Richard Karp

University Professor, Bioengineering and Electrical Engineering & Computer Science and Industrial Engineering & Operations Research and Mathematics Core Member, UCB/UCSF Graduate Group in Bioengineering 621 Soda mailcode: 1776 (510) 642-5799 fax: (510) 666-2956 This e-mail address is being protected from spambots. You need JavaScript enabled to view it Membership effective July 2006

Research Interests

Algorithms in computational biology, inference of regulatory structure from protein-protein interaction data.

Research Summary

I have worked on a variety of problems in computational molecular biology, including physical mapping, sequence assembly, sequence comparison, finding hidden structure in gene expression data, design of DNA probes, analysis of transcriptional regulation, discovery of regulatory structure from protein-protein interaction data, haplotype inference and estimation of haplotype frequencies from pooled genotype data.

Selected Publications

R. Karp A. Akella, S. Seshan, S. Shenker, C. Papadimitriou, Selfish Behavior and Stability of the Internet: A Game-Theoretic Analysis of TCP, Proc. Sigcomm, 2002.

R. KarpS. Ratnasamy, M. Handley, S. Shenker, Topologically-Aware Overlay Construction and Server Selection, Proceedings of Infocom 2002.

R. Karp, E. Xing, M. Jordan and S. Russell, A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Systems, Neural Information Processing Systems 2002.

R, Karp, M. Adler, E. Halperin, V. Vazirani, A Stochastic Process on the Hypercube with Applications to Peer-to-peerNetworks, Proc. Thirty-fifthAnnual ACM Symposium on Theory of Computing STOC, 2003.

R, Karp E. Eskin and E. Halperin, Large-Scale reconstruction of Haplotypes from Genotype Data, Proceedings of RECOMB 2003.

R. Karp J. Buhler, E. Halperin, R. Krauthgamer and B. Westover,, Detecting Protein Sequence Conservation Via Metric Embeddings, Proc. Intelligent Systems in Molecular Biology 2003.

R, Karp, C. Kenyon, A Gambling Game and Its Application to the Analysis of Adaptive Randomized Rounding, Proc. RANDOM 2003.

R. Karp, A. Rao,K. Lakshminarayanan, S. Surana and I. Stoica, Load Balancing in Structured P2P Systems, Proc. Second International Workshop on Peer-to-Peer Systems, 2003.

R. Karp, R. Sharan, I. Ovcharenko and A. Ben-Hur , CREME: A Framework for Identifying Cis-regulatory Modules in Human-mouseConserved Segments, Proc. Intelligent Systems in Molecular Biology 2003.

R. Karp, E. Xing, W. Wu and M. Jordan, A Modular Bayesian Model for Motif Detection, Proc. IEEE Computer Society Bioinformatics conference, 2003.