¬ Apostolico, A. and L. Parida, "Compression and the Wheel of Fortune." In Proceedings of Data Compression Conference (DCC). Snowbird, Utah, March 2003.

¬ Platt, D., C. Guerra, G. Zanotti and I. Rigoutsos, "Global secondary structure packing angle bias in proteins." In Proteins: Structure, Function and Genetics, In Press. 2003.

¬ Rigoutsos, I., J. Novotny, T. Huynh, S. Chin-Bow, L. Parida, D. Platt, D. Coleman and T. Shenk, "In Silico Pattern-based Analysis of the Human Cytomegalovirus (HHV5) Genome." In Journal of Virology. In Press. 2003.

¬ Iliopoulos, I., S. Tsoka, M. A. Andrade, A. J. Enright, M. Carroll, P. Poullet, V. Promponas, T. Liakopoulos, G. Palaios, C. Pasquier, S. Hamodrakas, J. Tamames, A. T. Yagnik, A. Tramontano, D. Devos, C. Blaschke, A. Valencia, D. Brett, D. Martin, C. Leroy, I. Rigoutsos, C. Sander and C. A. Ouzounis, "Evaluation of Annotation Strategies Using an Entire Genome Sequence. " In Bioinformatics. In Press. 2003.

¬ Dehal, P., Y. Satou, R. K. Campbell, J. Chapman, B. Degnan, A. DeTomaso, B. Davidson, A. Di Gregorio, M. Gelpke, D. M. Goodstein, et al., "The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins." In Science. 2157-2167, 2002.

¬ Rigoutsos, I., T. Huynh, A. Floratos, L. Parida and D. Platt, "Dictionary-driven Protein Annotation." In Nucleic Acids Research. 30(17), 2002.

¬ Wang, X., J. T.L. Wang, D. Shasha, B. A. Shapiro, I. Rigoutsos and K. Zhang, "Finding Patterns in Three Dimensional Graphs: Algorithms and Applications to Scientific Data Mining. " In IEEE Transactions on Data and Knowledge Engineering. 14(4):731-749, July/August 2002.

¬ Shibuya, T. and I. Rigoutsos, Dictionary-driven Prokaryotic Gene Finding. In Nucleic Acids Research. 30(12), 2002.

¬ Novotny, J., I. Rigoutsos, D. Coleman and T. Shenk, "In Silico Structural and Functional Analysis of the Human Cytomegalovirus (HHV5) Genome" In Journal of Molecular Biology 310(5):1151-1166, July 2001.

¬ Parida, L., I. Rigoutsos and D. E. Platt, "An Output-sensitive Flexible Pattern Discovery Algorithm." In Proceedings 12th Annual Symposium on Combinatorial Pattern Matching. July 2001. Jerusalem, Israel.

¬ Floratos, A., I. Rigoutsos, L. Parida and Y. Gao, "DELPHI: A pattern-based method for detecting sequence similarity." In IBM Journal of Research and Development 45(3/4), May/July 2001.

¬ Platt, D. E., L. Parida, Y. Gao, A. Floratos and I. Rigoutsos, "QSAR in Grossly Underdetermined Systems: Opportunities and Issues." In IBM Journal of Research and Development. 45(3/4), May/July 2001.

¬ Riek, R. P., I. Rigoutsos, J. Novotny and R. M. Graham, "Non-a-Helical Elements Modulate Polytopic Membrane Architecture." In Journal of Molecular Biology. 306(2):349-362, February 2001.

¬ Rigoutsos, I., A. Floratos, L. Parida, Y. Gao and D. E. Platt, "The Emergence of Pattern Discovery Techniques in Computational Biology." In Metabolic Engineering. 2(3):159-177, July 2000.

¬ Parida, L., I. Rigoutsos, A. Floratos, D. E. Platt, and Y. Gao, "Pattern Discovery on Character Sets and Real Valued Data: Linear Bound on Irredundant Motifs and an Efficient Polynomial Time Algorithm." In Proceedings 11th Annual ACM/SIAM Symposium on Discrete Algorithms (SODA '00).  San Francisco, CA. January 2000.

¬ Rigoutsos, I., A. Floratos, C. Ouzounis, Y. Gao and L. Parida, "Dictionary Building Via Unsupervised Hierarchical Motif Discovery In The Sequence Space of Natural Proteins." Journal of Proteins: Structure, Function and Genetics, 37(2). November 1999.

¬ Rigoutsos, I., Y. Gao, A. Floratos and L. Parida, "Building Dictionaries Of 1D and 3D Motifs by Mining the Unaligned 1D Sequence of 17 Archaeal and Bacterial Genomes." In Proceedings Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB '99), pp. 223-233, Heidelberg, Germany. August 1999.

