Papers in Refereed Journals

1. ``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), Journal of Computational Biology, (In press) 2004.

2. ``A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology,'' (with A. Yan and C. Langmead) The International Journal of Robotics Research Special Issue on Robotics Techniques Applied to Computational Biology, (In press) 2004.

3. ``Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure'' (with L. Wang), Journal of Biomolecular NMR 2004; 29(3):223-242.

4. ``An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments'' (with C. Langmead), Journal of Biomolecular NMR 2004; 29(2):111-138.

5. ``A Polynomial-Time Nuclear Vector Replacement Algorithm for bAutomated NMR Resonance Assignments,'' (with C. Langmead, A. Yan, R. Lilien, and L. Wang) Journal of Computational Biology 2004; 11(2-3):277-298.

6. ``A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry'' (with R. Lilien, C. Bailey-Kellogg, and A. Anderson). Acta Crystallographica D: Biological Crystallography 2004; D60, 1057-1067.

7. ``The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme,'' (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Eukaryotic Microbiology 2003; 50(6):555-556. Cover article.

8. ``Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase,'' (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.

9. ``Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum,'' (with R. Lilien and H. Farid), Journal of Computational Biology, 10(6) 2003 pp. 925-946.

10. ``Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns'', (with C. Langmead, A. Yan, and C. R. McClung), Journal of Computational Biology 10(3-4) 2003, pp. 521-536.

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) Journal of Computational Biology 8(1):19-36, 2001.

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), Journal of Computational Biology, 7(3-4) (2000) pp. 537-558.