Predrag Radivojac

Online Preprints

1. The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. arXiv:2205.05897
2. Ramola R, et al. The field of protein function prediction as viewed by different domain scientists. bioRxiv 2022.04.18.488641
3. Pejaver V, et al. Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria. bioRxiv 2022.03.17.484479
4. Pagel KA, et al. The influence of genetic predisposition and physical activity on risk of Gestational Diabetes Mellitus in the nuMoM2b cohort. (2022) medRxiv 2022.03.08.22271868
5. Guerrero RF, et al. Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas. (2022) medRxiv 2022.02.28.22271641
6. Karanam A, et al. Explaining deep tractable probabilistic models: the sum-product network case. (2021) arXiv:2110.09778
7. Jain S, et al. Nonparametric semi-supervised learning of class proportions. (2016) arXiv:1601.01944
8. Radivojac P. A (not so) quick introduction to protein function prediction. (2013). PDF

Complete Publication List

1. ☀️ Radivojac P. Advancing remote homology detection: a step towards understanding and accurately predicting protein function. Cell Syst., accepted.
2. ☀️ Jiang Y, Urresti J, Pagel KA, Pramod AB, Iakoucheva LM, Radivojac P. Prioritizing de novo autism risk variants with calibrated gene- and variant-scoring models. Hum. Genet., accepted. PDF PubMed
3. ☀️ Karanam A, Hayes AL, Kokel H, Haas DM, Radivojac P, Natarajan S. A probabilistic approach to extract qualitative knowledge for early prediction of gestational diabetes. Proceedings of the 19th International Conference on Artificial Intelligence in Medicine, AIME 2021, Virtual Event, pp. 497-502. PDF
4. ☀️ Lugo-Martinez J, Zeiberg D, Gaudelet T, Malod-Dognin N, Przulj N, Radivojac P. Classification in biological networks with hypergraphlet kernels. Bioinformatics (2021), 37(7): 1000-1007. PDF PubMed
5. Wang RJ, Radivojac P, Hahn MW. Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis. Genetics (2021), 217(1): iyaa014. PDF PubMed
6. Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nat. Commun. (2020), 11(1): 5918. PDF PubMed Web
7. Peng Y, Jain S, Li YF, Gregus M, Ivanov AR, Vitek O, Radivojac P. New mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics. Bioinformatics (2020) 36(Supplement_2):i745-i753. PDF PubMed Supp
8. Stamboulian M, Guerrero RF, Hahn MW, Radivojac P. The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinformatics (2020) 36(Supplement_1):i219-i226. PDF PubMed
9. Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res. (2020) 30(6):826-834 PDF PubMed
10. Naidu JS, Delano JD, Mathews S, Radivojac P. An examination of citation-based impact of the computational biology conferences. Bioinformatics (2020) 36(9):2958-2962. PDF PubMed Code/Data
11. Jain S, Delano JD, Sharma H, Radivojac P. Class prior estimation with biased positives and unlabeled examples. AAAI Conference on Artificial Intelligence, AAAI 2020, pp. 4255-4263, New York, New York, U.S.A., February 2020. PDF AAAI
12. Zeiberg D, Jain S, Radivojac P. Fast nonparametric estimation of class proportions in the positive-unlabeled classification setting. AAAI Conference on Artificial Intelligence, AAAI 2020, pp. 6729-6736, New York, New York, U.S.A., February 2020. PDF AAAI
13. Brenner SE, Bulyk ML, Crawford DC, Morgan AA, Radivojac P, Tatonetti NP. Precision medicine: addressing the challenges of sharing, analysis, and privacy at scale. Pac. Symp. Biocomput. (2020) 25:547-550. PDF
14. Kurgan L, Radivojac P, Sussman JL, Dunker AK. On the importance of computational biology and bioinformatics to the origins and rapid progression of the intrinsically disordered proteins field. Pac. Symp. Biocomput. (2020) 25:149-158. PDF
15. Jain S, Levine M, Radivojac P, Trosset MW. Identifiability of two-component skew normal mixtures with one known component. Scand. J. Stat. (2019) 46(4): 955-986. PDF
16. Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkiran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernandez JM, Gemovic B, Perovic VR, Davidovic RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Toronen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijevic V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Bjorne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Smuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. (2019) 20(1):244. PDF PubMed

