List of Publications -- List of Patents
Books
Systems Biology: Genomics. I. [Rigoutsos</b>] and G. Stephanopoulos, Eds. Oxford University Press. August 2006.
Systems Biology: Networks, Models and Applications. I. [Rigoutsos</b>] and G. Stephanopoulos, Eds. Oxford University Press. August 2006.
Papers and Extended Abstracts
Styczynski, M., K. Jensen, I. Rigoutsos and G. Stephanopoulos, "Miscalculations in BLOSUM62 surprisingly improve search performance." Nature Biotechnology. In Press.
Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, Rigoutsos I and PT Nelson, "The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1." J Neurosci. 2008 Jan 30;28(5):1213-23.
Warnecke, F., P. Luginbühl, N. Ivanova, M. Ghassemian, T. Richardson§, J. Stege, M. Cayouette, G. Djordjevic, N. Aboushadi, R. Sorek, S. Tringe, M. Podar, H. Garcia Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N. Kyrpides, E. Matson, E. Ottesen5, X. Zhang, A. McHardy, M. Hernández, C. Murillo, L. Acosta, I. Rigoutsos, G. Tamayo, B. Green, C. Chang, E. Rubin, E. Mathur§, D. Robertson, P. Hugenholtz, and J. Leadbetter, "Metagenomic and functional analysis of hindgut microbiota of a wood feeding higher termite." Nature, 450(7169):560-5, November 2007.
Tay, Y., W.-L. Tam, Y.-S. Ang, P. Gaughwin, H. Yang, W. Weijia, L. Rubing, J. George, H.-H. Ng, R. Perera, T. Lufkin, I. Rigoutsos, A. Thomson, and B. Lim, "MicroRNA-134 modulates the differentiation of mouse embryonic stem cells where it causes post-transcriptional attenuation of Nanog and LRH1." Stem Cells, 26(1):17-29, January 2008. Epub Oct 4 2007.
McHardy, A. and I. Rigoutsos, "What’s in the mix: phylogenetic classification of metagenome sequence samples." Curr Opinion in Microbiology, 10(5):499-503, October 2007.
Mavromatis, K., N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A.C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz and N.C. Kyrpides, "Use of simulated data sets to evaluate the fidelity of metagenomic processing methods." Nature Methods, 4(6):495-500, June 2007. Epub 2007 Apr 29.
McHardy, A. C., H. G. Martín, A. Tsirigos, P. Hugenholtz and I. Rigoutsos, "Accurate phylogenetic classification of DNA fragments based on sequence composition." Nature Methods, 4(1):63-72, January 2007. Epub 2006 Dec 10.
Höhl, M., I. Rigoutsos and M.A. Ragan, "Pattern-based phylogenetic distance estimation and tree reconstruction." Evolutionary Bioinformatics Online, 2006:2 357-373.
Rigoutsos, I., T. Huynh, Y. Tay, W.-L. Tam, A. Thomson, B. Lim, Revisiting the Topics of Microrna Target Detection and Microrna Precursor Discovery. Extended Abstract. Keystone Symposium on RNAi for Target Validation and as a Therapeutic, Keystone, Colorado. January 2007.
Rigoutsos, I. A. Tsirigos, A. McHardy, T. Huynh, Pyknons: Collections of RNAi Related Regulatory Elements that are Organism-specific. Extended Abstract. Keystone Symposium on MicroRNAs and siRNAs: Biological Functions and Mechanisms, Keystone, Colorado. January 2007.
Loose, C., K Jensen, I. Rigoutsos and G. Stephanopoulos, A Linguistic Model for the Rational Design of Antimicrobial Peptides, Nature, (7113):867-9, October 2006.
Martin, H.G, N. Ivanova, V. Kunin, F. Warnecke, K. Barry, A. C. McHardy, C. Yeates, S. He, A. Salamov, E. Szeto, E. Dalin, N. Putnam, H. J. Shapiro, J. L. Pangilinan, I. Rigoutsos, N. C. Kyrpides, L. L. Blackall, K. D. McMahon and P. Hugenholtz, Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24(10):1263-9, October 2006. Epub Sep 24 2006.
