This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
January-March 2004 (vol. 1 no. 1)
pp. 1

[1] B.A. Shapiro and K. Zhang, “Comparing Multiple RNA Secondary Structures Using Tree Comparisons,” Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309-318, 1990.
[2] F. Corpet and B. Michot, “RNAlign Program: Alignment of RNA Sequences Using Both Primary and Secondary Structures,” Computer Applications in the Biosciences, vol. 10, no. 4, pp. 389-399, 1994.
[3] T. Jiang, G. Lin, B. Ma, and K. Zhang, “A General Edit Distance between RNA Structures,” J. Computational Biology, vol. 9, no. 2, pp. 371-388, 2002.
[4] K. Wojciech and B. Shapiro, “Stem Trace: An Interactive Visual Tool for Comparative RNA Structure Analysis. ” Bioinformatics, vol. 15, no. 1, pp. 16-31, 1999.
[5] B. Shapiro, “An Algorithm for Comparing Multiple RNA Secondary Stuctures,” Computer Applications in the Biosciences, vol. 4, no. 3, pp. 387-393, 1988.
[6] S. Siebert and R. Backofen, “MARNA: A Server for Multiple Alignment of Rnas,” Proc. German Conf. Bioinformatics, pp. 135-140, 2003.
[7] C. Notredame, D. Higgins, and J. Heringa, “T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment,” J. Molecular Biology, vol. 302, pp. 205-217, 2000.
[8] T. Jiang, J. Wang, and K. Zhang, “Alignment of Trees–An Alternative to Tree Edit,” Theoretical Computer Science, vol. 143, no. 1, pp. 137-148, 1995.
[9] J. Thompson, D. Higgins, and T. Gibson, “CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position Specific Gap Penalties and Weight Matrix Choice,” Nucleic Acids Research, vol. 22, pp. 4673-4680, 1994.
[10] D. Feng and F. Doolittle, “Progressive Sequence Alignment as a Prerequisite to Correct to Correct Phylogenetic Trees,” J. Molecular Evolution, vol. 25, pp. 351-360, 1987.
[11] P. Kilpeläinen and H. Mannila, “Ordered and Unordered Tree Inclusion,” SIAM J. Computing, vol. 24, pp. 340-356, 1995.
[12] D. Reis, P. Golgher, A. Silva, and A. Laender, “Automatic Web News Extraction Using Tree Edit Distance,” Proc. 13th Conf. World Wide Web, pp. 502-511, 2004.
[13] B. Rössler, J. Zhang, and M. Höchsmann, “Visual Guided Grasping and Generalization Using Self-Valuing Learning,” Proc. IEEE/RSJ Int'l Conf. Intelligent Robots and Systems, 2002.
[14] T. Sebastian, P. Klein, B. Kimia, “Recognition of Shapes by Editing Their Shock Graphs,” IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 26, pp. 550-571, 2004.
[15] M. Höchsmann, T. Toller, R. Giegerich, and S. Kurtz, “Local Similarity in RNA Secondary Structures,” Proc. IEEE Computational Systems Bioinformatics Conf., pp. 159-168, 2003.
[16] I. Hofacker, W. Fontana, P. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster, “Fast Folding and Comparison of RNA Secondary Structures,” Monatshefte f. Chemie, vol. 125, pp. 167-188, 1994.
[17] K. Tai, “The Tree-to-Tree Correction Problem,” J. ACM, vol. 26, pp. 422-433, 1979.
[18] L. Wang and T. Jiang, “On the Complexity of Multiple Sequence Alignment,” J. Computational Biology, vol. 1, pp. 337-348, 1994.
[19] P. Bonizzoni and G. Della Vedova, “The Complexity of Multiple Sequence Alignment with Sp-Score that is a Metric,” Theoretical Computer Science, vol. 259, no. 1, pp. 63-79, 2001.
[20] S. Le, R. Nussinov, and J. Mazel, “Tree Graphs of RNA Secondary Structures and Their Comparison,” Computational Biomedical Research, vol. 22, pp. 461-473, 1989.
[21] T. Lowe and S. Eddy, “tRNAscan-se: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence,” Nucleic Acids Research, vol. 25, pp. 955-964, 1997.
