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REFINER

Associate Investigator NCBI, NLM, NIH Computational Biology Branch Building 38A 8S814 Bethesda, MD 20894 Tel: 301-435-5891 Fax: 301-480-9241 Email: panch@ncbi.nlm.nih.gov

 Anna R. Panchenko, PhD

View my Publications and Curriculum vitae

 Research Interests:

• Protein-protein interactions
• Protein structural evolution
• Prediction of protein function and functionally important sites
• Prediction of tertiary protein structure
• Methods of sequence alignments

More details on ongoing research projects

 Teaching Experience:

• The course  Introduction to Bioinformatics  at George Washington University
• The course  Computational Aspects of Molecular Structure  at Johns Hopkins University
• Tutorial  Protein-protein interactions: structures and systems approaches to analyze diverse genomic data  at ISMB2006, Fortaleza, Brazil

 Organized conferences:

DIMACS Workshop on Sequence, Structure and Systems Approaches to Predict Protein Function Rutgers University, May 2006.

Book

 Recent Publications:

• Saikat Chakrabarti, Stephen Bryant and Anna R. Panchenko Functional specificity lies within the properties and evolutionary changes of amino acids J Mol Biol, v. 373(3), p. 801 (2007).
• Benjamin Shoemaker and Anna R. Panchenko Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners PLoS Comput Biol, 3(4) (2007).
• Thomas Madej, Anna R. Panchenko, Jie Chen and Stephen Bryant Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins  BMC Structural Biology, 7:23 (2007).
• Benjamin Shoemaker and Anna R. Panchenko Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases PLoS Comput Biol, 3(3) (2007).
• Yuri Wolf, Thomas Madej, Vladimir Babenko, Benjamin Shoemaker and Anna R. Panchenko Long-term trends in evolution of indels in protein sequences  BMC Evol Biol, v.7 (2007).
• Jessica H. Fong, Lewis Y. Geer, Anna R. Panchenko and Stephen H. Bryant  Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony  J Mol Biol, v. 366, p.307 (2007).
• Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant  State of the art: refinement of multiple sequence alignments,  BMC Bioinformatics, v.7 (2006).
• Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant  Refining multiple sequence alignments with conserved core regions  Nucleic Acids Res., v.34(9), p.2598 (2006).
• Benjamin A. Shoemaker, Anna R. Panchenko and Stephen H. Bryant Finding biologically relevant domain interactions: Conserved Binding Mode analysis,  Protein Science, v.15(2), p.352 (2006).