| From Corynebacterium Glutamicum to Mycobacterium Tuberculosis - Towards Transfers of Gene Regulatory Networks and Integrated Data Analyses with MycoRegNet | J. Krawczyk, T. A. Kohl, A. Goesmann, J. Kalinowski, and J. Baumbach | Nucleic Acids Research, Vol. 37, No. 14, e97 | August 2009 | Algorithms | [PDF]
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| Torque: Topology-Free Querying of Protein Interaction Networks | S. Bruckner, F. Hueffner, R. M. Karp, R. Shamir, and R. Sharan | Nucleic Acids Research, Vol. 37, pp. 106-108 | July 2009 | Algorithms | [PDF]
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| On the Power and Limits of Evolutionary Conservation -- Unraveling Bacterial Gene Regulatory Networks | J. Baumbach | Nucleic Acids Research, Vol. 38, No. 22, pp. 7877-7884 | December 2010 | Algorithms | [PDF]
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| AltAnalyze and DomainGraph: Analyzing and Visualizing Exon Expression Data | D. Emig, N. Salomonis, J. Baumbach, T. Lengauer, B. R. Conklin, and M. Albrecht | Nucleic Acids Research, Vol. 38, Web Server Issue, pp. W755-W762 | July 2010 | Algorithms | [PDF]
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| Dynamic programming meets the principle of inclusion and exclusion | R. M. Karp | Operations Research Letters, Vol. 1, No. 2, pp. 49-51 | April 1982 | Algorithms | |
| Review of F. V. Fomin and D. Kratsch, "Exact Exponential Algorithms" | M. Mnich | Operations Research Letters, Vol. 39, No. 3, pp. 229-230 | May 2011 | Algorithms | |
| Knowledge Discovery for Time Series | M. Saffell | Ph.D. Thesis, OGI School of Science and Engineering, Oregon Health and Science University | September 2005 | Algorithms | |
| Curve Reconstruction and the Traveling Salsman Problem. | E. Althaus | Ph.D. Thesis, Universitat des Saarlandes. 2001. | 2001 | Algorithms | |
| Stochastic Manhattan Learning: Time-Evolution Operator for the Ensemble Dynamics | T. Leen and J. Moody | Physical Review E, 1997. | 1997 | Algorithms | |
| Probabilistic Convergence Guarantees for Type-II Pulse-Coupled Oscillators | J. Nishimura and E. Friedman | Physical Review E, Vol. 86, Issue 2 | August 2012 | Algorithms | |
| Calculations for Cosmic Axion Detection | L. Krauss, J. Moody, F. Wilczek, and D. Morris | Physical Review Letters, Vol. 55, Issue 17, pp. 1797-1800 | 1985 | Algorithms | |
| Macroscopic T Nonconservation: Prospects for a New Experiment | W. Bialek, J. Moody, and F. Wilczek | Physical Review Letters, Vol. 56, pp. 1623 | 1986 | Algorithms | |
| Realizations of Magnetic Monopole Gauge Fields: Diatoms and Spin-Precession | J. Moody, A. Shapere, and F. Wilczek | Physical Review Letters, Vol. 56, pp. 893 | 1986 | Algorithms | |
| A Stellar Energy Loss Mechanism Involving Axions | L.M. Krauss, J. Moody, and F. Wilczek | Physics Letters, Vol. 144B, pp. 391 | 1984 | Algorithms | |
| Joint Analysis of Multiple Metagenomic Samples | Y. Baran and E. Halperin | PLOS Computational Biology, accepted for publication | 2012 | Algorithms | |
| Genome-Wide Association Data Reveal a Global Map of Genetic Interaction Among Protein Complexes | G. Hannum., R. Srivas., A. Guénolé, H. van Attikum, N. J. Krogan, R. M. Karp, and T. Ideker | PLoS Genetics, Vol. 5, Issue 12, e1000782 | December 2009 | Algorithms | [PDF]
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| Presymptomatic Risk Assessment for Chronic Non-Communicable Diseases | B. Padhukasahasram, E. Halperin, J. Wessel, D. J. Thomas, E. Silver, H. Trumbower, M. Cargill, and D. A. Stephan | PLoS ONE Vol. 5, No. 12. doi:10.1371/journal.pone.0014338 | December 2010 | Algorithms | |
| Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma | C. F. Skibola, P. M. Bracci, E. Halperin, A. Nieters, A. Hubbard, R. A. Paynter, D. R. Skibola, A. Agana, N. Becker, P. Tessler, M. S. Forrest, S. Sankararaman, L. Conde, E. A. Holly, and M. T. Smith | PLoS ONE, Vol. 3, Issue 7, e2816 | June 2008 | Algorithms | [PDF]