Miranda, K., T. Huynh, Y. Tay, Y.-S. Ang, W.-L. Tam, A. Thomson, B. Lim and I. Rigoutsos, A pattern-based method for the identification of micro-RNA target sites and their corresponding heteroduplexes. Cell, 126, 1203-1217, September 2006.
Rigoutsos, I., T. Huynh, K. Miranda, A. Tsirigos, A. McHardy, and D. Platt. Short Blocks from the Noncoding Parts of the Human Genome have Instances within Nearly All Known Genes and Relate to Biological Processes. PNAS, 103(17):6605-10, April 2006.
Rigoutsos, I., T. Huynh, K Miranda, A. Tsirigos, A Mchardy, D Platt, "The Untranslated and Amino-Acid Coding Regions of Nearly All Human Genes Contain Mosaics of Statistically-Significant Blocks Each of Which is Also Present in Numerous Copies in the Non-Coding Parts of the Human Genome." Extended Abstract. ASM Conference on Mobile DNA. Banff, Alberta, Canada. March 2006.
Rigoutsos, I., T. Huynh, K Miranda, A. Tsirigos, A McHardy, D Platt, "Extremely-Well-Conserved Blocks Link The Non-Coding And Gene-Coding Regions Of The Human Genome And Suggest The Existence Of An Endogenous, Previously-Unseen Layer Of Cell Process Regulation." Extended Abstract. Keystone Symposium on Signaling Networks. Vancouver, British Columbia, Canada. February 2006.
Miranda, K., T. Huynh and I. Rigoutsos, "A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes." Extended Abstract. Keystone Symposium on RNAi and Related Pathways. Vancouver, British Columbia, Canada. January 2006.
Jensen, K., M. Styczynski, I. Rigoutsos and G. Stephanopoulos, "A Generic Motif Discovery Algorithm for Sequential Data." Bioinformatics, 22(1):21-8, January 2006.
Mullins, I. M., M. S. Siadaty, J. Lyman, K. Scully, C. T. Garrett, W. G. Miller, R. Muller, B. Robson, C. Apte, S. Weiss, I. Rigoutsos, D. Platt, S. Cohen and W. A. Knaus, "Data mining and clinical data repositories: Insights from a 667,000 patient data set." Computers in Biology and Medicine, 36(12):1351-77, December 2005. Epub Dec 22, 2005.
Darzentas, N., I. Rigoutsos and C. Ouzounis, "Sensitive Detection of Sequence Similarity Using Combinatorial Pattern Discovery: a Challenging Study of Two Distantly Related Protein Families." Proteins, 61(4):926-37, December 2005.
Rigoutsos, I., T. Huynh, K. Miranda, A. Tsirigos, A. McHardy, and D. Platt. "The Potential Value On Oligonucleotide Therapy Of Millions Of Variable-Length Blocks Which Are Conserved Between The Non-Coding And Gene-Coding Regions Of The Human Genome." Poster Presentation. 1st Meeting of the Oligonucleotide Therapeutics Society, Rockefeller University, New York, NY. September 2005.
Tsirigos, A and I. Rigoutsos, "A Sensitive Method Capable of Detecting Horizontal Gene Transfers in Viral, Archaeal and Bacterial Genomes." Nucleic Acids Research, 33(12):3699-3707, July 2005.
Hoehl, M, I. Rigoutsos and M. Ragan, "Pattern-based phylogenetic distance estimation and tree reconstruction" (Extended Abstract). Proceedings 13th International Conference on Intelligent Systems for Molecular Biology (ISMB '05).
Wouters, M., I. Rigoutsos, C. Chu, L. Feng, D. Sparrow and S. Dunwoodie, "Evolution of Distinct EGF Domains with Specific Functions." Protein Science, 14(4):1091-1103, April 2005.
Tsirigos, A. and I. Rigoutsos, "A New Computational Method for the Detection of Horizontal Gene Transfer Events." Nucleic Acids Research, 33(3):922-933, February 2005.