• Coverage in Genome Web

17. Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH. Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Hum. Mutat. (2019) 40(9):1519-1529. PDF PubMed
18. Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, Jiang Y, Joseph T, Katsonis P, Kotte S, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Moult J, Pal LR, Poitras J, Radivojac P, Rao A, Sivadasan N, Sunderam U, Saipradeep VG, Yin Y, Zaucha J, Brenner SE, Meyn MS. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Hum Mutat. (2019) 40(9):1373-1391. PDF PubMed
19. Bromberg Y, El-Mabrouk N, Radivojac P. ISMB/ECCB 2019 proceedings. Bioinformatics (2019) 35(14): i1-i2. PDF PubMed
20. Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, de la Cruz X, Díez O, Gutiérrez-Enríquez S, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Moles-Fernández A, Montalban G, Mooney SD, O'Conner R, Ootes L, Özkan S, Padilla N, Pagel KA, Pejaver V, Radivojac P, Riera C, Savojardo C, Shen Y, Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE, ENIGMA Consortium. Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Hum. Mutat. (2019) 40(9):1546-1556. PDF PubMed
21. Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat. 40(9):1530-1545. PDF PubMed
22. Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum. Mutat. (2019) 40(9):1495-1506. PDF PubMed
23. Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner S, Kann MG. Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum. Mutat. (2019) 40(9):1612-1622. PDF PubMed
24. Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SCE, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum. Mutat. (2019) 40(9):1330-1345. PDF PubMed
25. McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan RG, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, Savojardo C, Martelli PL, Casadio R, Pal LR, Moult J, Brenner S, Altman R. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum. Mutat. (2019) 40(9):1314-1320. PDF PubMed
26. Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput. Biol. (2019) 15(6): e1007112. PDF PubMed Web
27. Yang R, Jiang Y, Mathews S, Housworth EA, Hahn MW, Radivojac P. A new class of metrics for learning on real-valued and structured data. Data Min. Knowl. Disc. (2019) 33(4): 995-1016. PDF Supp SupTable
28. Misal SA, Li S, Tang H, Radivojac P, Reilly JP. Identification of N-terminal protein processing sites by chemical labeling mass spectrometry. Rapid Commun. Mass Spectrom. (2019) 33(11): 1015-1023. PDF PubMed
29. Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC, Baboon Genome Analysis Consortium. The comparative genomics and complex population history of Papio baboons. Sci. Adv. (2019) 5(1): eaau6947. PDF PubMed
30. Brenner SE, Bulyk M, Crawford DC, Mesirov JP, Morgan AA, Radivojac P. Precision medicine: improving health through high-resolution analysis of personal data. Pac. Symp. Biocomput. (2019) 24: 220-223. PDF PubMed
31. Ramola R, Jain S, Radivojac P. Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. Pac. Symp. Biocomput. (2019) 24: 124-135. PDF PubMed
32. Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G. New Drosophila long-term memory genes revealed by assessing computational function prediction methods. G3 (2019) 9(1): 251-267. PDF PubMed
33. Mohammed Ismail W, Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P. The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS One (2018) 13(12): e0208901. PDF PubMed
34. Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A. Target site specificity and in vivo complexity of the mammalian arginylome. Sci. Rep. (2018) 8(1): 16177. PDF PubMed
35. Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive longevity predicts mutation rates in primates. Curr. Biol. (2018) 28(19): 3193-3197. PDF PubMed
36. Ramalho RF, Li S, Radivojac P, Hahn MW. Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in mammals. IEEE-ACM Trans. Comput. Biol. Bioinform. (2018) 15(4): 1284-1289. PDF IEEE-Xplore PubMed
37. Natarajan S, Das S, Ramanan N, Kunapuli G, Radivojac P. On whom should I perform this lab test next? An active feature elicitation approach. Proceedings of the International Joint Conference on Artificial Intelligence, IJCAI 2018, pp. 3498-3505, Stockholm, Sweden, July 2018. PDF IJCAI
38. Bromberg Y, Radivojac P. ISMB 2018 proceedings. Bioinformatics (2018) 34(13): i2-i3. PDF PubMed
39. Peng Y, Jiang Y, Radivojac P. Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. Bioinformatics (2018) 34(13): i313-i322. PDF Supp Code PubMed
40. Yamada M, Tang J, Lugo-Martinez J, Hodzic E, Shrestha R, Saha A, Ouyang H, Yin D, Mamitsuka H, Sahinalp C, Radivojac P, Menczer F, Chang Y. Ultra high-dimensional nonlinear feature selection for big biological data. IEEE Trans. Knowl. Data Eng. (2018) 30(7): 1352-1365. PDF IEEE-Xplore
41. Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat R, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman R, Klein TE, Hoskins R, Repo S, Brenner SE, Morgan AA. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum. Mutat. (2017) 38(9): 1182-1192. PDF PubMed
42. Pejaver V, Mooney SD, Radivojac P. Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges. Hum. Mutat. (2017) 38(9): 1092-1108. PDF PubMed
43. Pagel KA, Pejaver V, Lin GN, Nam H, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics (2017) 33(14): i389-i398. PDF PubMed Web