¬ Parida, L., A. Floratos and I. Rigoutsos, "An Approximation Algorithm for Alignment of Multiple Sequences Using Motif Discovery." Journal Of Combinatorial Optimization,  3(2/3):247-275, July 1999.

¬ Floratos, A., I. Rigoutsos, L. Parida, G. Stolovitzky and Y. Gao, "Sequence Homology Detection Through Large-Scale Pattern Discovery." In Proceedings Third Annual ACM International Conference on Computational Molecular Biology (RECOMB '99). Lyon, France. April 1999.

¬ Rigoutsos, I., D. E. Platt, A. Califano, and B. D. Silverman, "Representation and Matching Of Small Flexible Molecules In Large Databases Of 3D-Molecular Information." In Pattern Discovery In Molecular Biology. J. Wang, B. Shapiro and D. Shasha, Editors. Oxford University Press. 1999.

¬ Stolovitzky, G., Y. Gao, A. Floratos, and I. Rigoutsos, "Tandem Repeat Detection using Pattern Discovery with Applications to the Identification of Yeast Satellites." IBM Research Report, RC 21508. May 1999.

¬ Rudin, N., K. Inman, G. Stolovitzky and I. Rigoutsos, "DNA-Based Identification." In Biometrics: Personal Identification In Networked Society. A. Jain, R. Bolle and S. Pankanti, Editors, Kluwer Academic Publishers. 1999.

¬ Silverman, D., D. E. Platt, M. Pitman, and I. Rigoutsos, "Comparative Molecular Moment Analysis (CoMMA)." In Perspectives in Drug Discovery and Design, vols. 12/13/14 (3D QSAR in Drug Design: Recent Advances. H. Kubinyi, G. Folkers, and Y. C. Martin (Eds.), Kluwer/Escom. 1998.

¬ Parida, L., A. Floratos and I. Rigoutsos, "MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences." In Proceedings 9th Workshop on Genome Informatics. Tokyo, Japan. December 1998.

¬ Rigoutsos, I., A. Floratos, C. Ouzounis, and Y. Gao, "From Motif Discovery To Functional Characterization and Structure Prediction: A Feasible Journey." Proceedings Second Annual TIGR Conference on Computational Genomics, Reston, VA. November 1998. (Extended Abstract)

¬ Silverman, B. D., M. Pitman, D. E. Platt, and I. Rigoutsos, "Molecular Moment Similarity between Clozapine and Substituted [(4-Phenylpiperazinyl)-methyl] benzamides: Selective Dopamine D4 Agonists." Journal of Computer-Aided Molecular Design, vol. 12, num. 6, pp. 525-532. 1998.

¬ Floratos, A. and I. Rigoutsos, "On The Time Complexity Of The Teiresias Algorithm." IBM Research Report, RC 21161. April 1998.

¬ Rigoutsos, I., "Well-behaved, Tunable 3D Affine Invariants." Proceedings IEEE Conference On Computer Vision and Pattern Recognition (CVPR '98). Santa Barbara, CA. June 1998.

¬ Rigoutsos, I. and A. Floratos, "Motif Discovery Without Alignment Or Enumeration." In Proceedings Second Annual ACM International Conference on Computational Molecular Biology (RECOMB 98). New York, NY. March 1998.

¬ Rigoutsos, I., "2D Affine-Invariants that Distribute Uniformly and Can be Tuned to any Convex Feature Domain." Proceedings International Conference On Computer Vision (ICCV '98) Bombay, India. January 1998.

¬ Rigoutsos, I. and A. Floratos, "Combinatorial Pattern Discovery In Biological Sequences: The TEIRESIAS Algorithm." In Bioinformatics, vol.14, num. 1. 1998.

¬ Wang X., J. Wang, D. Shasha, B. Shapiro, S. Dikshitulu, I. Rigoutsos and K. Zhang, "Automated Discovery Of Active Motifs In Three Dimensional Molecules." In Proceedings 3rd International Conference On Knowledge Discovery And Data Mining (KDD-97). Newport Beach, CA. August 1997.

¬ Rigoutsos, I., A. Floratos, and C. Ouzounis, "Preliminary Results On the Discovery of Patterns of Amino Acids Common to Sequences of Leghemoglobins." IBM Research Report, RC 20806. April 1997.

¬ Rigoutsos, I., A. Floratos, and C. Ouzounis, "Preliminary Results On the Discovery of Patterns of Amino Acids Common to Sequences of Core Histones 3 & 4." IBM Research Report, RC 20804. April 1997.

¬ Rigoutsos, I., A. Floratos, and C. Ouzounis, "Case Studies In Pattern Discovery Without Alignment Results Using The Teiresias Algorithm." IBM Research Report, RC 20803. April 1997.

¬ Rigoutsos, I. and A. Califano, "Searching In Parallel for Similar Strings." IEEE Computational Science and Engineering, vol. 1, num. 2. Summer 1994.