| Integrated Analysis and Reconstruction of Microbial Transcriptional Gene Regulatory Networks Using CoryneRegNet | J. Baumbach, T. Wittkop, C. K. Kleindt, and A. Tauch | Nature Protocols, Vol. 4, Issue 6, pp. 992-1005 | June 2009 | Algorithms | |
| Towards the Integrated Analysis, Visualization, and Reconstruction of Microbial Gene Regulatory Networks | J. Baumbach, S. Rahmann, and A. Tauch | Briefings in Bioinformatics, Vol. 10, Issue 1, pp. 75-83 | January 2009 | Algorithms | [PDF]
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| Reliable Transfer of Transcriptional Gene Regulatory Networks Between Taxonomically Related Organisms | J. Baumbach, S. Rahmann, and A. Tauch | BMC Systems Biology, Vol. 3, Issue 8 | January 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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| Computing the Similarity of Two Sequences with Nested Arc Annotations | J. Alber, J. Gramm, J. Guo, and R. Niedermeier | Theoretical Computer Science, Vol. 312, Issues 2-3, pp. 337-358 | January 2004 | Algorithms | |
| 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 | |
| Incomplete Directed Perfect Phylogeny | I. Pe'er, T. Pupko, R. Shamir, and R. Sharan | SIAM Journal on Computing 33(3), pp. 590-607 | January 05 2004 | Algorithms | |
| Scoring Clustering Solutions by Their Biological Relevance | I. Gat-Viks, R. Sharan, and R. Shamir | Bioinformatics, 19,pp 2381-2389 | 2003 | Algorithms | |
| Reconstructing Chain Functions in Genetic Networks | I. Gat-Viks, R. Shamir, R.M. Karp, and R. Sharan | Proceedings of the Ninth Pacific Symposium on Biocomputing (PSB'04), pp. 498-509 | January 05 2004 | Algorithms | |
| A Simplex variant solving an m*d linear program in O(min(m2, d2)) expected number of pivot steps | I. Adler, R. M. Karp, and R. Shamir | Journal of Complexity, Vol. 3, No. 4, pp. 372-87 | December 1987 | Algorithms | |
| A family of simplex variants solving an m*d linear program in expected number of pivot steps depending on d only | I. Adler, R. M. Karp, and R. Shamir | Mathematics of Operations Research, Vol. 11, No. 4, pp. 570-90 | November 1986 | Algorithms | |
| Coalescing Times for IID Random Variables | I. Adler, H.S. Ahn, R.M. Karp, and S.M. Ross | Random Structures and Algorithms | 2003 | Algorithms | |
| A Probabilistic Model for the Survivability of Cells | I. Adler, H-S Ahn, R. M. Karp, and S.M. Ross | Journal of Applied Probability, Vol. 42, No. 4, pp. 919-931 | December 2005 | Algorithms | |
| Data Visualization and Feature Selection: New Algorithms for Nongaussian Data | H. Yang and J. Moody | Advances in Neural Information Processing Systems, Vol.12, S.A. Solla, T.K. Leen and K.R. Muller (eds.), MIT Press, 2000. | 2000 | Algorithms | |
| Feature Selection Based on Joint Mutual Information | H. Yang and J. Moody | Advances in Intelligent Data Analysis (AIDA), Computational Intelligence Methods and Applications (CIMA), International Computer Science Conventions, Rochester, New York, June 22-25, 1999. | June 1999 | Algorithms | |
| Online Scheduling for Sorting Buffers | H. Racke, C. Sohler, and M. Westermann | European Symposium on Algorithms, 820-832, 2002. | 2002 | 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 Method for Obtaining Randomized Algorithms with Small Tail Probabilities | H. Alt, L. Guibas, K. Mehlhorn, R. M. Karp, et al. | Algorithmica, Vol. 16, No. 4-5, pp. 543-547 | October 1996 | Algorithms | |
| Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction | G.E. Blelloch, K. Dhamdhere, E. Halperin, R. Ravi, R. Schwartz, and S. Sridhar | Proceedings of the 33rd International Colloquium on Automata, Languages, and Programming (ICALP 2006), Venice, Italy, pp. 667-678 | July 2006 | Algorithms | |
| 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 | |
| Failure correction techniques for large disk arrays | G.A. Gibson, L. Hellerstein, R. M. Karp, R.H. Katz, and D.A. Patterson | Proceedings of the Third International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS-III), Boston, Massachusetts, pp.123-32 | April 1989 | Algorithms | |
| Hardness of Approximation for Vertex-Connectivity Network Design Problems | G. Kortsarz, R. Krauthgamer, and J.R. Lee | Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization (APPROX), 185-199, Springer, 2002. | 2002 | Algorithms | |
| Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification and Population Stratification | G. Kimmel, R. Sharan, and R. Shamir | INFORMS Journal on Computing, in press | January 05 2004 | Algorithms | |
| Idetifying Blocks and Sub-Populations in Noisy SNP Data | G. Kimmel, R. Sharan, and R. Shamir | Proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI'03), pp. 303-319 | 2003 | Algorithms | |
| Association Mapping and Significance Estimation via the Coalescent | G. Kimmel, R. M. Karp, M. A. Jordan, and E. Halperin | Journal of Human Genetics, Vol. 83, Issue 6, pp. 675-683 | December 2008 | Algorithms | [PDF]
