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2005-2008

Reviews

  1. Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Front Biosci. (2008) 13: 3391-3407.

  2. Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Protein disorder and functional proteomics. Biophys J. (2007) 92(5): 1439-1456.

Research Papers

  1. Radivojac P, Baenziger PH, Kann MG, Mort ME, Hahn MW, Mooney SD. Gain and loss of phosphorylation sites in human cancer. Bioinformatics. (2008) 24(16): i241-i247.

  2. Li YF, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H. A Bayesian approach to protein inference problem in shotgun proteomics. The 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008, pp. 167-180, Singapore, 2008.

  3. Mohan A, Sullivan WJ Jr, Radivojac P, Dunker AK, Uversky VN. Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes. Mol Biosyst. (2008) 4 (4): 328-340.

  4. Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD. An integrated approach to inferring gene-disease associations in humans. Proteins.(2008) 72 (3): 1030-1037. (www.phenopred.org) (data)

  5. Abi-Haidar A, Kaur J, Maguitman A, Radivojac P, Rechtsteiner A, Verspoor K, Wang Z, Rocha LM. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome Biol. (2008) 9 (S2): S11.

  6. Alves P, Arnold RJ, Clemmer DE, Li Y, Reilly JP, Sheng Q, Tang H, Xun Z, Zeng R, Radivojac P. Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics. (2008) 24 (1): 102-109.

  7. Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK. Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res. (2007) 6(6): 2351-66.

  8. Youn E, Peters BJ, Radivojac P, Mooney SD. Evaluation of features for catalytic residue prediction in novel folds. Protein Sci. (2007) 16(2): 216-226.

  9. Alves P, Arnold RJ, Novotny MV, Radivojac MV, Reilly JP, Tang H. Advancements in protein inference from shotgun proteomics using peptide detectability. Pac Symp Biocomput. (2007) 409-420.

  10. Tang H, Arnold RJ, Alves P, Xun Z, Clemmer DE, Novotny MV, Reilly JP, Radivojac P. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics. (2006) 22(14): e481-e488.

  11. Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN. Analysis of molecular recognition features (MoRFs). J Mol Biol. (2006) 362(5): 1043-1059.

  12. Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM. Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol. (2006) 2(8): e100.

  13. Dalkilic MM, Clark WT, Costello JC, Radivojac P. Using compression to detect classes of inauthentic texts. SIAM International Conference on Data Mining, SDM 2006, pp. 604-608, Bethesda, Maryland, U.S.A., April 2006.

  14. Roy S, Schnell S, Radivojac P. Unraveling the nature of the segmentation clock: intrinsic disorder of clock proteins and their interaction map. Comput Biol Chem. (2006) 30(4): 241-248.

  15. Vacic V, Iakoucheva LM, Radivojac P. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics. (2006) 22(12): 1536-1537.

  16. Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ, Cortese  MS, Sickmeier M, LeGall T, Obradovic Z, Dunker AK. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A. (2006) 103(22):8390-8395.

  17. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics. (2006) 7(1): 208.

  18. Radivojac P, Vucetic S, O'Connor TR, Uversky VN, Obradovic Z, Dunker AK. Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition. Proteins. (2006) 63(2): 398-410.

  19. Arnold RJ, Jayasankar N, Aggarwal D, Tang H, Radivojac P. A machine learning approach to predicting peptide fragmentation spectra. Pac Symp Biocomput. (2006) 219-230.

  20. Daily KM, Radivojac P, Dunker AK. Intrinsic disorder and protein modifications: building an SVM predictor for methylation. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, pp. 475-481, San Diego, California, U.S.A., November 2005.

  21. Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins. (2005) 61(S7): 176-182.

  22. Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z. Optimizing intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol. (2005) 3(1): 35-60.

Database Papers

  1. Saha S, Harrison SH, Shen C, Tang H, Radivojac P, Arnold RJ, Zhang X, Chen JY. HIP2: An online database of human plasma proteins from healthy individuals. BMC Med Genomics. (2008), 1 (1): 12.

