C. L. Tang, E. Alexov, A. M. Pyle, and B. Honig. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of molecular biology, Academic Press, volume 366, issue 5, pages 1475-1496, 2007.

C. L. Tang, D. Petrey, M. Fasnacht, M. Kosloff, E. Alexov, and B. Honig. Use of limited suboptimal alignment in homology modeling. Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2004.

C. L. Tang, L. Xie, I. Y. Koh, S. Posy, E. Alexov, and B. Honig. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. Journal of molecular biology, Elsevier, volume 334, issue 5, pages 1043-1062, 2003.

D. Petrey, Z. Xiang, C. L. Tang, L. Xie, M. Gimpelev, T. Mitros, C. S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, and others. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins: Structure, Function, and Bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 53, issue 6, pages 430-435, 2003.

C. Tang, E. Alexov, A. Pyle, and B. Honig. Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation. BIOPHYSICAL JOURNAL, volume 82, issue 1, pages 131A-131A, 2002.