- S.D. Mooney, C.C. Huang, P.A. Kollman, T.E. Klein, “Computed Free Energy Differences Between Point Mutations in a Collagen-like Peptide,” Biopolymers 58:347-353, 2001.
- T.E. Klein, J.T. Chang, K.L. Easton, R. Fergerson, M. Hewett, Z. Lin, Y. Liu, S. Liu, D.E. Oliver, D.L. Rubin, J.M. Stuart and R.B. Altman, “Integrating Genotype and Phenotype Information: An Overview of the PharmGKB Project,” The Pharmacogenomics Journal 1:167-170, 2001.
- D.L. Rubin, M. Hewett, D.E. Oliver, T.E. Klein and R.B. Altman, " Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML,” Pacific Symposium on Biocomputing 7:88-99, 2002.
- D.E. Oliver, D.L. Rubin, J.M. Stuart, M. Hewett, T.E. Klein and R.B. Altman, "Ontology Development for a Pharmacogenetics Knowledge Base,” Pacific Symposium on Biocomputing 7:65-76, 2002.
- M. Hewett M, D.E. Oliver, D.L. Rubin, K.L. Easton, J.M. Stuart, R.B. Altman and T.E. Klein, “PharmGKB: the Pharmacogenetics Knowledge Base," Nucleics Acids Research 1:163-165, 2002.
- S.D. Mooney, P.A. Kollman and T.E. Klein, "Conformational Preferences of Substituted Prolines in the Collagen Triple Helix,” Biopolymers 64:57-62, 2002.
- R.B. Altman and T.E. Klein, "Challenges for Biomedical Informatics and Pharmacogenenomics,” Annual Review of Pharmacology and Toxicology 42:113-133, 2002
- R. Hewett, J. Leuchner, C. M. Teng, S.D. Mooney and T.E. Klein, “Compression-based Induction and Genome Data,” Proceedings of the 15th International FLAIRS Conference, May, Pensacola, FL, 2002.
- S.D. Mooney and T.E. Klein, “The Functional Importance of Disease-Associated Mutation,” BMC Bioinformatics 2002, 3:24.
- M.L. Green and T.E. Klein, “A multidomain TIGR/olfactomedin protein family with conserved structural similarityin the N-terminal region and conserved motifs in the C-terminal region," Mol Cell Proteomics 1:394-403, 2002.
- S.D. Mooney, T.E. Klein. “Structural Models of Osteogenesis Imperfecta-associated Variants in the COL1A1
Gene.” Mol Cell Proteomics. 1:868-75, 2002.
- R.B. Altman, D.A. Flockhart, S.T. Sherry, D.E. Oliver, D.L. Rubin, T.E. Klein. “Indexing pharmacogenetic
knowledge on the World Wide Web.” Pharmacogenetics. 2003 Jan;13(1):3-5.
- R. Hewett, J. Leuchner, S.D. Mooney and T.E. Klein, “An Analysis of Mutations in the COLIAI Gene with
Second-Order Rule Induction," International Journal of Pattern Recognition and Artificial Intelligence, 17:721-7240, 2003.
- S.D. Mooney, T.E. Klein, R.B. Altman, M.A. Trifiro, and B. Gottlieb, “A Functional Analysis of Disease-associated
Mutations in the Androgen Receptor Gene," Nucleic Acids Research 31: e42 2003
- M.P. Liang, D.R. Banatao, T.E. Klein, D.L. Brutlag, R.B. Altman, “WebFEATURE: An interactive web tool for
identifying and visualizing functional sites on macromolecular structures”, Nucleic Acids Research 31:3324-3327, 2003.
- D.R. Banatao, R.B. Altman and T.E. Klein. “Microenvironment analysis and identification of magnesium binding
sites in RNA," Nucleic Acids Research 31:4450-4460, 2003.
- S. Liu, S. Lin, M. Woon, T.E. Klein and R.B. Altman, “A Personalized and Automated dbSNP Surveillance
System," Proceedings of the Computational Systems Bioinformatics (CSB ‘’03), 132-136, 2003.
- D. R. Banatao, I.S. Gabashvili, T.E. Klein, R.B. Altman, “Computational screen for magnesium binding sites
suggests ion-binding cores in ribosomal subunits," J. Mol. Biol. (in review).
- R.J. Radmer and T.E. Klein, “The Severity of Osteogenesis Imperfecta and the Structure of a Collagen-like Peptide Modeling a Lethal Mutation Site," Biochemistry (in review).