The following list includes references to only selected computational-biology-related publications by members of the group. For a comprehensive list that includes non-biology-related publications, please visit the individual pages of the group's members.
Books
Systems Biology: Genomics. I. Rigoutsos and G. Stephanopoulos, Eds. Oxford University Press. August 2006.
Systems Biology: Networks, Models and Applications. I. Rigoutsos and G. Stephanopoulos, Eds. Oxford University Press. August 2006.
Book Chapters
R. Zhou. Dewetting in Nanoscale Hydrophobic Plates Collapse and Protein Complex Folding, Ed. Uli Hansmann, NIC Series on Protein Folding and System Biology, p480-486, Berlin, 2006.
R. Zhou. Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method, Ed. Albert Zomaya, "Parallel Computing for Bioinformatics and Computational Biology", p397-425, John Wiley & Sons Publisher, New Jersey, 2006.
Papers and Extended Abstracts
Silverman, B.D. Modeling the Effect of Growth Rate and Survivability Trade-Offs on Species Coexistence and Spatial Topology at a Traveling Invasive Wave-Front. Ecological Modeling. In Press.
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. In Press.
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.
Krause, L., A.C. McHardy, T.W. Nattkemper, A. Puhler, J. Stoye and F. Meyer. GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Research, December 2006.
Jensen, K., M. Styczynski, I. Rigoutsos and G. Stephanopoulos, Computational Methods of a Generic Motif Discovery Algorithm for Sequential Data. Extended Abstract. 2006 AiChE Annual Meeting, San Francisco, CA. November 2006.<\LI>
Lan, H., X. Huang, R. Zhou and B.J. Berne. Water dynamics in the salvation shell of a multi-domain protein, J. Phys. Chem. B., 110, 3704-3711, 2006.
Lwin, T.Z., R. Zhou and R. Luo. Is Poisson-Boltzmann theory insufficient for protein folding simulations? J. Chem. Phys. 124, 34902-34907, 2006.
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.
Krause, A., A. Ramakumar, D. Bartels, F. Battistoni, T. Bekel, J. Boch, M. Bohm, F. Friedrich, T. Hurek, L. Krause, B. Linke, A.C. McHardy, A. Sarkar, S. Schneiker, A.A. Syed, R. Thauer, F.J. Vorholter, S. Weidner, A. Puhler, B. Reinhold-Hurek, O. Kaiser and A. Goesmann. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nature Biotechnology, 24(11):1385-91, November 2006. Epub 2006 Oct 22.
Eleftheriou, R., A. Germain, A. Royyuru and R. Zhou. Thermal denaturing of mutant lysozyme with both OPLSAA and CHARMM force fields, J. Am. Chem. Soc. 128, 13388-13395, 2006.
McHardy, A.C., H. Neuweger, L. Krause and F. Meyer. REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Applied Bioinformatics, 5(3):193-8, 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.
Li, J., X. Li, M. Eleftheriou, and R. Zhou. Hydration and Dewetting near Fluoronated Superhydrophobic Plates, J. Am. Chem. Soc. 128, 12439-12447, 2006.
Zhou, R., L. Parida, K. Kapila, and S. Mudur. PROTERAN: Animated Terrain Evolution for Visual Analysis of Patterns in Protein Folding Trajectory, Bioinformatics, in press, 2006.
Silverman, B.D. Hydrophobic and acidic moments of a nucleoplasmin NP-core chaperone. Journal of Biomolecular Structure and Dynamics, 24(1):49-56, August 2006.
Zhou, R., A. Royyuru, P. Athma, F. Suits and B.D. Silverman. Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins, Int. J. Bioinf. Res. Appl. 2, 161-176, 2006.