  2. Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, Mooney SD. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. (2008) 36(Database issue): D815-819.

  3. Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK. DisProt: A database of protein disorder. Bioinformatics. (2005) 21(1): 137-140.

Book Chapters and Other Articles

  1. Lussier YA, Lee Y, Radivojac P, Ofran Y, Punta M, Butte AJ, Kann MG. Molecular bioinformatics for disease: protein interactions and phenomics. Pacific Symposium on Biocomputing, PSB 2008, pp. 228-230, The Big Island of Hawaii, U.S.A., January 2008. Introductory article to the conference session Protein Interactions and Disease.

  2. Uversky VN, Radivojac P, Iakoucheva LM, Obradovic Z, Dunker AK. Prediction of intrinsic disorder and its use in functional proteomics. Book Chapter in Methods in Molecular Biology, vol. 408: Gene Function Analysis. Edited by: M. F. Ochs. pp. 69-92. Humana Press Inc., Totowa, NJ. 2007.

  3. Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pacific Symposium on Biocomputing, PSB 2007, pp. 1-3, Wailea, Hawaii, U.S.A., January 2007. Introductory article to the conference session Protein Interactions and Disease.

  4. Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pacific Symposium on Biocomputing, PSB 2006, pp. 351-353, Wailea, Hawaii, U.S.A., January 2006. Introductory article to the conference session Protein Interactions and Disease.

  5. Dalkilic MM, Kim S, Radivojac P, Tang H. Transforming biology into an information science. I-Conference 2005, University Park, Pennsylvania, U.S.A., September 2005.

2001-2004

Research Papers

  1. Radivojac P, Obradovic Z, Dunker AK, Vucetic S. Feature selection filters based on the permutation test. European Conference on Machine Learning, ECML 2004, pp. 334-346, Pisa, Italy, September 2004.

  2. Radivojac P, Chawla NV, Dunker AK, Obradovic Z. Classification and knowledge discovery in protein databases. J Biomed Inform. (2004) 37(4): 224-239.

  3. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK. The importance of intrinsic disorder for protein phosphorylation. (joint first authors LMI and PR), Nucleic Acids Res. (2004) 32 (3): 1037-1049.

  4. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK. Protein flexibility and intrinsic disorder. Protein Sci. (2004) 13 (1): 71-80. (data)

  5. Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK. Predicting intrinsic disorder from amino acid sequence. Proteins. (2003) 53 (S6): 566-572.

  6. Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G. Improved amino acid flexibility parameters. Protein Sci. (2003), 12 (5):1060-1072.

  7. Radivojac P, Korad U, Sivalingam KM, Obradovic Z. Learning from class-imbalanced data in wireless sensor networks. IEEE Semiannual Vehicular Technology Conference, VTC-Fall 2003, Vol. 5, pp. 3030-3034, Orlando, Florida, U.S.A., October 2003.

  8. Radivojac P, Obradovic Z, Brown CJ, Dunker AK. Prediction of boundaries between intrinsically ordered and disordered protein regions. Pac Symp Biocomput. (2003), 216-227.

  9. Senk V, Radivojac P, Radujkov I. The systolic bidirectional algorithm for decoding trellis codes. IEEE International Symposium on Information Theory, ISIT'02, p. 260, Lausanne, Switzerland, July 2002.

  10. Radivojac P, Obradovic Z, Brown CJ, Dunker AK. Improving sequence alignments for intrinsically disordered proteins. Pac Symp Biocomput. (2002), 589-600. 

  11. Vucetic S, Radivojac P, Dunker AK, Brown CJ, Obradovic Z. Methods for improving protein disorder prediction. International Joint INNS-IEEE Conference on Neural Networks, Vol. 4, pp. 2718-2723, Washington DC, U.S.A., July 2001.

