49. Radivojac, P., Iakoucheva, L. M., Oldfield, C.J., Obradovic, Z., Uversky, V.N., Dunker, A.K. Intrinsic Disorder and Functional Proteomics. Biophys. J. (In press, 2007).

48. Dunker, A.K. Disordered Proteins. In: Encyclopedia for the Life Sciences. John Wiley & Sons. London (In Press, 2007)

47. Vacic, V., Oldfield, C.J., Mohan, A., Radivojac, P., Cortese, M.S., Uversky, V.N., and Dunker, A.K. Characterization of molecular recognition features, MoRFs, and their binding partners. Journal of Proteome Research (In Press, 2007)

46. Oldfield, C.J., Van, Y. Dunker, A.K. Prediction of intrinsic protein disorder: applications in structural genomics. In: Methods Mol. Biol. Structural Genomics (M.A. Kennedy, ed.). (In Press, 2007)

45. Uversky, Radivojac, P., V.N., Iakoucheva, L.M., Obradovic, Z., Dunker, A.K. Prediction of Intrinsic Disorder in Functional Proteomics. In: Methods in Molecular Biology: Gene Function Analysis. (Michael F. Ochs, ed.) Humana Press. Totowa, NJ. (In Press, 2007)

44. Uversky V.N., Dunker A.K., Intrinsically Disordered Proteins. Vol. 1: Longhi S., Measles Virus Nucleoprotein. Nova Science Publishers, Inc., Hauppauge, NY, USA. (In press, 2007)

43. Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Obradovic, Z. and Uversky, V.N. Functional anthology of intrinsic disorder. III. Biological processes and functions of proteins with long disordered regions. J. Proteome. Res. (In press, 2007)

42. Vucetic, S., Xie, H., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Obradovic, Z. and Uversky, V.N., Functional anthology of intrinsic disorder. II. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome. Res. (In press, 2007)

41. Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Uversky, V.N., and Obradovic, Z. Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome. Res. (In press, 2007)

40. Uversky, V. N., Dunker, A.K. Understanding protein non-folding. To fold or not to fold: Some current concepts of protein chemistry. (Zbilut, J., Scheibel, T., eds.) (2006) Nova Science Publishers, Inc. Hauppauge, NY. (In Press)

39. Midic, U. Dunker, K. and Obradovic, Z. Exploring alternative knowledge representations for protein secondary-structure prediction. Int’l Journal of Data Mining and Bioinformatics. (In press)

38. Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N., Obradovic, Z., and Dunker, A.K. DisProt: The database of disordered proteins. Nucleic Acids Res. 35 (Database issue): D786-93. (2007)

37. Le Gall, T., Romero, P., Cortese, M.S., Uversky, V.N., and Dunker, A.K., Intrinsic disorder in the Protein Data Bank. J. Biomol. Struct. Dyn. 24: 325-42. (2007)

36. Uversky, V.N., Roman, A., Oldfield, C.J., Dunker, A.K. Protein intrinsic disorder and human papillomaviruses: Increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. J. Proteome Res. 5: 1829-1842 (2006)

35. Romero, P., S. Zaidi, S., and Dunker, A. K. Roles of Intrinsic Disorder in Protein Families and Isozymes; Proceedings of the 13th International Congress on Genes, Gene Families and Isozymes (Xiong X.G., Yan Z.Z., Liang W.Y., eds.) Medimond Publishers, Bologna, Italy, pp 7-13 (2006)

34. Romero, P. R., Zaidi, S., Fang, Y.Y., Uversky, V.N., Radivojac, P., Cortese, M., Sickmeier, M., Obradovic, Z., and Dunker, A.K. Alternative splicing in concert with protein intrinsic disorder enables functional diversity in multicellular organisms. Proc. Nat’l. Acad. Sci. USA 103: 8390-8395 (2006)

33. Radivojac, P., Vucetic, S., O’Connor, T.R., Uversky, V.N., Obradovic, Z., and Dunker, A.K. Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition mechanism. Proteins: Structure, Function, and Bioinformatics 63: 398-410 (2006)