Schneiker, S., V.A. Martins dos Santos, D. Bartels, T. Bekel, M. Brecht, J. Buhrmester, T.N. Chernikova, R. Denaro, M. Ferrer, C. Gertler, A. Goesmann, O.V. Golyshina, F. Kaminski, A.N. Khachane, S. Lang, B. Linke, A.C. McHardy, F. Meyer, T. Nechitaylo, A. Puhler, D. Regenhardt, O. Rupp, J.S. Sabirova, W. Selbitschka, M.M. Yakimov, K.N. Timmis, F.J. Vorholter, S. Weidner, O. Kaiser O and P.N. Golyshin. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nature Biotechnology, 24(8):997-1004, August 2006. Epub 2006 Jul 30.
Liu, P., X. Huang, R. Zhou and B.J. Berne. Hydrophobic Aided Replica Exchange Method for Protein Folding, J. Phys. Chem. B 110, 19018 - 19022, 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.
Eleftheriou, M., A. Rayshubski, J. Pitera, B. Fitch, R. Zhou and R. Germain. Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L, International Parallel and Distributed Processing Symposium HiCOMB 2006.
Eleftheriou, M., A. Rayshubski, J. Pitera, B. Fitch, R. Zhou and R. Germain. Large Scale Parallel Implementation of Replica Exchange on Blue Gene/L, SIAM Conference on Parallel Processing for Scientific Computing San Francisco, California, USA February 22-24, 2006.
Fitch, B.G, A. Rayshubskiy, M. Eleftheriou, T.J.C. Ward, M. Giampapa, Y. Zhestkov, M.C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, S. Feller, and and R. Germain. Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. In V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, editors, International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846-854. Springer-Verlag, 2006.
Liu, T., L. Ye, H. Chen, J. Li, Z. Wu and R. Zhou. A Combined Steepest Descent and Genetic Algorithm (SD/GA) Approach for the Optimization of Solvation Parameters, Mol. Simul. 32, 427-435, 2006.
Zhou, R., Replica Exchange Molecular Dynamics Method for Protein Folding, Ed. Y. Bai and R. Nussinov, "Methods in Molecular Biology", The Humana Press, 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.
Zhou, R. and B. J. Berne, Recent Progress in Protein Folding Kinetics, Ann. Rev. of Phys. Chem., 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.
Lan, H., X. Huang, R. Zhou and B. J. Berne, Water dynamics in the salvation shell of a multi-domain protein, J. Phys. Chem. B. 109, 2005.
Silverman, B. David, "Asymmetry in the burial of hydrophobic residues along the histone chains of Eukarya, Archaea, and a transcription factor." BMC Structural Biology, 5:20, 2005
Lei, L., J. Li, T. Liu, Z. Wu and R. Zhou, Wavelets approach for protein trajectory analysis. J. Bioinfo. Comp. Biol., 3, 2005.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Buttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klosgen U, Patschkowski T, Ruckert C, Rupp O, Schneiker S, Schuster SC, Vorholter FJ, Weber E, Puhler A, Bonas U, Bartels D, Kaiser O. Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence. J. Bacteriol. 187:7254-66, 2005.[
Zhou, R., A. Royyuru, P. Athma, F. Suits and B. D. Silverman, Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins. Int. J. Bioinfo. Res. Appl., 2, in press, 2005
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.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucl. Acids Res. 33:5691-702, 2005.[
Silverman, B. David, "Underlying Hydrophobic Sequence Periodicity of Protein Tertiary Structure." Journal of Biomolecular Structure and Dynamics 22, 411-423, 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.
Silverman, B. David, "The Hydrophobicity of the H3 Histone Fold differs from the Hydrophobicity of the other three Folds." Journal of Molecular Evolution, 60, 354-364, 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.
