Publication Search Results

Title	Author	Bibliographic	Date	Group	Links
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
Optimal Fully Dynamic Algorithms for Cograph Recognition	R. Shamir and R. Sharan	Discrete Applied Mathematics 136, pp. 329-340	January 05 2004	Algorithms
Cluster Graph Modification Problems	R. Shamir, R. Sharan, and D. Tsur	Discrete Applied Mathematics	January 05 2004	Algorithms
CREME: Cis-Regulatory Module Explorer for the Human Genome	R. Sharan, A. Ben-Hur, G.G. Loots, and I. Ovcharenko	Nucleic Acids Research 32, pp. W253-W256	January 05 2004	Algorithms
Multiplexing Schemes for Generic SNP Genotyping Assays	R. Sharan, A. Ben-Dor, and Z. Yakhini	Proceedings of PSB'04, pp. 140-151	January 05 2004	Algorithms
Comparing Verboseness for Finite Automata and Turing Machines	T. Tantau	Theory of Computing Systems, Vol. 31, No. 1, pp. 95-109	January 05 2004	Algorithms
A Logspace Approximation Scheme for the Shortest Path Problem for Graphs with Bounded Independence Number	T. Tantau	Proceedings of STACS 2004, Lecture Notes on Computer Science, Springer-Verlag	January 05 2004	Algorithms
Avoiding Forbidden Submatrices by Row Deletions	S. Wernicke, J. Alber, J. Gramm, J. Guo, and R. Niedermeier	Proceedings of SOFSEM 04, LNCS, Vol. 2832, pp. 349-360, Springer	January 05 2004	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
Revealing Modularity and Organization in the Yeast Molecular Network by Integrated Analysis of Highly Heterogeneous Genome-Wide Data	A. Tanay, R. Sharan, M. Kupiec, and R. Shamir	Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 9, pp. 2981-2986. DOI:10.1073/pnas.0308661100.	March 2004	Algorithms	[PDF]
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]
A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns	J. Gramm	Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway	September 05 2004	Algorithms
Perfect Path Phylogeny Haplotyping with Missing Data is Fixed-Parameter Tractable	J. Gramm, T. Nierhoff, and T. Tantau	Proceedings of the First International Workshop on Parameterized and Exact Computation (IWPEC 2004), Bergen, Norway	September 05 2004	Algorithms
A 1.5-Approximation Algorithm for Sorting by Transpositions and Transversals	T. Hartman and R. Sharan	Proceedings of WABI	September 05 2004	Algorithms
Stochastic Direct Reinforcement: Application to Simple Games with Recurrence	J. Moody, Y. Liu, M. Saffell, and K. Youn	Proceedings of the 2004 AAAI Fall Symposium on Artificial Multiagent Learning, Arlington, Virginia, pp. 23-34	October 2004	Algorithms	[PDF]
Optimization Problems Related to Internet Congestion Control	R. M. Karp	Graph Theory, Combinatorics and Algorithms: Interdisciplinary Applications, M.C. Golumbic and I.B.-A. Hartman, eds., Springer-Verlag, New York	2005	Algorithms
Whole-Genome Patterns of Common DNA Variation in Three Human Populations	D. A. Hinds, L. L. Stuve, G. B. Nilsen, E. Halperin, E. Eskin, D. G. Ballinger, K. A. Frazer, and D. R. Cox	Science, Vol. 307, No. 5712, pp. 1072-1079. DOI:10.1126/science.1105436	February 2005	Algorithms	[PDF]
Performance Aspects of Distributed Caches Using TTL-Based Consistency	E. Cohen, E. Halperin, and H. Kaplan	Theoretical Computer Science, Vol. 331, Issue 1, pp. 73-96	February 2005	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]
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
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks	J. Scott, T. Ideker, R. M. Karp, and R. Sharan	Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05), Cambridge, Massachusetts, pp. 133-144	May 2005	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]
Generalization Error Bounds Using Unlabeled Data	M. Kaariainen	Proceedings of the 18th Annual Conference on Learning Theory (COLT 2005), Bertinoro, Italy, pp. 127-142	June 2005	Algorithms
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data	R. Sharan, T. Ideker, B. P. Kelley, R. Shamir, and R. M. Karp	Journal of Computational Biology, Vol. 12, Issue 6, pp. 835-846; also in Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB'04), San Diego, California, pp. 282-289, March 2004	July 2005	Algorithms
Asymmetric K-Center Is Log* N-Hard to Approximate	J. Chuzhoy, S. Guha, E. Halperin, S. Khanna, G. Kortsarz, R. Krauthgamer, and J. Naor	Journal of the ACM, Vol. 52, Issue 4, pp. 538-551	July 2005	Algorithms