• Ian Lawson Van Toch Memorial Award at ISMB/ECCB 2017.

44. Jain S, White M, Radivojac P. Recovering true classifier performance in positive-unlabeled learning. AAAI Conference on Artificial Intelligence, AAAI 2017, pp. 2066-2072, San Francisco, California, U.S.A., February 2017. PDF Supp AAAI
45. Friedberg I, Radivojac P. Community-wide evaluation of computational function prediction. Book Chapter in Methods in Molecular Biology, vol. 1446: The Gene Ontology Handbook. Edited by: C. Dessimoz and N. Škunca, pp. 133-146. Springer, New York, NY. 2017. PDF PubMed
46. Bromberg Y, Hahn MW, Radivojac P. Computational approaches to understanding the evolution of molecular function. Pac. Symp. Biocomput. (2017) 22: 1-2. PDF PubMed
47. Reddy KD, Malipeddi J, DeForte S, Pejaver V, Radivojac P, Uversky VN, Deschenes RJ. Physicochemical sequence characteristics that influence S-palmitoylation propensity. J. Biomol. Struct. Dyn. (2017) 35(11): 2337-2350. PDF PubMed
48. Jain S, White M, Radivojac P. Estimating the class prior and posterior from noisy positives and unlabeled data. Advances in Neural Information Processing Systems, NIPS 2016, pp. 2693-2701, Barcelona, Spain, December 2016. PDF
49. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am. J. Hum. Genet. (2016), 99(4): 877-885. PDF PubMed
50. Li S, Dabir A, Misal SA, Tang H, Radivojac P, Reilly JP. Impact of amidination on peptide fragmentation and identification in shotgun proteomics. J. Proteome Res. (2016) 15(10): 3656-3665. PDF PubMed
51. Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P. The loss and gain of functional amino acid residues is a common mechanism causing human inherited disease. PLoS Comput. Biol. (2016) 12(8): e1005091. PDF Supp Data PubMed
52. Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. (2016) 17(1): 184. PDF Supp Data Figures PubMed
53. Rost B, Radivojac P, Bromberg Y. Protein function in precision medicine: deep understanding with machine learning. FEBS Lett. (2016) 590(15): 2327-2341. PDF PubMed
54. Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD. Regulatory single-nucleotide variant predictor increases predictive performance of functional regulatory variants. Hum. Mutat. (2016) 37(11): 1137-1143. PDF PubMed
55. Ji C, Li S, Reilly JP, Radivojac P, Tang H. XLSearch: a probabilistic database search algorithm for identifying cross-linked peptides. J. Proteome Res. (2016) 15(6): 1830-1841. PDF Code PubMed
56. Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T. Applying, evaluating and refining bioinformatics core competencies (an update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput. Biol. (2016) 12(5): e1004943. PDF PubMed
57. Glover MS, Dilger JM, Acton MD, Arnold RJ, Radivojac P, Clemmer DE. Examining the influence of phosphorylation on peptide ion structure by ion mobility spectrometry-mass spectrometry. J. Am. Soc. Mass Spectrom. (2016) 27(5):786-794. PDF PubMed
58. Khanal N, Pejaver V, Li Z, Radivojac P, Clemmer DE, Mukhopadhyay S. The position of proline mediates the reactivity of S-palmitoylation. ACS Chem. Biol. (2015) 10(11): 2529-2536. PDF PubMed
