer to recognize and categorize real-world objects the way a human does?
To tackle this question, we are developing new formal methods for structure- or symbolic-based machine learning and pattern recognition. While applying these methods to the classical applications of pattern recognition, we also hope that the methods will help us answering a biological question:
Q2: What can we learn about structure, function, and evolution of macromolecular assemblies and larger biological systems?
In collaboration with experimental scientists, we try to answer this question for specific biological systems. In particular, we study molecular assemblies of a chemical synapse, a complex biological system that is linked to the basic cognitive processes, such as learning and memory. We hope that one day, the discovered molecular mechanisms behind those processes can be incorporated into a machine learning framework.
- Wang Q, Korkin D, Shang Y. "A Fast Multiple Longest Common Subsequence (MLCS) Algorithm", IEEE T KDE, in press
- 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
- 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
- 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
- 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
- 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