Zhou, R., Protein Folding Free Energy Landscape with Parallel Replica Exchange Molecular Dynamics, Ed. Albert Zomaya, "Parallel Computing for Bioinformatics and Computational Biology", John Wiley & Sons Publisher, 2005
Huang, X., R. Zhou, and B. J. Berne, Drying and Hydrophobic Collapse of Paraffin Plates, J. Phys. Chem. B 109, 3546-3552, 2005
Parida, L., and R. Zhou, Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-hairpin, PLoS Comp. Biol. 1, 32-40, 2005
Li, J., H. Chen, T. Liu, L. Ye, H. Fang, X. Tang, Z. Wu and R. Zhou, Water Hydration Near Graphite-CH3 and Graphite-COOH Surfaces, J. Phys. Chem. B 109, 13639-13648, 2005
Liu, P., X. Huang, R. Zhou and B. J. Berne, Drying and Hydrophobic Collapse of Melittin Tetramer, Nature, 437, 159-162, 2005
Zhou, R., Sampling Protein Folding Free Energy Landscape: Coupling Replica Exchange Method with P3ME/RESPA Algorithm , J. Mol. Grap. Model. 22, 451-463, 2004
A.C. McHardy, A. Goesmann, A. Pühler, F. Meyer. Development of joint application strategies for two microbial gene finders, Bioinformatics, 20:1622-31, 2004.
Zhou, R., G. Dent, A. Royyuru, and P. Athma, Assessment of Protein Structure Refinement with Replica exchange Method, Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 390-391, 2004
Zhou, R., A. Royyuru, P. Athma, and B. D. Silverman, Hydrophobicity of Multi-domain Proteins: Spatially Profiling their Distribution, Eds, A. Gramada, P. E. Bourne, RECOMB2004 - Currents in Computational Molecular Biology, 441-442, 2004
Zhou, R., G. Krilov and B. J. Berne, Comment on "Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?": The Poisson-Boltzman Model, J. Phys. Chem. B 108, 7528 - 7530, 2004
Swope, W., J. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. Fitch, R. Germain, A. Rayshubskiy, T. J. C. Ward, Y. Zhestkov, and R. Zhou, Describing Protein Folding Kinetics by Molecular Dynamics Simulations: II. Application to a beta-hairpin Peptide, J. Phys. Chem. B 108, 6582-6594, 2004
A.C. McHardy, J. Kalinowski, A. Pühler, F. Meyer. Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics, Proteomics 4: 46-58, 2004.
Zhou, R., X. Huang, C. Margulius and B. J. Berne, Hydrophobic Collapse in Multi-domain Protein Folding, Science, 305, 1605-1609, 2004
Feng, J., R. Zhou, and L. Parida, Pattern Discovery Analysis for Protein Folding Trajectories, Ed. Y. P. Chen and L. S. Wong, Proc. 3rd Asia-Pac. Bioinfo. Conf., p95-99, Imperial College Press, London, UK, 2004
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.
Eres, R., G.M. Landau and L. Parida, "Permutation Pattern Discovery in Biosequences." In Journal of Computational Biology. To Appear. 2004.
Chattaraj A. and L. Parida, "An inexact suffix tree based algorithm for extensible pattern discovery." In Theoretical Computer Science. To Appear. 2004
Huynh, T. and I. Rigoutsos, "The Web Server of IBM’s Bioinformatics and Pattern Discovery Group: 2004 update." In Nucleic Acids Research, 32:10-15, 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.
Apostolico, A. M. Comin and L. Parida, "Motifs in Ziv-Lempel-Welch Clef." In Proceedings of IEEE Data Compression Conference (DCC '04). Snowbird, Utah, March 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.
Apostolico, A. and L. Parida, "Incremental Paradigms of Motif Discovery." In Journal of Computational Biology 11(1):15-25, January 2004.
Kaminski, G., R. A. Friesner and R. Zhou, A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulation, J. Comp. Chem. 24, 267-276, 2003
Silverman, B. David, "Hydrophobicity of Transmembrane Proteins: Spatially profiling the distribution." Protein Science 12, 586-599, 2003
A. Wilke, C. Rückert, D. Bartels, M. Dondrup, A. Goesmann, A. Hüser, S. Kespohl, B. Linke, M. Mahne, A. McHardy, A. Pühler, F. Meyer. Bioinformatics support for high-throughput proteomics, J. Biotechnol. 106: 147-56, 2003.