59. Ji C, Li YF, Bellinger EP, Li S, Arnold RJ, Radivojac P, Tang H. A maximum-likelihood approach to absolute protein quantification in mass spectrometry. ACM Conference on Bioinformatics, Computational Biology and Health Informatics, ACM BCB 2015, pp. 296-305, Atlanta, Georgia, U.S.A., September 2015. PDF ACM-DL
60. Glover MS, Bellinger EP, Radivojac P, Clemmer DE. Penultimate proline in neuropeptides. Anal. Chem. (2015) 87(16): 8466-8472. PDF PubMed
61. Friedberg I, Wass MN, Mooney SD, Radivojac P. Ten simple rules for a community computational challenge. PLoS Comput. Biol. (2015) 11(4): e1004150. PDF PubMed
62. Shin Y, Myers S, Gupta M, Radivojac P. A link graph-based approach to identify forum spam. Security Comm. Networks (2015) 8(2): 176-188. PDF
63. Glover MS, Shi L, Fuller DR, Arnold RJ, Radivojac P, Clemmer DE. On the split personality of penultimate proline. J. Am. Soc. Mass Spectrom. (2015) 26(3): 444-452. PDF PubMed
64. Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, Görg C, Hunter LE, Muse SV, Radivojac P, Moore JH. Training the next generation of quantitative biologists in the era of big data. Pac. Symp. Biocomput. (2015) 20: 488-492. PDF PubMed
65. Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Sci. Rep. (2014) 4: 7155. PDF PubMed
66. Jiang Y, Clark WT, Friedberg I, Radivojac P. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics (2014) 30(17): i609-i616. PDF Supp PubMed
67. Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci. (2014) 23(8): 1077-1093. PDF Supp Web PubMed
68. Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. Bioinformatics curriculum guidelines: toward a definition of core competencies. PLoS Comput. Biol. (2014) 10(3): e1003496. PDF PubMed
69. Li Z, Dilger JM, Pejaver V, Smiley D, Arnold RJ, Mooney SD, Mukhopadhyay S, Radivojac P, Clemmer DE. Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides. Int. J. Mass Spectrom. (2014) 368: 6-14. PDF PubMed
70. Lugo-Martinez J, Radivojac P. Generalized graphlet kernels for probabilistic inference in sparse graphs. Network Science (2014) 2(2): 254-276. PDF Code
71. Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I. The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinformatics (2014) 30(14): 2091-2092. PDF PubMed
72. Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biol. (2014) 15: R19. PDF PubMed
73. Clark WT, Radivojac P. Vector quantization kernels for the classification of protein sequences and structures. Pac. Symp. Biocomput. (2014) 19: 316-327. PDF PubMed
74. Li S, Arnold RJ, Tang H, Radivojac P. Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM BCB 2013, pp. 316-323, Washington, District of Columbia, U.S.A., September 2013. PDF ACM-DL
75. Clark WT, Radivojac P. Information-theoretic evaluation of predicted ontological annotations. Bioinformatics (2013) 29(13): i53-i61. PDF Supp Code/Data PubMed

• Ian Lawson Van Toch Memorial Award at ISMB/ECCB 2013.