32. Radivojac, P., Iakoucheva, L.M., Oldfield, C.J., Obradovic, Z., Uversky, V.N., and Dunker, A.K. Intrinsic Disorder and Functional Proteomics. Biophys J. [Epub ahead of print]. (2006)

31. Peng, K., Radovojac, P., Vucetic, S., Dunker, A.K., and Obradovic, Z. Length-dependent prediction of protein intrinsic disorder, BMC Bioinformatics 7: 208 (2006)

30. Mohan, A., Radivojac, P., Oldfield, C.J., Vacic, V., Cortese, M.S., Uversky, V.N., Dunker, A.K. A dataset of molecular recognition features (MoRFs). J. Mol. Biol. 362: 1043-59 (2006)

29. Liu, J., Perumal, N.B., Uversky, V.N., Oldfield, C.J., Su, E.W., Dunker, A.K. Intrinsic disorder in transcription factors. Biochemistry 45: 6873-6888 (2006)

28. Dosztányi, Z., Chen, J., Dunker, A.K., Simon, I., and Tompa, P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J. Proteome Res. 5: 2985-95 (2006)

27. Cheng, Y., LeGall, T., Oldfield, C.J., Mueller, J.P., Van, Y.Y., Romero, P., Cortese, M.S, Uversky, V.N., and Dunker, A.K. Rational drug design via intrinsically disordered protein. Trends Biotechnol. 24: 435-42. (2006)

26. Cheng Y., Le Gall T., Oldfield C.J., Dunker A.K., Uversky V.N. Abundance of intrinsic disorder in proteins associated with cardiovascular disease. Biochemistry. 45: 10448-10460 (2006)

25. Chen, J.W., Romero, P., Uversky, V.N., and Dunker, A.K. Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder, J. Proteome Res. 5: 888-898 (2006)

24. Chen, J.W., Romero, P., Uversky, V.N., and Dunker, A.K. Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions, J. Proteome Res.5: 879-887 (2006)

23. Vucetic, S., Obradovic, Z., Vacic, V., Radivojac, P., Peng, K., Iakoucheva, L.M., Lawson, J.D., Brown, C.J., Sikes, J.G., Newton, C.D., Dunker, A.K. DisProt: a database of protein disorder. Bioinformatics. 21: 137-140. (2005).

22. Peng, K., Vucetic, S., Radivojac, P., Brown, C.J., Dunker, A.K., Obradovic, Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. and Comp. Bio. 3: 35-60. (2005).

21. Park, I.Y., Kim, E.J., Park, H.J., Fields, K., Dunker, A.K., Kang, C.H. Interaction between cardiac calsequestrin and drugs with known cardiotoxicity. Mol. Pharmacol. 67: 97-104 (2005).

20. Oldfield, C.J., Ulrich, E.L., Cheng, Y., Dunker, A.K., and Markley, J.L. Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins: Structure, Function, and Bioinformatics. 59: 444-453 (2005).

19. Oldfield, C.J., Cheng, Y., Cortese, M.S., Brown, C.J., Uversky, V.N., and Dunker, A.K. Comparing and combining predictors of mostly disordered proteins. Biochemistry. 44: 1989-2000. (2005).

18. Oldfield, C.J., Cheng, Y., Cortese, M., Romero, P., Uversky, V.N., and Dunker, A.K. Coupled folding and binding with -helical molecular recognition elements. Biochemistry. 44: 12454-12470 (2005).

17. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., and Dunker, A.K. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins: Structure, Function, Bioinformatics. 61: 176-182 (2005)

16. Midic, U., Dunker, A.K., and Obradovic, Z. Improving Protein Secondary-Structure Prediction by Predicting Ends of Secondary-Structure Segments. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, pp. 490-497, San Diego, California, USA, (2005)

15. Daly, K., Radivojac, P., and Dunker, A. K. Intrinsic disorder and protein modifications: building an SMV predictor for methylation. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, pp. 475-481, San Diego, California, USA, (2005)

14. Cortese, M.C., Baird, J.P., Uversky, V.N., and Dunker, A.K. Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatment. J. Proteome Res. 4: 1610-1618 (2005)

13. Radivojac, P., Obradovic, Z., Dunker, A.K., Vucetic, S. Feature selection filters based on the permutation test. 15th European Conference on Machine Learning. ECML 2004: 334-345 (2004).