Styczynski, M., K. Jensen, I. Rigoutsos and G. Stephanopoulos, "An extension and novel solution to the (l,d)-motif challenge problem," Proceedings 15th International Conference on Genome Informatics, Yokohama, Japan. December 2004.
Rigoutsos I. and T. Huynh, "Chung-Kwei: a Pattern-discovery-based System for the Automatic Identification of Unsolicited E-mail Messages (SPAM)." In Proceedings First Conference on Email and Anti-Spam (CEAS2004), Mountain View, CA. July 2004.
Moxley, J., G. Stephanopoulos and I. Rigoutsos, "Systems Biology: Using Systems Approaches to Manage Biological Complexity." In Foundations of Computer Aided Process Design Conference on Discovery though Product and Process Design (FOCAPD 2004), Princeton University, Princeton, NJ. July 2004.
Huynh, T. and I. Rigoutsos, "The Web Server of IBM’s Bioinformatics and Pattern Discovery Group: 2004 update." In Nucleic Acids Research, 32(Web Server issue):10-15, July 2004
Paredes, C., I. Rigoutsos and E. Papoutsakis, "Transcriptional Organization of the Clostridium acetobutylicum Genome." In Nucleic Acids Research, 32(6):1973-1981, April 2004.
Wong, M. S., R. M. Raab, I. Rigoutsos, G. N. Stephanopoulos, and J. K. Kelleher, "Metabolic and Transcriptional Patterns Accompanying Glutamine Depletion and Repletion in Mouse Hepatoma Cells: A model for Physiological Regulatory Networks." In Physiological Genomics 16(2):247-55, January 2004.
Azumi*, K., R. De Santis*, A. De Tomaso*, I. Rigoutsos*, F. Yoshizaki*, M. R. Pinto, R. Marino, K. Shida, M. Ikeda, M. Arai, Y. Inoue, T. Shimizu, N. Satoh, D.S. Rokhsar, L. Du Pasquier, M. Kasahara, M. Satake and M. Nonaka, "Genomic Analysis of Immunity in a Urochordate and the Emergence of the Vertebrate Immune System: Waiting for Godot." In Immunogenetics, 55(8):570-581, November 2003. ('*' indicates joint first authorship)
Murphy, E., I. Rigoutsos, T. Shibuya and T. Shenk, "Re-evaluation of Human Cytomegalovirus Coding Potential." In Proc. Nat. Acad. Sciences USA, 100(23):13585-13590, November 2003.
Rigoutsos, I., P. Riek, R. M. Graham and J. Novotny, "Structural Details (Kinks and Non-a Conformations) in Transmembrane Helices are Intrahelically Determined and can be Predicted by Sequence Pattern Descriptors." In Nucleic Acids Research, 31(15):4625-31, August 2003.
Huynh, T., I. Rigoutsos, D. Platt, L. Parida and T. Shibuya, "The Web Server of IBM’s Bioinformatics and Pattern Discovery Group." In Nucleic Acids Research, 31(13):3645-3650, July 2003.
Platt, D., C. Guerra, G. Zanotti and I. Rigoutsos, "Global secondary structure packing angle bias in proteins." In Proteins: Structure, Function and Genetics, 53(2): 252-261, November 2003.
Hoehl, M, I. Rigoutsos and M. Ragan, "Freeing Phylogenies from Artifacts of Alignments," Poster Presentation 11th International Conference on Intelligent Systems for Molecular Biology (ISMB '03) , Brisbane, Australia, June 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 19(6): 717-726, June 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 77(7):4326-4344, April 2003.