Zhou, R., B. D. Silverman, A. Royyuru, and P. Athma, Spatial Profiling of Protein Hydrophobicity: Native vs. Decoy Structures , Proteins, 52, 561-572, 2003
Zhou, R., Folding free energy landscape of protein folding in water: explicit vs. implicit solvent, Proteins 53, 148-161, 2003
A. Goesmann, B. Linke, O. Rupp, L. Krause, D. Bartels, M. Dondrup, A.C. McHardy, A. Wilke, A. Pühler, F. Meyer. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology, J. Biotechnol. 106: 157-67, 2003.
Fitch, B. R., R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, F. Suits, W. Swope, T. J. C. Ward, Y. Zhestkov, and R. Zhou, Blue Matter, An Application Framework for Molecular Simulation on Blue Gene , J. Parallel & Distrib. Comput. 63, 759-773, 2003
Zhou, R., Trp-cage: Folding Free Energy Landscape in Explicit Water, Proc. Natl. Acad. Sci., 100, 13280-13285, 2003
Zhou, R., Exploring Protein Folding Free Energy Landscape: Replica Exchange Monte Carlo , Eds, J. E. Gubernatis, The Monte Carlo Method in the Physical Sciences, Celebrating the 50th Anniversary of the Metropolis Algorithm, AIP Conf. Proc. Vol 690, 406-408, 2003
Murphy, E., I. Rigoutsos, T. Shibuya and T. Shenk, "Re-evaluation of Human Cytomegalovirus Coding Potential." Proc. Nat. Academy of Sciences, USA. In Proc. Nat. Acad. Sciences USA, 100(23):13585-13590, November 2003
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.
Silverman, B. David, "Hydrophobic Moments of Protein Tertiary Structure." Proteins: Structure, Function and Genetics 53, 880-888, 2003
J. Kalinowski, B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B.J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Krämer, B. Linke, A.C. McHardy, F. Meyer, B. Mockel, W. Pfefferle, A. Pühler, D.A. Rey, C. Rückert, O. Rupp, H. Sahm, V.F. Wendisch, I. Wiegräbe, A. Tauch. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins, J. Biotechnol. 104: 5-25, 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.
Miranda, K.C., J.R. Shannon, A.S. Yap, R.D.Teasdale, and J.L. Stow, "Contextual Binding of p120ctn to E-cadherin at the Basolateral Plasma Membrane in Polarized Epithelia." In Journal of Biological Chemistry, 278:43480 - 43488, October 2003.
R. Eres, G. M Landau and L. Parida, "A Combinatorial Approach to Automatic Discovery of Cluster Patterns." In Proceedings of WABI '03, Budapest, Hungary, September 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." Nucleic Acids Research, 31(13):3645-3650, July 2003.
A.C. McHardy, A. Tauch, C. Rückert, A. Pühler, J. Kalinowski. Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum, J. Biotechnol. 104: 229-40, 2003.
Grimmond S.M., K.C. Miranda, Z. Yuan, M.J. Davis, D.A. Hume, K. Yagi, N. Tominaga, H. Bono, Y. Hayashizaki, T. Okazaki, R.D. Teasdale, "The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment." In Genome Research, 13(6b):1350-1359, June 2003.
Hoehl, M, I. Rigoutsos and M. Ragan, "Freeing Phylogenies from Artifacts of Alignments," Poster Presentation in 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.
F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, A. Pühler. GenDB--an open source genome annotation system for prokaryote genomes, Nucleic Acids Res. 31: 2187-95, 2003.
Apostolico, A. and L. Parida, "Compression and the Wheel of Fortune." In Proceedings of IEEE Data Compression Conference (DCC '03). Snowbird, Utah, March 2003.