12. Radivojac, P., Chawla, N.V., Dunker, A.K., Obradovic, Z. Classification and knowledge discovery in protein databases. Journal of Biomedical Informatics. 37: 224-239 (2004).

11. Radivojac, P., Obradovic, Z., Smith, D.K., Zhu, G., Vucetic, S., Brown, C.J., Lawson, J.D., and Dunker, A.K. Protein flexibility and intrinsic disorder. Protein Sci. 13(1): 71-80. 2004.

10. Iakoucheva, L.M., Radivojac, P., Brown, C.J., O’Connor, T.R., Sikes, J.G., Obradovic, Z., and Dunker, A.K. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Research. 32(3): 1037-1049. 2004

9. Bourhis J-M, Johansson K, Receveur-Brechot V, Oldfield CJ, Dunker KA, Canard B, Longhi S. The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinisically disordered proteins that fold upon binding to their physiological partner. Virus Res. 99(2): 157-167. 2004.

8. Park, H., Park, I.Y., Kim, E., Youn, B., Fields, K., Dunker, A.K., and Kang, C. Comparing skeletal and cardiac calsequestrin structures and their calcium binding: a proposed mechanism for coupled calcium binding and protein phosphorylation. J. Biol. Chem. 279(17): 18026-18033. 2004.

7. Yang, J., Powers, J.R., Clark, S., Dunker, A.K. & Swanson, B.G. Ligand and flavor binding functional properties of β-lactoglobulin in the molten globule state induced by high pressure. J. Food Science. 68: 444-452 (2003).

6. Smith, D.K., Radivojac, P., Obradovic, Z., Dunker, A.K., and Zhu, G. Improved amino acid flexibility parameters. Protein Science. 12: 1060-1072 (2003).

5. Radivojac, P., Obradovic, Z., Brown, C.J. and Dunker A.K. Prediction of boundaries between intrinsically ordered and disordered protein. Pac. Symp. Biocomput. 8: 216-227 (2003).

4. Park, H.J., Wu, S., Dunker, A.K., and Kang, C.H. Polymerization of calsequestrin: implications for calcium regulation. J. Biol. Chem. 278: 16176-16182 (2003).

3. Vucetic, S., Brown, C.J., Dunker, A.K., and Obradovic, Z. Flavors of protein disorder. Proteins. 52(4): 573-584. 2003.

2. Obradovic Z, Kang P, Vucetic S, Radivojac P, Brown CJ, Dunker AK. Predicting intrinsic disorder from amino acid sequence. Proteins: Structure, Function, and Genetics. 53:566-572. 2003.

1. Iakoucheva LM, Dunker AK. Order, disorder, and flexibility: prediction from protein sequence. Structure. 11:1316-1317. 2003.

11. Jung J, Sun B, Foroud TM, Eckert GJ, Wetherill, LF, Edenberg HJ, Xuei X, Chun TY, Pratt JH. An association of the calcium-sensing receptor gene with blood pressure in African American. (2008)

10. Jung J, Sun B, Kwon D, Koller DL, Foroud TM. Allelic based Gene-Gene interaction associated with Quantitative traits. (2008)

9. Jung J, Zhong M, Liu L, Fan R. Bivariate combined linkage and association mapping of quantitative trait loci. Genet Epidemiol. 2008 Feb 15. [Epub ahead of print]

8. Fan R, Liu L, Jung J, Zhong M. Combined linkage and association mapping of quantitative trait Loci with missing completely at random genotype data. Behav Genet. 2008 May; 38(3):316-36. Epub 2008 Feb 27

7. Fan RZ, Jung JS, and Jin L. (2006) High Resolution Association Mapping of Quantitative Trait Loci, A population Based Approach. Genetics. 172:663-686

6. Jung JS, Weeks, DE and Feingold, E (2006) Gene Dropping vs. Empirical Variance estimation for allele-sharing linkage statistics (in press)

5. Fan RZ, Jung JS, Liu L, and Zhong M (2006) Combined Linkage and Association Mapping of Quantitative trait loci with missing genotype data. (submitted)

