RESEARCH INTEREST

Development and application of structural bioinformatics methods to study  structure, function, and evolution of macromolecular assemblies; studying structural mimicry in host-pathogen interactions.


RESEARCH

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.


SELECTED PUBLICATIONS

Journals

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


Technical reports