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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)

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)

Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps, Akinc M, Bekris KE, Chen BY, Ladd AM, Plaku E, Kavraki LE, Dario P. and Chatila R , Robotic Research: The Eleventh International Symposium, p.80-89, (2005)

Sampling-Based Roadmap of Trees for Parallel Motion Planning, Plaku E, Bekris KE, Chen BY, Ladd AM, Kavraki LE , IEEE Transactions on Robotics, Volume 21, Number 4, p.597-608, (2005)

2003
Multiple Query Probabilistic Roadmap Planning Using Single Query Planning Primitives, Bekris KE, Chen BY, Ladd AM, Plaku E, Kavraki LE , 2003 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS), October, Las Vegas, NV, p.656-661, (2003)