4. Jung JS, Fan RZ and Jin L. (2005) Combined Linkage and Association Mapping of Quantitative Trait Loci by Multiple Markers. Genetics . 170(2):881-898

3. Fan RZ, Jung JS (2004) High Resolution joint linkage disequilibrium and linkage mapping of Quantitative Trait Loci based on sibship data. Hum. Hered 56:166-187

2. Fan RZ, Spinka C, Jin L., and Jung, JS (2004) Pedigree Linkage Disequilibrium Mapping of Quantitative Trait Loci. European Journal of Human genetics 13:216-31

1. Fan RZ, Jung JS (2003) Association Studies of QTL for multi-allelic Markers by Mixed Models. Hum. Hered. 54:132-150.

14. Ma X., Zhang K., Lebo M., Cheng C., Sun F., Li X. Evolution of Drosophila Ribosomal Protein Gene Core Promoters. Submitted.

13. Cai, X., Hu H., Li X. A novel method for genome-wide identification of motif modules. Submitted.

12. Hu H., Li X. Networking Pathways unveils Association between Obesity and Non-Insulin Dependent Diabetes Mellitus. Pac Symp Biocomput. 2008.

11. Humphreys TL, Li L, Li X, Janowicz DM, Fortney KR, Zhao Q, Li W, McClintick J, Katz BP, Wilkes DS, Edenberg HJ, Spinola SM. Dysregulated Immune Profiles in Skin and Dendritic Cells are Associated with Increased Host Susceptibility to Haemophilus ducreyi Infection in Human Volunteers. Infect Immun. 2007 Sep 24; [Epub ahead of print].

10. Hu H., Li X. Transcriptional regulation in eukaryotic ribosomal protein genes. Genomics. 2007; 90(4):421-3.

9. Cai, X., Hu H., Li XS. Tree Gibbs Sampler: Identifying Conserved Motifs without Aligning Orthologous Sequences. Bioinformatics. 2007 May 31; [Epub ahead of print].

8. Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP. A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics. 2006 Sep 15;22(18):2210-6.

7. Li X. Cancer Bioinformatics - From Therapy Design to Treatment. Briefings in Bioinformatics. 2006.

6. LaRocque R., Harris JB, Dziejman M., Li X. et al. Transcriptional Profiling of Vibrio cholerae Recovered Directly from Early and late human infection. Infection and Immunity. 73(8):4488-93, 2005.

5. Li X. & Wong WH. Sampling motifs on phylogenetic trees. Proc Natl Acad Sci USA, 102(27), 9481-9486, 2005.

4. Li X., Zhong S. & Wong WH. Reliable transcription factor binding sites prediction in eukaryotes by phylogenetic verification. Proc Natl Acad Sci U S A. 102(47):16945-50, 2005.

3. Bjorkbacka H, Fitzgerald KA, Huet F, Li X, et al. The induction of macrophage gene expression by LPS predominantly utilizes MyD88-independent signaling cascades. Physiol Genomics, 19(3):319-30, 2004.

2. Li X., Waterman M. Estimate the repeat structure of a genome without assembly. Genome Research, 13(8):1916-22, 2003.

1. Yeh RF, Speed T., Waterman MS & Li X. Predicting progress in shotgun sequencing with paired ends. Center for Bioinformatics & Molecular Biostatistics, 2002.

21. Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells, Wang, G., Wang, Y., Feng, W., Wang, X., Yang, J.Y., Zhao, Y, Wang, Y., Liu, Y., BMC Genomics (in press)

20. A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology, Feng, W.*, Liu, Y.*, Wu, J., Nephew, K.P., Huang, T.H., and Li, L. BMC Genomics (in press). * co-first author

19. Wang X., Wang K., Wang G., Sanford, J.R., Liu Y., Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing, 8th IEEE International Conference on BioInformatics and BioEngineering, Athens, Greece, October 2008.

18. Hamamura K., Liu Y., and Yokota H. Microarray Analysis of Thapsigargin-Induced Stress to Endoplasmic Reticulum of Mouse Osteoblasts, Journal of Bone and Mineral Metabolism, 2008;26(3):231-40. Epub 2008 May 11.