[22] D. Dowell and S. Eddy, “Evaluation of Several Lightweight Stochastic Context-Free Grammars for RNA Secondary Structure Prediction,” BMC Bioinformatics, vol. 5, no. 71, 2004.
[23] M. Gribskov, A. McLachlan, D. Eisenberg, “Profile Analysis Detection of Distantly Related Proteins,” Proc. Nat'l. Academy of Science, no. 88, vol. 43, pp. 55-58, 1987.
[24] H. Carillo and D. Lipman, “The Multiple Sequence Alignment Problem in Biology,” SIAM J. Applied Math., vol. 48, no. 5, pp. 1073-1082, 1988.
[25] M. Zuker and P. Stiegler, “Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information,” Nucleic Acids Research, vol. 9, pp. 133-148, 1981.
[26] K. Zhang and D. Shasha, “Simple Fast Algorithms for the Editing Distance between Trees and Related Problems,” SIAM J. Computing, vol. 18, no. 6, pp. 1245-1262, 1989.
[27] P.N. Klein, “Computing the Edit-Distance between Unrooted Ordered Trees,” Proc. Sixth Ann. European Symp., no. 1461, pp. 91-102, 1998.
[28] S. Dulucq and H. Touzet, “Analysis of Tree Edit Distance Algorithms,” Proc. 14th Ann. Symp. Combinatorial Pattern Matching, pp. 83-95, 2003.
[29] S. Dulucq and L. Tichit, “RNA Secondary Structure Comparison: Exact Analysis of the Zhang-Sasha Tree Edit-Algorithm,” Theoretical Computer Science, vol. 306, pp. 471-484, 2003.
[30] D. Konings and P. Hogeweg, “Pattern Analysis of RNA Secondary Structure: Similarity and Consensus of Minimal-Energy Folding,” J. Molecular Biology, vol. 207, pp. 597-614, 1989.
[31] F. Chetouani, P. Monestie, P. Thebault, C. Gaspin, and B. Michot, “ESSA: An Integrated and Interactive Computer Tool for Analysing RNA Secondary Structure,” Nucleic Acids Research, vol. 25, no. 17, pp. 3514-3522, 1997.
[32] G. Pesole, S. Liuni, G. Grillo, F. Licciulli, F. Mignone, C. Gissi, and C. Saccone, “Utrdb and Utrsite: Specialized Database of Sequences and Functional Elements of 5' and 3' Untranslated Regions of Eukaryotic mRNAs,” Nucleic Acids Research, vol. 30, pp. 335-340, 2002.
[33] M. Zuker, “Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.
[34] I. Hofacker, “Vienna RNA Secondary Structure Server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3429-3431, 2003.
[35] A. Wong and D. Chiu, “An Event-Covering Method for Effective Probabilistic Inference,” Pattern Recognition, vol. 20, pp. 245-255, 1987.
[36] D. Chiu and T. Kolodziejczak, “Inferring Consensus Structure from Nucleic Acid Sequences,” Computer Applications in the Biosciences, vol. 7, pp. 347-352, 1991.
[37] J. Gorodkin, L. Heyer, S. Brunak, and G. Stormo, “Displaying the Information Contents of Structural RNA Alignments,” Bioinformatics, vol. 13, pp. 583-586, 1997.
[38] M. Mandal, B. Boese, J. Barrick, W. Winkler, and R. Breaker, “Riboswitches Control Fundamental Biochemical Pathways in Bacillus Subtilis and Other Bacteria,” Cell, vol. 113, no. 5, pp. 577-586, 2003.
[39] S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. Eddy, “Rfam: An RNA Family Database,” Nucleic Acids Research, vol. 31, no. 1, pp. 439-441, 2003.
[40] I. Hofacker, M. Fekete, and P. Stadler, “Secondary Structure Prediction for Aligned RNA Sequences,” J. Molecular Biology, vol. 319, pp. 1059-1066, 2002.
[41] K. Zhang, “Computing Similarity between RNA Secondary Structures,” Proc. IEEE Int'l Joint Symp. Intelligence and Systems, pp. 126-132, 1998.

Citation:
Michael R. Williams, "Welcome Message," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 1, Jan.-March 2004, doi:10.1109/TCBB.2004.13
Usage of this product signifies your acceptance of the Terms of Use.