  12. Senk V, Radivojac P. A new bidirectional algorithm for decoding trellis codes. IEEE International Conference on Trends in Communications, EUROCON 2001, pp. 34-36, Bratislava, Slovak Republic, July 2001.

Book Chapters and Other Articles

  1. Book review: Igor F. Tsigelny (editor). Protein structure prediction: bioinformatics approach. International University Line, La Jolla, CA, 2002. Briefings in Bioinformatics, 5 (2), pp. 207-209, June 2004. Henry Stewart Publications, London UK.

1995-2000

Reviews

  1. Senk V, Radivojac P, Stanojevic I. An overview of decoding procedures for trellis codes. Proceedings of Telecommunication Forum, TELFOR’99, pp. 257-264, Belgrade, Yugoslavia, November 1999, invited paper.

Research Papers

  1. Senk V, Radivojac P, Todic O. An application of the bidirectional stack algorithm to speech coding. IEEE International Conference on Telecommunications in Modern Satellite, Cable, and Broadcasting Services, TELSIKS’99, Vol. I, pp. 259-262, Nis, Yugoslavia, October 1999.

  2. Senk V, Radivojac P. Universal trellis coding of speech. International Conference on Telecommunications, ICT'98, Vol. II, pp. 273-277, Porto Carras, Greece, June 1998.

  3. Radivojac P, Senk V, Savic M. Filter bank based trellis coding of speech. Australian Workshop on Signal Processing Applications, WoSPA'97, pp. 51-54, Brisbane, Australia, November 1997.

  4. Senk V, Radivojac P. The bidirectional stack algorithm. IEEE International Symposium on Information Theory, ISIT'97, p. 500, Ulm, Germany, July 1997.

  5. Senk V, Radivojac P. A multi-path stack algorithm for decoding trellis codes. Proceedings of the 3-rd International Conference on Telecommunications in Modern Satellite, Cable, and Broadcasting Services, TELSIKS’97, Vol. II, pp. 780-783, Nis, Yugoslavia, October 1997.

  6. Savic M, Radivojac P. A heuristic procedure for extracting stationary modes of a speech source. Proceedings of XLI Yugoslav Conference on ETRAN, Vol. 2, pp. 200-202, Zlatibor, June 1997.

  7. Radivojac P, Vucetic S. An improved trellis code search procedure for speech compression. Proceedings of XLI Yugoslav Conference on ETRAN, Vol. 2, pp. 203-205, Zlatibor, June 1997.

  8. Senk V, Radivojac P, Stanojevic M. The tunneled M-algorithm. Proceedings of XL Yugoslav Conference on ETRAN, Vol. 2, pp. 269-272, Budva, June 1996.

  9. Radivojac P, Senk V. An improved simulation procedure for estimating the error probability of channel codes. Proceedings of YU-INFO'96, Symposium on Computer Science, Brezovica, April 1996.

  10. Senk V, Radivojac P. The bidirectional stack algorithm - simulation results. Proceedings of TELSIKS’95, 2-nd Conference on Telecommunications in Modern Satellite and Cable Services, Vol. I, pp. 349-352, Nis, Yugoslavia, October 1995.

  11. Senk V, Radivojac P. An efficient simulation procedure for estimating the error probability of channel codes. Proceedings of ITP'95, Symposium on Information Technology and Application, Novi Sad, September 1995.

  12. Radivojac P, Senk V. The generalized Viterbi-T algorithm. Proceedings of XXXIX Yugoslav Conference on ETRAN, Vol. 2, pp. 13-16, Zlatibor, June 1995.

  13. Despotovic M, Senk V, Sveljo O, Radivojac P. New channel trellis codes on precoded partial-response 1+D channel. Proceedings of XXXIX Yugoslav Conference on ETRAN, Vol. 2, pp. 17-19, Zlatibor, June 1995.

Last modified: September 05, 2008