17. Wang, X., Wang, G., Shen, C., Li, L., Edenberg, H.J., Sanford, J., Liu, Y., Refining Detection of Protein Binding Regions Using Pyrosequencing-derived RNA Fragments, BMC Genomics, 9 (Suppl 1):S17 (2008)

16. Wang, G., Wang, X., Li, L., Nephew, N.P., Edenberg, H.J., Zhou, F.C., Liu, Y. Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data, BMC Genomics, 9 (Suppl 1):S19 (2008)

15. McClintick, J.N.*, Liu, Y.*, Edenberg, H.J., Mapping of trans-acting regulatory factors from microarray data, BMC Genetics, BMC Proceedings 2007, 1 (Suppl 1):S155 (18 December 2007). *co-first author.

14. Chen, A., Hamamura, K., Wang, G., Xing, W., Mohan, S., Yokota, H, and Liu, Y., Model-Based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone, Genomics, Proteomics and Bioinformatics, Aug-Nov 5 (3-4), 158-65 (2007).

13. Liu, Y., Computational Genome Analysis: an Introduction (book review), Briefings in Bioinformatics, doi:10.1093/bib/bbm020

12. Zhang, P., Su, M., Liu, Y., Hsu, A. and Yokota, H. Knee Loading Dynamically Alters Intramedullary Pressure in Mouse Femora. Bone 40(2):538-43 (2007).

11. Liu, Y. & Edenberg, H. Identification and Evaluation of Transcription Factor Binding Sites Responsive to PEG-IFN-alpha in PBMC in vitro. Genomics 2006, 88: 452-461.

10. Su, M., Jiang, H., Zhang, P., Liu, Y., Tanaka, S., and Yokota, H. Load-Driven Molecular Transport Using FRAP, Annals of Biomedical Engineering, Oct;34(10):1600-1606. (2006).

9. Liu, Y. & Yokota, H. Artificial Ants Deposit Pheromone to Search for Regulatory DNA Elements. BMC Genomics, Aug 30;7:221 (2006)

8. Liu, Y. and Yokota, H. Modeling Transcriptional Regulation in Chondrogenesis Using Particle Swarm Optimization. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 311-317, San Diego, CA (2005).

7. Liu, Y., Vincenti, M. P. & Yokota, H. Principal Component Analysis for Predicting Transcription-Factor Binding Motifs from Array-Derived Data. BMC Bioinformatics 2005, 6:276.

6. Sun, I., Liu, Y., Tanaka, S., Sun, H. & Yokota, H. Biochemical Aspects of High-Impact Exercises in Joint Degradation. Journal of Sports Sci. and Med 3, 37-43 (2004).

5. Liu, Y. & Yokota, H. Modeling of Dynamic Transcriptional Regulation in Human Chondrogenesis. Systems Biology 1, 85-92 (2004).

4. Sun, H. B., Liu, Y., Qian, L. & Yokota, H. Model-based analysis of matrix metalloproteinase expression under mechanical shear. Ann Biomed Eng 31, 171-80 (2003).

3. Liu, Y., Sun, H. B. & Yokota, H. Regulating Gene Expression Using Optimal Control Theory. Third IEEE Symposium Bioinformatics and Bioengineering 313 -318, Bethesda, MD (2003).

2. Qian, L., Liu, Y., Sun, H. B. & Yokota, H. Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues. Front Biosci 7, a126-34 (2002).

1. Du, X. & Liu, Y. Network Management for Enterprise Intranet, (In Chinese), Journal of Automation, China (1999).

47. Liang, S.; Li, L.; Hsu, W-L; Uversky, V.; Zhou, Y.; Dunker, A. K.; Meroueh, S. O. Molecular Design of Protein Interaction Sites with a New Algorithm that Incorporates Receptor Flexibility J. Mol. Biol. (2008). Submitted

46. Liang, S.; Meroueh S. O.; Zhou Yaoqi Enriching near-native structures from protein-protein docking decoys using an empirical scoring function. Bioinformatics (2008) Submitted

