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Publications - Keith Dunker Lab

In Press 

49.  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)

48.  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)

47.  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)

46.  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)

45.  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)

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.  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)

42.  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)

41.  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)

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

39.  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).

2007 

38.  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)

37.  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)

2006 

36.  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)

35.  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)

34.  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)

33.  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)

32.  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)

31.  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)

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

28.  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)

27.  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)

26.  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)

25.  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)

24.  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)

2005 

23.  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)

22.  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)

21.  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)

20.  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)

19.  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).

18.  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).

17.  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).

16.  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).

15.  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).

14.  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).

2004 

13.  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.

12.  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.

11.  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

10.  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.

9.  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).

8.  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).

2003 

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

6.  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.

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

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

1.  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).