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| Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse | E. Lindfors, P. V. Gopalachrayulu, E. Halperin, and M. Oresic | PLoS, Vol. 4, Issue 10, e7323 | October 2009 | Algorithms | [PDF]
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| Active Learning Under Arbitrary Distributions | C. Monteleoni and M. Kaariainen | Poster at the Value of Information in Inference, Learning, and Decision-Making Workshop at the 19th Annual Conference on Neural Information Processing Systems (NIPS), Vancouver, Canada | December 2005 | Algorithms | |
| Algorithms for Comparing Pedigree Graphs | B. Kirkpatrick, H. Finucane, Y. Reshef, and R. Karp | Presented at the 10th Workshop on Algorithms in Bioinformatics (WABI 2010), Liverpool, United Kingdom | September 2010 | Algorithms | [PDF]
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| Genomic Privacy and Limits of Individual Detection in a Pool | S. Sankararaman, G. Obozinski, M. I. Jordan, and E. Halperin | Presented at the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, Massachusetts | July 2010 | Algorithms | |
| Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes | R. Srivas, G. Hannum, A. Guénolé, H. van Attikum, N. J. Krogan, R. M. Karp, and T. Ideker | Presented at the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, Massachusetts | July 2010 | Algorithms | |
| A Model-Based Approach for Analysis of Spatial Structure in Genetic Data | W. Yang, J. Novembre, E. Eskin, and E. Halperin | Presented at the Annual Meeting of the American Society of Human Genetics, San Francisco, California | November 2012 | Algorithms | |
| Lower Bounds for Reductions | M. Kaariainen and J. Langford | Presented at the Atomic Learning Workshop, Chicago, Illinois | March 2006 | Algorithms | |
| Effective Heuristics for NP-Hard Problems | R. M. Karp | Presented at the Michael Rabin Celebration, Cambridge, Massachusetts | August 2011 | Algorithms | |
| Understanding Science Through the Lens of Computation | R. Karp | Presented at the Symposium on Transformational Information Engineering and Science, Singapore | January 2010 | Algorithms | |
| Theory of Computation as an Enabling Tool for the Sciences | R. Karp | Presented at the Turing Centennial Celebration, Princeton, New Jersey. Also presented at the 9th Annual Conference on Theory and Applications of Models of Computation (TAMC 2012), Turing Centenary Meeting, Beijing, China | May 2012 | Algorithms | |
| Competitive analysis of financial games | R. El-Yaniv, A. Fiat, R. M. Karp, and G. Turpin | Proceedings 33rd Annual Symposium on Foundations of Computer Science (Cat. No. 92CH3188-0), Pittsburgh, Pennsylvania, pp. 327-33 | October 1992 | Algorithms | |
| Selfish Behavior and Stability of the Internet: A Game-Theoretic Analysis of TCP | A. Akella, R.M. Karp, S. Seshan, S. Shenker, and C. Papadimitriou. | Proceedings ACM SIGCOMM 2002. | 2002 | Algorithms | |
| CLIFF: Clustering of High-Dimensional Microarray Data via Iterative Feature Filtering Using Normalized Cuts | E. P. Xing and R. M. Karp | Proceedings for the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, Denmark, Vol. 17, Supplement 1, pp. S306-S315 | July 2001 | Algorithms | [PDF]
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| Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles | I. Ulitzky, R. M. Karp, and R. Shamir | Proceedings of 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, pp. 347-359 | March 2008 | Algorithms | |
| Mapping the Genome: some combinatorial problems arising in molecular biology | R. M. Karp | Proceedings of 25th Annual Symposium on the Theory of Computing, San Diego, California, pp. 278-85 | May 1993 | Algorithms | |
| Linked Decomposition of Networks and the Power of Choice in Polya Urns | H. Lin, C. Amanatidis, M. Sideri, R. M. Karp, and C. Papadimitriou | Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 2008), pp. 993-1002, San Francisco, California | January 2008 | Algorithms | |
