Papers in Refereed Conferences

1. ``Algorithmic Challenges in Structural Molecular Biology and Proteomics,'' Sixth International Workshop on the Algorithmic Foundations of Robotics (WAFR), Utrecht/Zeist, The Netherlands. July 11-13, 2004 pp. 1-10 (Invited).

2. ``High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment'' (with C. Langmead), the IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA, pp. 278-289 (August, 2004).

3. ``Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings'' (with L. Wang), the IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA, pp. 319-330 (August, 2004).

4. ``A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme,'' (with R. Lilien, B. Stevens, and A. Anderson), Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego (March 27-31, 2004) pp. 46-57.

5. ``3D Structural Homology Detection via Unassigned Residual Dipolar Couplings,'' (with C. Langmead), Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August 10, 2003) pp. 209-217. ISBN 0-7695-2000-6.

6. ``A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments,'' (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.

7. ``A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns'', (with C. Langmead and C. R. McClung), Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 14-16, 2002) pp. 237-245.

8. ``Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns'', (with C. Langmead, T. Yan, and C. R. McClung), Proceedings of The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (2002). pp. 205-215.

9. ``Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data'' (with C. Langmead), The Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Montreal, April 22-25 (2001) pp. 164-175.

10. ``Physical Geometric Algorithms for Structural Molecular Biology'' (with C. Bailey-Kellogg, J. Kelley, and R. Lilien) invited paper at the Special Session on Computational Biology & Chemistry, Proc. IEEE International Conference on Robotics and Automation (ICRA) 2001, Seoul, Korea, pp. 940-947.

11. ``Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling'' (with C. Bailey-Kellogg, J. Kelley, and C. Stein) Proc.  International Conference on Intelligent Systems for Molecular Biology (ISMB'2000), AAAI Press, (August 20-23, 2000) La Jolla, CA, pp. 13-24.

12. ``The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data,'' (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Tokyo, Japan, April 8 -- 11, 2000, pp. 33-44.