76. Lugo-Martinez J, Radivojac P. Vertex classification in graphs. Biomedical Computation Review. p. 25. June 2013. PDF BCR
77. Xue L, Wang P, Wang L, Renzi E, Radivojac P, Tang H, Arnold RJ, Zhu JK, Tao WA. Quantitative measurement of phosphoproteome response to osmotic stress in Arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC). Mol. Cell. Proteomics (2013) 12(8): 2354-2369. PDF PubMed
78. Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L. Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PLoS One (2013) 8(3): e58993. PDF PubMed
79. Ji C, Arnold RJ, Sokoloski KJ, Hardy RW, Tang H, Radivojac P. Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra. Proteomics (2013) 13(5): 756-765. PDF PubMed
80. Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction. Nat. Methods (2013) 10(3): 221-227. PDF Supp Data PubMed
81. Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. ISCB computational biology Wikipedia competition. PLoS Comput. Biol. (2013) 9(9): e1003242. PDF PubMed
82. Bagchi A, Mort M, Li B, Xin F, Carlise C, Oron T, Powell C, Youn E, Radivojac P, Cooper DN, Mooney SD. Analysis of features from protein-protein hetero-complex structures to predict protein interaction interfaces using machine learning. Procedia Technology (2013) 10: 62-66. PDF
83. Li YF, Radivojac P. Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics (2012) 13(Suppl 16): S4. PDF PubMed
84. Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum. Mutat. (2013) 34(1): 255-265. PDF PubMed
85. Xin F, Radivojac P. Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinformatics (2012) 28(22): 2905-2913. PDF PubMed
86. Nussinov R, Tsai CJ, Xin F, Radivojac P. Allosteric post-translational modification codes. Trends Biochem. Sci. (2012) 37(10): 447-455. PDF PubMed
87. Kosti I, Radivojac P, Mandel-Gutfreund Y. An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PLoS Comput. Biol. (2012) 8(7): e1002603. PDF PubMed
88. Li B, Radivojac P, Mooney SD. Bioinformatics approaches to the functional profiling of genetic variants. Mutations in Human Genetic Disease. Edited by: D. N. Cooper and J. M. Chen, pp. 233-250, InTech, 2012. PDF
89. Li YF, Arnold RJ, Radivojac P, Tang H. Protein identification problem from a Bayesian point of view. Stat. Interface. (2012) 5(1): 21-37. PDF PubMed
90. Xin F, Radivojac P. Computational methods for identification of functional residues in protein structures. Curr. Protein Pept. Sci. (2011) 12(6): 456-469. PDF Data PubMed
91. Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP. Investigation of VUV photodissociation propensities using peptide libraries. Int. J. Mass Spectrom. (2011) 308(2-3): 142-154. PDF PubMed
92. Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD. Prediction of functional regulatory SNPs in monogenic and complex disease. Hum. Mutat. (2011) 32(10): 1183-1190. PDF PubMed
93. Nehrt NL, Clark WT, Radivojac P, Hahn MW. Testing the ortholog conjecture with comparative functional genomics data from mammals. PLoS Comput. Biol. (2011) 7(6): e1002073. PDF PubMed