45. Shi, Q.; Meroueh, S. O.; Fisher, J.; Mobashery S. Investigation of the Mechanism of the Cell Wall DD-Carboxypeptidase Reaction of Penicillin-Binding Protein 5 of Escherichia coli by QM/MM Calculations JACS (2008) In Press

44. Jewell, J.; Oh, E.; Bennett, S. M.; Meroueh, S. O., and Thurmond, D. The tyrosine phosphorylation of Munc18c induces a switch in binding specificity from syntaxin 4 to Doc2beta J. Biol. Chem. (2008). In Press

43. Li, Liwei and Meroueh, S. O. Receptor-Ligand Interactions in Biological Systems. In: Encyclopedia for the Life Sciences. John Wiley & Sons. London (2008) In press

42. Li, Liwei; O’Callaghan, B. J.; Dantzer, J. J. and Meroueh S. O. PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-Dimensional structures and Binding Thermodynamics from Isothermal Titration Calorimetry. Chem. Biol. & Drug Design. (2008) 71:529-32.

41. Samy Meroueh: Normal Mode Analysis Theoretical and Applications to Biological and Chemical Systems. Briefings in Bioinformatics 8(5): 378-379 (2007)

40. Li, Liwei; Uversky N. V.; Dunker, K. A.; Meroueh, S. O. A Computational Investigation of Allostery in the Catabolite Activator Protein. J. Am. Chem. Soc. (2007) 129(50), 15668-76

39. Zhang, W.; Shi, Q.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Catalytic Mechanism of Penicillin-Binding Protein 5 of Escherichia coli. J. Biol. Chem. 2007, 46, 10113-10121.

38. Rosenblum, G.*; Meroueh, S.*; Toth, M.; Fisher, J. F.; Fridman, R.; Mobashery, S.; Sagi, I. Molecular Structures and Dynamics of the Stepwise Activation of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma, J. Am. Chem. Soc. 2007 129(44),13566-74. (Authors contributed equally)

37. Meroueh, S. O. and Mobashery, S., Conformational Transition in the Aminoacyl t-RNA Site of the Bacterial Robosome both in the Presence and Absence of an Aminoglycoside Antibiotic. Chemical Biology and Drug Design 2007, 69, (5), 291-297.

36. Meroueh, S. O.; Cha, J.; Mobashery, S. Inhibition of Class A ß-Lactamases, In Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition, Bonomo, R. A.; Tolmasky, M. E., Eds.; ASM Press, 2007, pp101-114, Washington D.C.

35. Li, J.; Cross, J. B.; Vreven, T.; Meroueh, S. O. ; Mobashery, S.; Schlegel, H. B., Lysine Carboxylation in Proteins: OXA-10 Beta-Lactamase. Proteins 2005, 61, (2), 246-257.

34. Osenkowski, P.; Meroueh, S. O. ; Pavel, D.; Mobashery, S.; Fridman, R., Mutational and Structural Analyses of the Hinge Region of Membrane Type 1-Matrix Metalloproteinase and Enzyme Processing. J. Biol. Chem. 2005, 280, (28), 26160-26168.

33. Murray, J. B.; Meroueh, S. O.; Russell, R. J.; Lentzen, G.; Haddad, J.; Mobashery, S., Interactions of Designer Antibiotics and the Bacterial Ribosomal Aminoacyl-tRNA Site. Chem. Biol. 2006, 13, (2), 129-38.

32. Hesek, D.; Toth, M.; Meroueh, O.; Brown, S.; Zhao, H.; Sakr, W.; Fridman, R.; Mobashery, S., Design and Characterization of a Metalloproteinase Inhibitor-Tethered Resin for the Detection of Active MMPs in Biological Samples. Chem. Biol. 2006, 13, 379-388.

31. Meroueh, S. O.; Bencze, K. Z.; Hesek, D.; Lee, M.; Fisher, J. F.; Stemmler, T. L.; Mobashery, S., Three-Dimensional Structure of the Bacterial Cell Wall Peptidoglycan. Proc. Natl. Acad. Sci. USA 2006, 103, (12), 4404-4409.

30. Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Nanomolecular and Supramolecular Paths toward the Bacterial Peptidoglycan Structure. Microbe 2006, 1, 420-427.