Dehal, P., Y. Satou, R. Campbell, J. Chapman, B. Degnan, A. De Tomaso, B. Davidson, A. Di Gregorio, M. Gelpke, D. M. Goodstein, N. Harafuji, K. E. M. Hastings, I. Ho, K. Hotta, W. Huang, T. Kawashima, P. Lemaire, D. Martinez, I. A. Meinertzhagen, S. Necula, M. Nonaka, N. Putnam, S. Rash, H. Saiga, M. Satake, A. Terry, L. Yamada, H.-G. Wang, S. Awazu, K. Azumi, J. Boore, M. Branno, S. Chin-bow, R. DeSantis, S. Doyle, P. Francino, D. N. Keys, S. Haga, H. Hayashi, K. Hino, K. S. Imai, K. Inaba, S. Kano, K. Kobayashi, M. Kobayashi, B.-I. Lee, K. W. Makabe, C. Manohar, G. Matassi, M. Medina, Y. Mochizuki, S. Mount, T. Morishita, S. Miura, A. Nakayama, S. Nishizaka, H. Nomoto, F. Ohta, K. Oishi, I. Rigoutsos, M. Sano, A. Sasaki, Y. Sasakura, E. Shoguchi, T. Shin-i, A. Spagnuolo, D. Stainier, M. M. Suzuki, O. Tassy, N. Takatori, M. Tokuoka, K. Yagi, F. Yoshizaki, S. Wada, C. Zhang, P. D. Hyatt, F. Larimer, C. Detter, N. Doggett, T. Glavina, T. Hawkins, P. Richardson, S. Lucas, Y. Kohara, M. Levine, N. Satoh, and D. S. Rokhsar, "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):455-474, 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):533-544, 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. 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). 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." In Proteins: Structure, Function and Genetics, 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." In 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. 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.
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.
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.
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." In Proceedings Second Annual TIGR Conference on Computational Genomics. Reston, VA. November 1998.
Rigoutsos, I. and A. Delis, "Managing Statistical Behavior of Large Data Sets in Networked Architectures." IEEE Transactions On Parallel And Distributed Systems. November 1998.
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." In Journal of Computer-Aided Molecular Design, vol. 12, num. 6, pp. 525-532. 1998.
Rigoutsos, I., "Well-behaved, Tunable 3D-Affine Invariants." Proceedings IEEE Conference On Computer Vision and Pattern Recognition . Santa Barbara, CA. June 1998.
Silverman, B. D., D. E. Platt, M. Pitman, and I. Rigoutsos, "Comparative Molecular Moment Analysis (CoMMA)." In 3D QSAR in Drug Design , H. Kubinyi, G. Folkers, and Y. C. Martin, Editors. Kluwer Escom, Dordrecht/Boston/London. 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.
Floratos, A. and I. Rigoutsos, "On The Time Complexity Of The Teiresias Algorithm." IBM Research Report, RC 21161. April 1998.
Rigoutsos, I. and A. Floratos, "Combinatorial Pattern Discovery In Biological Sequences: The TEIRESIAS Algorithm." Bioinformatics, Vol.14, num. 1. 1998.
Rigoutsos, "2D Affine-Invariants That Distribute Uniformly And Can Be Tuned To Any Convex Feature Domain." Proceedings IEEE International Conference On Computer Vision . Bombay, India. January 1998.
Wolfson, H. and I. Rigoutsos, "Geometric Hashing: An Overview." IEEE Computational Science & Engineering, vol. 4, num. 4,October-December 1997.
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. Delis, "The Impact Of Hashing Function Choice On The Load Balancing In Very Large Datasets." Proceedings 8th International Conference On Software Engineering and Knowledge Engineering (SEKE '98). Lake Tahoe, NE. June 1996.
Rigoutsos, I. and R. Hummel, "A Bayesian Approach to Model Matching with Geometric Hashing. " Computer Vision and Image Understanding, vol. 62, num. 1. July 1995.
Rigoutsos, I. and A. Califano, "Searching In Parallel for Similar Strings." In IEEE Computational Science and Engineering,, vol. 1, num. 2. Summer 1994.
Rigoutsos, I. and R. Hummel, "Distributed Bayesian Object Recognition." Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR '93), New York, NY. June 1993.