Zhou, R., and B. D. Silverman, Detecting native protein folds among large decoy sets with hydrophobic moments profiling, Proc. Paci. Symp. Biocomp. 2002, Eds. R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale and T. E. Klein, p673-684, World Scientific, Singapore, 2002
Kaminski, G., H. A. Stern, B. J. Berne, R. A. Friesner, Y. Cao, R. B. Murphy, R. Zhou, and T. A. Halgren, Development of a Polarizable Force Field for Proteins via ab initio Quantum Chemistry: First Generation Model and Gas phase Tests, J. Comp. Chem. 23, 1515-1531, 2002
Zhou, R., and B. J. Berne, Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?, Proc. Natl. Acad. Sci. 99, 12777-12782, 2002
Silverman, B. David, "A Two-Component Nucleation Model of Protein Hydrophobicity.’ Journal of Theoretical Biology 216, 130-146, 2002
Dehal, P., Y. Satou, R. K. Campbell, J. Chapman, B. Degnan, A. De Tomaso, 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, December 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
Rigoutsos, I., T. Huynh, A. Floratos, L. Parida and D. Platt, "Dictionary-driven Protein Annotation." In Nucleic Acids Research. 30(17), September 2002.
Shibuya, T. and I. Rigoutsos, "Dictionary-driven Prokaryotic Gene Finding." In Nucleic Acids Research. 30(12), July 2002.
Zhou, R., B. J. Berne and R. Germain, Free energy landscape of a beta-hairpin folding in explicit water, Proc. Natl. Acad. Sci. 98, 14931-14936, 2001
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.
Platt, D.E., "Are Mitochondria Mesoscopic?" In Biophysical Chemistry. 91(3):245-252 (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.
Miranda KC, T. Khromykh, P. Christy, T.L. Le, C.J. Gottardi, A.S. Yap, J.L. Stow and R.D. Teasdale, "A Dileucine Motif Targets E-cadherin to the Basolateral Cell Surface in Madin-Darby Canine Kidney and LLC-PK1 Epithelial Cells." In Journal of Biological Chemistry, 276(25):22565-72, June 2001.
Silverman, B. David, "Hydrophobic Moments of Protein Structures: Spatially Profiling the Distribution." Proceedings of the National Academy of Sciences 98, 4996-5001, 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.
Allen, F., G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni, M. Denneau, W. Donath, M. Eleftheriou, B. Fitch, B. Fleischer, C. J. Georgiou, R. Germain, M. Giampapa, D. Gresh, M. Gupta, R. Haring, H. Ho, P. Hochschild, S. Hummel, T. Jonas, D. Lieber, G. Martyna, K. Maturu, J. Moreira, D. Newns, M. Newton, R. Philhower, T. Picunko, J. Pitera, M. Pitman, R. Rand, A. Royyuru, V. Salapura, A. Sanomiya, R. Shah, Y. Sham, S. Singh, M. Snir, F. Suits, R. Swetz, W. C. Swope, N. Vishnumurthy, T. J. C. Ward, H. Warren, and R. Zhou, Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems Journal 40, 310-327, 2001
Zhou, R., E. Harder, H. Xu and B. J. Berne, Efficient multiple time step method for use with Ewald and Particle-Mesh Ewald for large biomolecular systems , J. Chem. Phys. 115, 2348-2358, 2001
Zhou, R., R. A. Friesner, A. Ghosh, R. C. Rizzo, W. L. Jorgensen, and R. M. Levy, New Linear Interaction Method for Binding Affinity Calculations using a Continuum Solvent Model, J. Phys. Chem. B105, 10388-10397, 2001
Silverman, B. David, "Molecular Moments for Computer-Aided Drug Discovery." Inaugural Issue of Mini-Reviews in Medicinal Chemistry 1(1), 1-4, 2001
Parida, L., "Some Results on Flexible-pattern Discovery." In Proceedings 11th Annual Symposium on Combinatorial Pattern Matching. June 2000. Montreal, Canada.
Silverman, B. David, "Three-Dimensional Moments of Molecular Property Fields." Journal of Chemical Information and Computer Science 40, 1470-1476, 2000
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.