29. Rekharsky, M.; Hesek, D.; Lee, M.; Meroueh, S. O.; Inoue, Y.; Mobashery, S., Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 2006, 128, (24), 7736-7737.

28. Cross, J. B.; Vreven, T.; Meroueh, S. O.; Mobashery, S.; Schlegel, H. B., Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A. J. Phys. Chem. B 2005, 109, (10), 4761-4769.

27. Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Bacterial Resistance to Beta-Lactam Antibiotics: Compelling Opportunism, Compelling Opportunity. Chem. Rev. 2005, 105, (2), 395-424.

26. Ikejiri, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Chang, M.; Fridman, R.; Mobashery, S., Design, Synthesis, and Evaluation of a Mechanism-Based Inhibitor for Gelatinase A. J. Org. Chem. 2005, 70, (14), 5709-5712.

25. Lee, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Fridman, R.; Mobashery, S., Synthesis of Chiral 2-(4-Phenoxyphenylsulfonylmethyl)-Thiiranes as Selective Gelatinase Inhibitors. Org. Lett. 2005, 7, (20), 4463-4465.

24. Meroueh, S. O. ; Fisher, J. F.; Schlegel, H. B.; Mobashery, S., Ab initio QM/MM Study of Class A Beta-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70. J. Am. Chem. Soc. 2005, 127, (44), 15397-15407.

23. Toth, M.; Osenkowski, P.; Hesek, D.; Brown, S.; Meroueh, S. O. ; Sakr, W.; Mobashery, S.; Fridman, R., Cleavage at the Stem Region Releases an Active Ectodomain of the Membrane Type 1 Matrix Metalloproteinase. Biochem. J. 2005, 387, 497-506.

22. T. Lim, S. O. Meroueh, M. Lee, M. J. Heeg, S. Mobashery "Strategy in Inhibition of Cathepsin B, A Target in Tumor Invasion and Metastasis" J. Am. Chem. Soc. 2004, 126, 10271-10277.

21. Birck, C.; Cha, J. Y.; Cross, J.; Schulze-Briese, C.; Meroueh, S. O.; Schlegel, H. B.; Mobashery, S.; Samama, J. P., X-ray Crystal Structure of the Acylated Beta-Lactam Sensor Domain of BlaR1 from Staphylococcus aureus and the Mechanism of Receptor Activation for Signal Transduction. J. Am. Chem. Soc. 2004, 126, (43), 13945-13947.

20. Brown, S.; Meroueh, S. O.; Fridman, R.; Mobashery, S., Quest for Selectivity in Inhibition of Matrix Metalloproteinases. Curr. Top. Med. Chem. 2004, 4, (12), 1227-1238.

19. Golemi-Kotra, D.; Meroueh, S. O.; Kim, C.; Vakulenko, S. B.; Bulychev, A.; Stemmler, A. J.; Stemmler, T. L.; Mobashery, S., The Importance of a Critical Protonation State and the Fate of the Catalytic Steps in Class A Beta-Lactamases and Penicillin-Binding Proteins. J. Biol. Chem. 2004, 279, (33), 34665-34673.

18. Kim, C.; Haddad, J.; Vakulenko, S. B.; Meroueh, S. O.; Wu, Y.; Yan, H.; Mobashery, S., Fluorinated Aminoglycosides and their Mechanistic Implication for Aminoglycoside 3 '-Phosphotransferases from Gram-Negative Bacteria. Biochemistry 2004, 43, (9), 2373-2383.

17. Fridman, R.; Toth, M.; Chvyrkova, I.; Meroueh, S. O.; Mobashery, S., Cell Surface Association of Matrix Metalloproteinase-9 (Gelatinase B). Cancer and Metastasis Rev 2003, 22, (2-3), 153-166.

16. Golemi-Kotra, D.; Cha, J. Y.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Resistance to Beta-Lactam Antibiotics and its Mediation by the Sensor Domain of the Transmembrane BlaR Signaling Pathway in Staphylococcus aureus. J. Biol. Chem. 2003, 278, (20), 18419-18425.