Rigoutsos, I. and R. Hummel, "Massively Parallel Model Matching: Geometric Hashing on the Connection Machine. " IEEE Computer: Special Issue on Parallel Processing for Computer Vision and Image Understanding, vol. 25, num. 2. February 1992.
Berger, M. and I. Rigoutsos, "An Algorithm for Point Clustering and Grid Generation." IEEE Transactions on Systems, Man and Cybernetics , vol. 21, num. 5. September/October 1991.
Rigoutsos, I. and R. Hummel, "Several Results on Affine Geometric Hashing." Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision, Tel Aviv, Israel. December 1991.
Rigoutsos, I. and R. Hummel, "Robust Similarity Invariant Matching in the Presence of Noise. " Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision, Tel Aviv, Israel. December 1991.
Rigoutsos, I., "Visuo-Tactual Coarseness Estimation Tasks: 1: Experiments, 2: Modeling." Proceedings Vision Interface '91, Calgary, Canada. June 1991.
Rigoutsos, I. and R. Hummel, "Implementation of Geometric Hashing on the Connection Machine." Proceedings IEEE Workshop on Directions in Automated CAD-Based Vision Systems, Maui, Hawaii. June 1991.
Aloimonos, J., and I. Rigoutsos, "Detection of 3-D Motion without Correspondence; Planar Surfaces: Theory and Experiments, Curved Surfaces: Theory." Proceedings AAAI-86, Philadelphia, PA. August 1986.
Aloimonos, J. and I. Rigoutsos, "How to Determine Structure, Depth and 3-D Motion of a Textured Plane, Without Correspondence." Proceedings Canadian Artificial Intelligence '86, Montreal, Canada. May 1986.
Aloimonos, J. and I. Rigoutsos, "Determining the 3-D Motion of a Rigid Planar Patch Without Correspondence, Under Perspective Projection." Proceedings IEEE Workshop on Motion, Charleston, SC. May 1986.
Patents
U.S. Patent # 7,248,971. "Methods and apparatus for discovering patterns in a set of sequences." July 24, 2007.
U.S. Patent # 6,785,672. "Methods and apparatus for performing sequence homology detection." August 31, 2004.
E.P. Patent # 0,985,995. "Method and apparatus for intrusion detection in computers and computer networks." August 13, 2003.
U.S. Patent # 6,571,199. "Method and apparatus for performing pattern dictionary formation for use in sequence homology detection." May 27, 2003.
U.S. Patent # 6,446,011. "Tandem repeat detection using pattern discovery." September 03, 2002.
E.P. Patent # 1,057,131. "Method and apparatus for performing pattern dictionary formation for use in sequence homology detection." May 22, 2002
U.S. Patent # 6,373,971. "Method and apparatus for pattern discovery in protein sequences." April 16, 2002.
U.S. Patent # 6,341,284. "Method and apparatus for exhaustive enumeration of correspondence in a set of descriptors." January 22, 2002.
U.S. Patent # 6,205,444. "Multiple sequence alignment system and method." March 20, 2001.
U.S. Patent # 6,108,666. "Method and apparatus for pattern discovery in 1-dimensional event streams." August 22, 2000.
U.S. Patent # 6,092,065. "Method and apparatus for discovery, clustering and classification of patterns in 1-dimensional event streams." July 18, 2000.
U.S. Patent # 5,977,890. "Method And Apparatus for Data Compression Utilizing Efficient Pattern Discovery." November 2, 1999.
U.S. Patent # 5,802,525. "Two-Dimensional Affine-Invariant Hashing Defined Over Any Two-Dimensional Convex Domain And Producing Uniformly-Distributed Hash Keys." September 1, 1998.
U.S. Patent # 5,799,312. "Three-Dimensional Affine-Invariant Hashing Defined Over Any Three-Dimensional Convex Domain And Producing Uniformly-Distributed Hash Keys." August 25, 1998.
US Patent #5,787,279. "System and Method For Conformationally-Flexible Molecular Recognition." July 28, 1998.
US Patent #5,752,019. "System And Method For Conformationally-Flexible Molecular Identification." May 12, 1998.