| A Rigorous Analysis of Population Stratification with Limited Data | K. Chaudhuri, E. Halperin, S. Rao, and S. Zhou | Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA), New Orleans, Louisiana, pp. 1046-1055 | January 2007 | Algorithms | [PDF]
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| Price Behavior and Hurst Exponents of Tick-By-Tick Interbank Foreign Exchange Rates | J. Moody and L. Wu | Proceedings of Computational Intelligence in Financial Engineering (IEEE IAFE 1995), New York, New York | 1995 | Algorithms | |
| Selecting Input Variables via Sensitivity Analysis: Application to Predicting the U.S. Business Cycle | J. Utans, J. Moody, S. Rehfuss, and H. Siegelmann | Proceedings of Computational Intelligence in Financial Engineering (IEEE IAFE 1995), New York, New York | April 1995 | Algorithms | |
| Stock Returns: Momentum, Volatility and Interest Rates | Y. Fang, S. Wada, and J. Moody | Proceedings of Computational Intelligence in Financial Engineering, IEEE Press | 2003 | Algorithms | |
| Running Time Analysis of ACO Systems for Shortest Path Problems | C. Horoba and D. Sudholt | Proceedings of Engineering and Stochastic Local Search Algorithms (SLS 2009), Brussels, Belgium, pp. 76-91 | September 2009 | Algorithms | [PDF]
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| Physical mapping of chromosomes using unique probes | F. Alizadeh, R. M. Karp, D.K. Weisser, and G. Zweig | Proceedings of Fifth Annual ACM-SIAM Symposium on Discrete Algorithms, Arlington, Virginia, pp. 489-500 | January 1994 | Algorithms | |
| Selection in the presence of noise: the design of playoff systems | M. Adler, P. Gemmell, M. Harchol-Balter, R. M. Karp, and C. Kenyon | Proceedings of Fifth Annual ACM-SIAM Symposium on Discrete Algorithms, Arlington, Virginia, pp. 564-72 | January 1994 | Algorithms | |
| The Minimum-Entropy Set Cover Problem | E. Halperin and R.M. Karp | Proceedings of ICALP | January 05 2004 | Algorithms | |
| LOGOS: A Modular Bayesian Model for de Novo Motif Detection | E.P. Xing, W. Wu, M. Jordan, and R.M. Karp | Proceedings of IEEE Computer Society Bioinformatic Conference IPTPS | 2003 | Algorithms | |
| Load Balancing in Dynamic Structured P2P Systems | B. Godfrey, R.M. Karp, K. Lakshminarayanan, S. Surana, and I. Stoica | Proceedings of INFOCOMM | January 05 2004 | Algorithms | |
| Approximating the Volume of Unions and Intersections of High-Dimensional Geometric Objects | K. Bringmann and T. Friedrich | Proceedings of International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, pp. 436-447 | December 2008 | Algorithms | [PDF]
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| Average Update Times for Fully-Dynamic All-Pairs Shortest Paths | T. Friedrich and N. Hebbinghaus | Proceedings of International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, pp. 693-704 | December 2008 | Algorithms | [PDF]
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| A Maximun Likelihood Polynomial Time Syndrome Decoder to Correct Linearly Independent Errors | G.B. Horn and R.M. Karp | Proceedings of International Symposium on Information Theory | 2001 | Algorithms | |
| Finite-Length Analysis of LT-codes | R.M. Karp, M. Luby, and A. Shokrollahi | Proceedings of International Symposium on Information Theory (ISIT) | January 05 2004 | Algorithms | |
| Global Synchronization in Sensornets | J. Elson, R.M. Karp, C.H. Papadimitriou, and S. Shenker | Proceedings of LATIN, 609-624, 2004. | 2004 | Algorithms | |
| Conserved Patterns of Protein Interaction in Multiple Species | R. Sharan, S. Sutharan, R. Kelley, T. Kuhn, S. McCuine, T.Sittler, R. Karp, and T. Ideker | Proceedings of National Academy of Science, Vol. 102, Issue 6, pp. 1974-1979 | February 2005 | Algorithms | [PDF]
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