Silverman, B. David, "The Thirty-one Benchmark Steroids Revisited: Comparative Molecular Moment Analysis (CoMMA) with Principal Component Regression." QSAR (Quantitative Structure Activity Relations) 19, 237-246, 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." 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. 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.
Silverman, B. David, Mike C. Pitman and Daniel E. Platt, "Molecular Moment Similarity Between Several Nucleoside Analogs of Thymidine and Thymidine." Journal of Biomolecular Structure and Dynamics, 16, 739-1102, 1999
Parida, L., "On the Approximability of Physical Map Problems using Single Molecule Methods." In Proceedings of Discrete Mathematics and Theoretical Computer Science (DMTCS 99), Auckland, New Zealand. January 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. and D. Platt, "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 Uniform Framework for Ordered Restriction Map Problems," In Journal of Computational Biology, vol. 5, num. 4. (winter) 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." In Proceedings Second Annual TIGR Conference on Computational Genomics, Reston, VA. November 1998. (Extended Abstract)
Silverman, 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.
Floratos, A. and I. Rigoutsos, "On The Time Complexity Of The Teiresias Algorithm." IBM Research Report, RC 21161. April 1998.
Parida, L. and B. Mishra, "Partitioning K Clones: Hardness Results and Practical Algorithms for the K-Populations Problem." In Proceedings Second Annual ACM International Conference on Computational Molecular Biology (RECOMB 98). New York, NY. March 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. and A. Floratos, "Combinatorial Pattern Discovery In Biological Sequences: The TEIRESIAS Algorithm." In Bioinformatics, 14(1). January 1998.
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.
Platt, D. E. and B. D. Silverman, "Registration, Orientation, and Similarity of Molecular Electrostatic Potentials through Multipole Matching." In Journal of Computational Chemistry, vol. 17. 1996.
Silverman, B. D. and D. E. Platt, "Comparative Molecular Moment Analysis (CoMMA): 3D-QSAR Without Molecular Alignment," In Journal of Medicinal Chemistry, vol. 39. 1995.
Rigoutsos, I. and A. Califano, "Searching In Parallel for Similar Strings." IEEE Computational Science and Engineering, vol. 1, num. 2. Summer 1994.
Platt, D. E. and F. Family, "Fractal and Multifractal Scaling," Physical Review E, vol. 47. 1993.
Platt, D. E. and F. Family, "Scaling of the Point-Point Correlation Function of DLA" Fractals, vol. 1. 1993.
In the last several years, there has been extensive press coverage of the work that has come out of our group. The following is a fairly extensive set of links and references to the relevant articles.
Monsanto And IBM Announce Strategic Techonology Alliance: 1 2
Big Blue Advancing In The Genomics Arena, ISB News Report, Spring 1998.
Linux Weekly News, November 05, 1998.
Teiresias on the Hacker Trail, Wired News 11/98
Technology Alliance Focuses on Research, IBM Research Magazine, Issue 1, 1998.
Pattern Of Deception, IBM Research Magazine, Issue 1, 1999.
Daring To Think Deep: Decoding Proteins, IBM Research Magazine, Issue 2, 1999.
Into the Big Blue Yonder, MIT Technology Review 07/99.
Algorithms solve business problems, USA Today, January 26, 1999.
All seeing software keeps eye on hackers, The London Sunday Times, November 8, 1998.
Policing the computer underworld, Science 282, 1223b, November 13,
1998.
Although the majority of our work focuses on bioinformatics applications for the
TEIRESIAS algorithm a research group at IBM's Global Security Analysis Laboratory in Zurich, Switzerland, has been successfully applying the algorithm in the development of computer-intrusion detection systems.
Wespi, A., M. Dacier and H. Debar, "An Intrusion-Detection System Based on the Teiresias Pattern-Discovery Algorithm" IBM Research Report, 1999.
Wespi, A., M. Dacier and H. Debar, "Intrusion Detection Using Variable-Length Audit Trail Patterns." IBM Research Report, RZ 3164. 1999.
