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2008
A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms, Fofanov VY, Chen BY, Bryant DH, Moll M, Lichtarge O, Kavraki LE, Kimmel M , IEEE Intl. Conf. on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, (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)

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)