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| A Randomization Test for Controlling Population Stratification in Whole-Genome Association Studies | G. Kimmel, M. I. Jordan, E. Halperin, R. Shamir, and R. M. Karp | American Journal of Human Genetics, Vol. 81, Issue 5, pp. 895-905 | November 2007 | Algorithms | [PDF]
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| 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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| A Few Ants Are Enough: ACO with Iteration-Best Update | F. Neumann, D. Sudholt, and C. Witt | Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2010), Portland, Oregon, pp. 63-70 | July 2010 | Algorithms | |
| UbiMASS - Ubiquitous Mobile Agent System for Wireless Sensor Networks | F. Bagci, J. Wolf, B. Satzger, and T. Ungerer | Proceedings of the Third IEEE International Conference on Sensor Networks, Ubiquitous, and Trustworthy Computing (SUTC2010), Newport Beach, California, pp. 245-252 | June 2010 | 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 | |
| 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 | |
| Bayesian Haplotype Inference via the Dirichlet Process | E.P. Xing, R. Sharan, and M.I. Jordan | Proceedings of the Second RECOMB Satellite Workshop on Computational Methods for SNP and Haplotypes, pp. 99-112; Also In Proceedings of ICML 2004 | January 05 2004 | Algorithms | |
| A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Sequences | E.P. Xing, M.I. Jordan, R.M. Karp, and S. Russell | Neural Information Processing Systems, 2002. | 2002 | Algorithms | |
| Distance Metric Learning, with Application to Clustering with Side-Information | E.P. Xing, A.Y. Ng, M.I. Jordan, and S. Russell | Neural Information Processing Systems, 2002. | 2002 | Algorithms | |
| MotifPrototyper: A Bayesian Profile Model for Motif Families | E.P. Xing and R.M. Karp | Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 29, pp. 10523-10528. DOI:10.1073/pnas.0403564101. | July 2004 | Algorithms | [PDF]
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| Internal Representations for Associative Memory | E.B. Baum, J. Moody, and F. Wilczek | Biological Cybernetics, Vol. 59, pp. 217-228 | 1988 | Algorithms | |
| A Discriminative Model for Identifying Spatial Cis-Regulatory Modules | E. Segal and R. Sharan | Proceedings of RECOMB 2004, pp. 141-149; also submitted to Journal of Computational Biology | January 05 2004 | Algorithms | |
| Feature Selection for High-Dimensional Genomic Microarray Data | E. P. Xing, M. I. Jordan, and R. M. Karp | Proceedings of the 18th International Conference on Machine Learning (ICML 2001), Williamstown, Massachusetts, pp. 601-608 | June 2001 | Algorithms | [PDF]
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| 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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| 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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| Detecting Protein Sequences via Metric Embeddings | E. Halperin, J. Buhler, R. M. Karp, R. Krauthgamer, and B. Westover | Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 122-129 | 2003 | Algorithms | |
| Integrality Ratio for Group Steiner Trees and Directed Steiner Trees | E. Halperin, G. Kortsarz, R. Krauthgamer, A. Srinivasan, and N. Wang | Proceedings of the Twelfth Symposium on Discrete Algorithms (SODA), 275-284 | 2003 | Algorithms | |
| Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy | E. Halperin, G. Kimmel, and R. Shamir | Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, Michigan, pp. 195-203 | June 2005 | Algorithms | [PDF]
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| Perfect Phylogeny and Haplotype Assignment | E. Halperin and R.M. Karp | In Proceedings of RECOMB | January 05 2004 | Algorithms | |
| The Minimum-Entropy Set Cover Problem | E. Halperin and R.M. Karp | Proceedings of ICALP | January 05 2004 | Algorithms | |
| Improved Approximation Algorithms for the Partial Vertex Cover Problem | E. Halperin and R. Srinivasan | Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization, (APPROX), 185-199, Springer, 2002. | 2002 | Algorithms | |
| The Minimum-Entropy Set Cover Problem | E. Halperin and R. M. Karp | Theoretical Computer Science, Vol. 348, Issue 2, pp. 240-250 | December 2005 | Algorithms | |
| Polylogarithmic Inapproximability | E. Halperin and R. Krauthgamer | Proceedings of the 35th Annual ACM Symposium on Theory of Computing (STOC), 585-594 | 2003 | Algorithms | |
| Estimating Haplotype Frequencies Efficiently | E. Halperin and E. Hazan | Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 553-568 | May 2005 | Algorithms | |
| Haplofreq - Estimating Haplotype Frequencies Efficiently | E. Halperin and E. Hazan | Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 553-568 | May 2005 | Algorithms | |
