31. Peters, B; Dirscherl, S; Dantzer, J; Cross, S; Li, X; Cornetta, K; Dinauer, MC; and Mooney, SD; “Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource” Submitted to Gene Therapy

30. Chen, JY; Youn, E; Mooney, SD; “Connecting protein interaction data, mutations and disease using bioinformatics” Methods in Molecular Biology, accepted

29. Radivojac, P; Peng, K; Clark, WT; Peters, BJ; Mohan, A; Boyle, SM; and Mooney SD. “An Integrated Approach to Inferring Gene-Disease Associations in Humans” Accepted to Proteins: Structure, Function and Bioinformatics

28. Firpi, H; Eun, Y; and Mooney, SD. (2008) \"Comparative Study of Particle Swarm Approaches for the Prediction of Functionally Important Residues in Protein Structures\" BioCom2008, Okinawa, Japan

27. Baenziger, P and Mooney SD (2007) “Extensible open source content management systems: A solution for many needs of a bioinformatics group” Briefings in Bioinformatics, in press, published online Dec 7th

26. Tocharoentanphol, C; Promso, S; Zelenika, D; Lowhnoo, T; Thongsima, S; Sura, T; Chantratita, W; Matsuda, F; and Mooney, SD; and Sakuntabhai, A. �Evaluation of re-sequencing on number of tag SNPs of 13 atherosclerosis related genes in Thai Population� In press, Journal of Human Genetics.53(1):74-86

25. Altman, RB; Benowitz, N; Gurwitz, D; Lunshof, J; Relling, M; Lamba, J; Wieben, E; Mooney, S; Giacomini, K; Weiss, S; Johnson, JA; McLeod, H; Flockhart, D; Weinshilboum, R; Shuldiner, AR; Roden, D; Krauss, RM; Ratain, M. (2007) "Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing." Pharmacogenomics.8(5):519.

24. Singh, A; Olowoyeye, A; Baenziger, PH; Dantzer, J; Kann, MG; Radivojac, P; Heiland, R; Mooney, SD. (2007) “MutDB: update on development of tools for the biochemical analysis of genetic variation.” Nucleic Acids Research

23. Wang, X; Wang, G; Shen, C; Li, L; Mooney, SD; Edenberg, HJ; Sanford, JR and Liu Y (2007) “Refining Detection of Protein Binding Regions Using Pyrosequencing-Derived RNA Fragments” BioComp ’07, Las Vegas, NV

22. Heiland, R; Mooney, SD; Boverhof, J; Jackson, K; Christie, M; Swat, M; Balter, A; Insley, J; (2007) \"Python for Scientific Gateways Development\", Proceedings of Grid Computing Environments (GCE) Workshop, Supercomputing 2007, Reno, NV.

21. Youn, E; Peters, B; Radivojac, P; and Mooney, SD. (2007) “Evaluation of Catalytic Residue Prediction in Novel Folds” Protein Science.16(2):216-26

20. Farrow, EG; Davis, SI; Mooney, SD; Beighton, P; Mascarenhas, L; Gutierrez, YR; Pitukcheewanont, P; and White, KE. (2006) "Extended Mutational Analyses of FGFR1 in Osteoglophonic Dysplasia (OD)" American Journal of Medical Genetics. 140A(5):537-539.

19. Peters, B; Moad, C; Youn, E; Buffington, K; Heiland, R; and Mooney, SD. (2006) "Identification of Structurally Similar Regions of Protein Structures Using the S-BLEST Website and Services." BMC Structural Biology, 6(4)

18. Babbitt P, Bourne, P and Mooney, SD (2005) "Informatics Applications in Structural Genomics: Introduction" Pacific Symposium on Biocomputing Vol. 8, Edited by Russ B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore.

17. Larsson, T, Davis, SI, Garringer, Mooney, SD, Draman, SM, Cullen, MJ, and White, KE (2005) "Mutant FGF23 Causing Familial Tumoral Calcinosis is Differentially Processed" Endocrinology, 146.9:3883-3891

16. Mooney SD, Liang MH, DeConde R, and Altman RB. (2005) "Structural characterization of proteins using residue environments". Proteins: Structure, Function and Bioinformatics, 61(4):741-7.

15. Dantzer, J, Moad, C, Heiland, R, and Mooney, SD, (2005) "MutDB Services: Interactve Stuctural Analysis of Mutation Data" Nucleic Acids Research, 33:W311-W314.

14. Mooney, SD, (2005) "Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis" (review) Briefings in Bioinformatics, 6(1):44-56.

13. Larsson, T, Yu, X, Davis, SI, Draman, M, Mooney, SD, Cullen, MJ, and White, KE, (2005) "A novel recessive mutation in Fibroblast growth factor-23 (FGF23) causes familial tumoral calcinosis" The Journal of Clinical Endocrinology & Metabolism, J Clin Endocrinol Metab. 90(4):2424-7.

12. Babbitt P and Mooney, SD (2004) “Informatics Applications in Structural Genomics: Introduction” Pacific Symposium on Biocomputing Vol. 8, Edited by Russ B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore.

11. Mooney, SD "Bioinformatics for Geneticists" (2004) Book Review, Briefings in Bioinformatics.

10. Mooney, SD “Microarrays for an Integrative Genomics” (2003) Book Review, Briefings in Bioinformatics.

9. Hewett, R; Leuchner J; Mooney, SD; and Klein, TE; (2003) "Analysis of mutations in COLIA1 gene with second-ordered rule induction" International Journal of Pattern Recognition and Artificial Intelligence, 17(5): 721-740.

8. Mooney, SD and Altman RB (2003) "MutDB: A platform for annotating mutations with functionally relevant data" Bioinformatics, 19: 1858-1860

7. Mooney, SD; Klein, TE; Altman, RB; Trifiro, MA; and Gottlieb, B (2003) "A Functional Analysis of Disease-associated Mutations in the Androgen Receptor Gene" Nucleic Acids Research, 31: e42

6. Babbitt P and Mooney, SD (2003) "Informatics Applications in Structural Genomics: Introduction" Pacific Symposium on Biocomputing Vol. 8, Edited by Russ B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore.

5. Mooney, SD; and Klein, TE (2002) "Structural Models of Osteogenesis Imperfecta Associated Mutations in the COLIA1 Gene" Molecular and Cellular Proteomics 1(11):868-875

4. Mooney, SD; and Klein, TE (2002) "The Functional Importance of Disease-associated Mutation" BMC Bioinformatics 3:24

3. Hewett, R; Leuchner J; Teng CM; Mooney, SD; and Klein, TE; (2002) "Compression-based Induction and Genome Data" 15th International Florida Artificial Intelligence Research Society Conference, May, Pensacola, FL

2. Mooney, SD; Kollman, PA; and Klein, TE (2002) "Conformational Preferences of Substituted Proline Residues in the Collagen Triple Helix" Biopolymers 64(2):63-71

1. Mooney, SD; Huang, CC; Kollman, PA; and Klein, TE. (2001) "Computed Free Energy Differences of a Collagen-like Peptide", Biopolymers 58(3):347-353