• Coverage: Nature Review Genetics

94. Clark WT, Radivojac P. Analysis of protein function and its prediction from amino acid sequence. Proteins (2011) 79(7): 2086-2096. PDF Software PubMed
95. Pereira L, Soares P, Radivojac P, Li B, Samuels DC. Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. Am. J. Hum. Genet. (2011) 88(4): 433-439. PDF PubMed
96. Li S, Arnold RJ, Tang H, Radivojac P. On the accuracy and limits of peptide fragmentation spectrum prediction. Anal. Chem. (2011) 83(3): 790-796. PDF Software PubMed
97. Li YF, Arnold RJ, Tang H, Radivojac P. The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J. Proteome Res. (2010) 9(12): 6288–6297. PDF PubMed
98. Bohrer BC, Li YF, Reilly JP, Clemmer DE, DiMarchi RD, Radivojac P, Tang H, Arnold RJ. Combinatorial libraries of synthetic peptides as a model for shotgun proteomics. Anal. Chem. (2010) 82(15): 6559-6568. PDF PubMed
99. Xin F, Myers S, Li YF, Cooper DN, Mooney SD, Radivojac P. Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Bioinformatics (2010) 26(16): 1975-1982. PDF Code Data PubMed
100. Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum. Mutat. (2010) 31(3) 335-346. PDF PubMed
101. Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM. Identification, analysis, and prediction of protein ubiquitination sites. Proteins (2010) 78(2): 365-380. PDF Web PubMed
102. Li S, Iakoucheva LM, Mooney SD, Radivojac P. Loss of post-translational modification sites in disease. Pac. Symp. Biocomput. (2010) 15: 337-347. PDF PubMed
103. Vacic V, Iakoucheva LM, Lonardi S, Radivojac P. Graphlet kernels for prediction of functional residues in protein structures. J. Comput. Biol. (2010) 17(1): 55-72. PDF Supp PubMed
104. Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics (2009) 25(21): 2744-2750. PDF Web PubMed
105. Mohan A, Uversky VN, Radivojac P. Influence of sequence changes and environment on intrinsically disordered proteins. PLoS Comput. Biol. (2009) 5(9): e1000497. PDF PubMed
106. Li YF, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H. A Bayesian approach to protein inference problem in shotgun proteomics. J. Comput. Biol. (2009) 16(8): 1183-1193. PDF PubMed
107. Lee E, Jung H, Radivojac P, Kim J-W, Lee D. Analysis of AML genes in dysregulated molecular interaction networks. BMC Bioinformatics (2009) 10 (Suppl 9): S2. PDF PubMed
108. Lussier YA, Lee Y, Radivojac P, Ofran Y, Butte A, Kann MG. Molecular bioinformatics for disease. Pac. Symp. Biocomput. (2009) 14: 464-466. PDF
109. 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. PDF PubMed
110. 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. PDF
111. 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. PDF PubMed
112. 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. PDF Data Web PubMed
113. Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Front. Biosci. (2008) 13: 3391-3407. PDF PubMed
114. 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. PDF PubMed
115. 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. PDF PubMed
116. 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. PDF PubMed
117. 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. PDF PubMed
118. Lussier YA, Lee Y, Radivojac P, Ofran Y, Punta M, Butte AJ, Kann MG. Molecular bioinformatics for disease: protein interactions and phenomics. Pac. Symp. Biocomput. (2008) 13: 228-230. PDF
119. Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Intrinsic disorder and functional proteomics. Biophys. J. (2007) 92(5): 1439-1456. PDF PubMed
120. 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. PDF PubMed
121. 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. PDF PubMed
122. 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. PDF PubMed
123. Alves P, Arnold RJ, Novotny MV, Radivojac P, Reilly JP, Tang H. Advancement in protein inference from shotgun proteomics using peptide detectability. Pac. Symp. Biocomput. (2007) 12: 409-420. PDF PubMed
124. Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pac. Symp. Biocomput. (2007) 12: 1-3. PDF
125. 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. PDF PubMed
126. 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. PDF PubMed
127. 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. PDF PubMed
128. 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. PDF Web