Optimal Flow Distribution Among Multiple Channels with Unknown Capacities	R. Karp, T. Nierhoff, and T. Tantau	Proceedings of the Second Brazilian Symposium of Graphs, Algorithms, and Combinatorics (GRACO 2005), Angra dos Reis, Brazil, pp. 225-231	July 2005	Algorithms	[PDF]
A Comparison of Tight Generalization Error Bounds	M. Kaariainen and J. Langford	Proceedings of the 22nd International Conference on Machine Learning (ICML 2005), Bonn, Germany, pp. 409-416	August 2005	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
Inference and Analysis of Haplotypes from Combined Genotyping Studies Deposited in dbSNP	N.A. Zaitlen, H.M. Kang, M.L. Feolo, S.T. Sherry, E. Halperin, and E. Eskin	Genome Research, Vol. 15, No. 11, pp.1594-1600	October 2005	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
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
On Active Learning in the Non-Realizable Case	M. Kaariainen	Proceedings of the Foundations of Active Learning Workshop at the 19th Annual Conference on Neural Information Processing Systems (NIPS), Vancouver, Canada	December 2005	Algorithms
Report of the SIGACT Committee on funding for Theoretical Computer Science	R. M. Karp	SIGACT (Special Interest Group on Algorithms and Computation Theory) News	December 2005	Algorithms
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
Optimal Flow Distribution Among Multiple Channels with Unknown Capacities	R. M. Karp, T. Nierhoff, and T. Tantau	Theoretical Computer Science: Essays in Memory of Shimon Even, O. Goldreich, A. L. Rosenberg, and A. L. Selman, eds., Lecture Notes in Computer Science, Vol. 3895, pp. 111-128, Springer-Verlag	2006	Algorithms	[PDF]
Fair Bandwidth Allocation Without Per-Flow State	R. M. Karp	In Essays in Theoretical Computer Science in Memory of Shimon Even, O. Goldreich, A. L. Rosenberg, and A. L. Selman, eds., pp. 88-110, Springer	2006	Algorithms
Lower Bounds for Reductions	M. Kaariainen and J. Langford	Presented at the Atomic Learning Workshop, Chicago, Illinois	March 2006	Algorithms
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals	J. Marchini, D. Cutler, N. Patterson, M. Stephens, E. Eskin, E. Halperin, S. Lin, S. Qin, G. Abecassis, H. Munro, and P. Donnelly	American Journal of Human Genetics, Vol. 78, Issue 3, pp. 437-450	March 2006	Algorithms
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks	J. Scott, T. Ideker, R. M. Karp, and R. Sharan	Journal of Computational Biology, Vol. 13, Issue 2 pp. 133-144	March 2006	Algorithms	[PDF]
George Dantzig's Impact on the Theory of Computation	R. M. Karp	Discrete Optimization, Vol. 5, Issue 2, pp. 174-185	May 2006	Algorithms
A Note on Optimally Phasing Long Genomic Regions Using Local Haplotype Predictions	E. Eskin, E. Halperin, and R. Sharan	Journal of Bioinformatics and Computational Biology, Vol. 4, No. 3, pp. 639-647	June 2006	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
Using DNA Pools for Genotyping Trios	K.B. Beckman, K.A. Abel, A. Braun, and E. Halperin	Nucleic Acids Research, Vol. 34, No. 19, electronic article no. 129	November 2006	Algorithms	[PDF]
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]
Noisy Binary Search	R. M. Karp and R. Kleinberg	Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), New Orleans, Louisiana, pp. 881-890	January 2007	Algorithms
Leveraging the HapMap Correlation Structure in Association Studies	N. Zaitlen, H. M. Kang, E. Eskin, and E. Halperin	American Journal of Human Genetics, Vol. 80, Issue 4, pp. 683-691	April 2007	Algorithms	[PDF]
An Efficient and Accurate Graph-based Approach to Detect Population Substructure	S. Sridhar, S. Rao, and E. Halperin	Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Oakland, California, pp. 503-517	April 2007	Algorithms	[PDF]
Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm	M. Narayanan and R. M. Karp	Journal of Computational Biology, Vol. 14, Issue 7, pp. 892-907	September 2007	Algorithms	[PDF]
Balancing the Traffic Load in Wireless Networks with Curveball Routing	L. Popa, A. Rostami, R. M. Karp, C. Papadimitriou, and I. Stoica	Proceedings of the 8th ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc 2007), Montreal, Canada	September 2007	Algorithms

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