15. Meroueh, S. O.; Minasov, G.; Lee, W.; Shoichet, B. K.; Mobashery, S., Structural Aspects for Evolution of Beta-Lactamases from Penicillin-Binding Proteins. J. Am. Chem. Soc. 2003, 125, (32), 9612-9618.

14. Rosenblum, G.; Meroueh, S. O.; Kleifeld, O.; Brown, S.; Singson, S. P.; Fridman, R.; Mobashery, S.; Sagi, I., Structural Basis for Potent Slow Binding Inhibition of Human Matrix Metalloproteinase-2 (MMP-2). J. Biol. Chem. 2003, 278, (29), 27009-27015.

13. Song, K. Y.; Meroueh, O.; Hase, W. L., Dynamics of Cr(CO)(6)(+) Collisions with Hydrogenated Surfaces. J. Chem. Phys. 2003, 118, (6), 2893-2902.

12. Wang, J. P.; Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Efficiency of Energy Transfer in Protonated Diglycine and Dialanine SID - Effects of Collision Angle, Peptide Ion Size, and Intramolecular Potential. Int. J. Mass. Spectrom. 2003, 230, (1), 57-64.

11. Wilkinson, A. S.; Bryant, P. K.; Meroueh, S. O.; Page, M. G. P.; Mobashery, S.; Wharton, C. W., A Dynamic Structure for the Acyl-Enzyme Species of the Antibiotic Aztreonam with the Citrobacter freundii Beta-Lactamase Revealed by Infrared Spectroscopy and Molecular Dynamics Simulations. Biochemistry 2003, 42, (7), 1950-1957.

10. Maveyraud, L.; Golemi-Kotra, D.; Ishiwata, A.; Meroueh, O.; Mobashery, S.; Samama, J. P., High-Resolution X-ray Structure of an Acyl-Enzyme Species for the Class D OXA-10 Beta-Lactamase. J. Am. Chem. Soc. 2002, 124, (11), 2461-2465.

9. Meroueh, O.; Hase, W. L., Dynamics of Energy Transfer in Peptide-Surface Collisions. J. Am. Chem. Soc. 2002, 124, (7), 1524-1531.

8. Meroueh, S. O.; Roblin, P.; Golemi, D.; Maveyraud, L.; Vakulenko, S. B.; Zhang, Y.; Samama, J. P.; Mobashery, S., Molecular Dynamics at the Root of Expansion of Function in the M69L Inhibitor-Resistant TEM Beta-Lactamase from Escherichia coli. J. Am. Chem. Soc. 2002, 124, (32), 9422-9430.

7. Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation. J. Phys. Chem. A 2002, 106, (42), 9983-9992.

6. Toth, M.; Hernandez-Barrantes, S.; Osenkowski, P.; Bernardo, M. M.; Gervasi, D. C.; Shimura, Y.; Meroueh, O.; Kotra, L. P.; Galvez, B. G.; Arroyo, A. G.; Mobashery, S.; Fridman, R., Complex Pattern of Membrane type 1 Matrix Metalloproteinase Shedding - Regulation by Autocatalytic Cell Surface Inactivation of Active Enzyme. J. Biol. Chem. 2002, 277, (29), 26340-26350.

5. Meroueh, O.; Hase, W. L., Effect of Surface Stiffness on the Efficiency of Surface-Induced Dissociation. Phys. Chem. Chem. Phys. 2001, 3, (12), 2306-2314.

4. Sun, L. P.; Claire, P. D.; Meroueh, O.; Hase, W. L., Dynamics of Ar+CH4/Ni{111} Collision-Induced Desorption. J. Chem. Phys. 2001, 114, (1), 535-544.

3. Meroueh, O.; Hase, W. L., Energy Transfer Pathways in the Collisional Activation of Peptides. Int. J. Mass. Spectrom. 2000, 201, (1-3), 233-244.

2. Sawilowsky, E. F.; Meroueh, O.; Schlegel, H. B.; Hase, W. L., Structures, Energies, and Electrostatics for Methane Complexed with Alumina clusters. J. Phys. Chem. A 2000, 104, (21), 4920-4927.

1. Meroueh, O.; Hase, W. L., Collisional Activation of Small Peptides. J. Phys. Chem. A 1999, 103, (20), 3981-3990.

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