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2008
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids, Kristensen DM, Ward RM, Lisewski AM, Edrin S, Chen BY, Fofanov VY, Kimmel M, Lichtarge O , BMC Bioinformatics, Volume 9, Issue 17, (2008)

2007
Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction, Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE , Journal of Bioinformatics and Computational Biology, Volume 5, Number 2a, p.353-382, (2007)

Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction, Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kimmel M, Lichtarge O, Kavraki LE , Computational Systems Bioinformatics Conference (CSB2007), p.343-355, (2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs, Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE , Journal of Computational Biology, Volume 14, Number 6, p.791-816, (2007)

2006
Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction, Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE , Systems Bioinformatics Conference (CSB), August, Volume 4, Stanford, CA, p.311-323, (2006)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction, Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE , Research in Computational Biology: 10th Annual International Conference (RECOMB), April, Venice, Italy, (2006)

Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity, Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O , Protein Science, Volume 15, Number 6, p.1530-1536, (2006)

2005
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs, Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE , Pacific Symposium on Biocomputing, Hawaii, USA, (2005)

2003
An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures, Yao H, Kristensen D, Mihalek I, Sowa M, Shaw C, Kimmel M, Kavraki LE, Lichtarge O , Journal of Molecular Biology, Volume 326, Number 1, p.255-261, (2003)