• Coverage: Slashdot, ACM Tech News, Der Spiegel

129. 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. PDF PubMed
130. 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. PDF Code/Web PubMed
131. 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. PDF PubMed
132. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics (2006) 7(1): 208. PDF PubMed
133. 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. PDF PubMed
134. Arnold RJ, Jayasankar N, Aggarwal D, Tang H, Radivojac P. A machine learning approach to predicting peptide fragmentation spectra. Pac. Symp. Biocomput. (2006) 11: 219-230. PDF PubMed
135. Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pac. Symp. Biocomput. (2006) 11: 351-353. PDF
136. 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. PDF IEEE-Xplore
137. 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. PDF PubMed
138. Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. Comput. Biol. (2005) 3(1): 35-60. PDF PubMed
139. 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. PDF Web PubMed
140. 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. PDF
141. Radivojac P, Chawla NV, Dunker AK, Obradovic Z. Classification and knowledge discovery in protein databases. J. Biomed. Inform. (2004) 37(4): 224-239. PDF Data PubMed
142. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. (2004) 32 (3): 1037-1049. PDF PubMed
143. 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. PDF PubMed
144. Book review: Igor F. Tsigelny (editor). Protein structure prediction: bioinformatics approach. International University Line, La Jolla, CA, 2002. Brief. Bioinform. 5 (2), pp. 207-209, June 2004. Henry Stewart Publications, London UK. PDF
145. 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. PDF PubMed
146. Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G. Improved amino acid flexibility parameters. Protein Sci. (2003), 12 (5):1060-1072. PDF PubMed
147. 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. PDF IEEE-Xplore
148. Radivojac P, Obradovic Z, Brown CJ, Dunker AK. Prediction of boundaries between intrinsically ordered and disordered protein regions. Pac. Symp. Biocomput. (2003) 8: 216-227. PDF PubMed
149. Senk V, Radivojac P, Radujkov I. The systolic bidirectional algorithm for decoding trellis codes. IEEE International Symposium on Information Theory, ISIT 2002, p. 260, Lausanne, Switzerland, July 2002. PDF IEEE-Xplore
150. Radivojac P, Obradovic Z, Brown CJ, Dunker AK. Improving sequence alignments for intrinsically disordered proteins. Pac. Symp. Biocomput. (2002) 7: 589-600. PDF PubMed
151. 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. PDF IEEE-Xplore
152. 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. PDF IEEE-Xplore
153. Senk V, Radivojac P, Stanojevic I. An overview of decoding procedures for trellis codes. Proceedings of the Telecommunication Forum, TELFOR 1999, pp. 257-264, Belgrade, Yugoslavia, November 1999. PDF
154. 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 1999, Vol. I, pp. 259-262, Nis, Yugoslavia, October 1999. PDF IEEE-Xplore
155. Senk V, Radivojac P. Universal trellis coding of speech. International Conference on Telecommunications, ICT 1998, Vol. II, pp. 273-277, Porto Carras, Greece, June 1998.
156. Radivojac P, Senk V, Savic M. Filter bank based trellis coding of speech. Australian Workshop on Signal Processing Applications, WoSPA 1997, pp. 51-54, Brisbane, Australia, November 1997.
157. Senk V, Radivojac P. The bidirectional stack algorithm. IEEE International Symposium on Information Theory, ISIT 1997, p. 500, Ulm, Germany, July 1997. PDF IEEE-Xplore
158. Senk V, Radivojac P. A multi-path stack algorithm for decoding trellis codes. Proceedings of the 3rd International Conference on Telecommunications in Modern Satellite, Cable, and Broadcasting Services, TELSIKS 1997, Vol. II, pp. 780-783, Nis, Yugoslavia, October 1997.
159. 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.
160. 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.
161. 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.
162. Radivojac P, Senk V. An improved simulation procedure for estimating the error probability of channel codes. Proceedings of YU-INFO 1996, Symposium on Computer Science, Brezovica, April 1996.
163. Senk V, Radivojac P. The bidirectional stack algorithm - simulation results. Proceedings of TELSIKS 1995, 2nd Conference on Telecommunications in Modern Satellite and Cable Services, Vol. I, pp. 349-352, Nis, Yugoslavia, October 1995.
164. Senk V, Radivojac P. An efficient simulation procedure for estimating the error probability of channel codes. Proceedings of ITP 1995, Symposium on Information Technology and Application, Novi Sad, September 1995.
165. Radivojac P, Senk V. The generalized Viterbi-T algorithm. Proceedings of XXXIX Yugoslav Conference on ETRAN, Vol. 2, pp. 13-16, Zlatibor, June 1995.
166. 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 update: May 26, 2022