Predrag Radivojac

Online Preprints

• Runyan M, et al. Improving splice site usage prediction with SPLAIRE. (2026) bioRxiv 2026.06.08.731019 
• Jiang FT, et al. Structure-aware protein function prediction at isoform resolution. (2026) bioRxiv 2026.04.24.720502 
• Ramola R, et al. On the state of protein function prediction: a report on the fourth CAFA challenge. (2026) bioRxiv 2026.05.06.722942  
• De Paolis Kaluza MC, et al. Advances in protein function prediction from the fifth CAFA challenge. (2026) bioRxiv 2026.04.27.716980 
• Abderrazzaq H, et al. Calibration of in-frame indel variant effect predictors for clinical variant classification. (2026) bioRxiv 2026.04.15.718599 
• Chen Y, et al. Gene- and domain-aware calibration increases the clinical utility of variant effect predictors. (2026) bioRxiv 2026.02.17.706269 
• Hoffing R, et al. Ancestry-specific performance of variant effect predictors in clinical variant classification. (2026) bioRxiv 2026.02.14.705914 
• Tejura M, et al. A scalable approach to resolving variants of uncertain significance. (2026) bioRxiv 2026.02.14.705848 
• Biar CG, et al. An integrated, scaled approach to resolve TSC2 variants of uncertain significance. (2026) bioRxiv 2026.01.16.699909 
• Zeiberg D, et al. Gene-based calibration of high-throughput functional assays for clinical variant classification. (2025) bioRxiv 2025.04.29.651326  
• Chao KR, et al. The landscape of regional missense mutational intolerance quantified from 125,748 exomes. (2024) bioRxiv 2024.04.11.588920  
• Jain S, et al. Nonparametric semi-supervised learning of class proportions. (2016) arXiv:1601.01944 
• Radivojac P. A (not so) quick introduction to protein function prediction. (2013) PDF 

Complete Publication List

• Mortensen GA, Schmidt H, Radivojac P, Ye Y, Haas DM. Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease. Microbiol. Spectr. (2026) 14(5): e0315525. PDF PubMed 
• Stewart R, Laval F, Coppin G, Spirohn-Fitzgerald K, Tixhon M, Hao T, Calderwood MA, Mort M, Cooper DN, Vidal M, Radivojac P. Predicting interaction-specific protein-protein interaction perturbations by missense variants with MutPred-PPI. The 30th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2026. Available on bioRxiv 2025.12.20.695738 
• Jiang J, Radivojac P, Gyori BM. Literature-driven extraction and computational prediction of causal statements linking genetic variants to biological processes, pathways and phenotypes. Pac. Symp. Biocomput. (2026) 31: 738-751. PDF PubMed Supp 
• Andreoletti G, Mangul S, Radivojac P, Brenner SE. Trust, reproducibility, and progress: the roles of independent blind prediction and assessment and benchmarking in computational biology. Pac. Symp. Biocomput. (2026) 31: 865-868. PDF PubMed 
• Li D, Liu S, Assis PR, Li M, Dong S, Whaling I, Jolanki O, Kagda M, Zhang W, Macias-Velasco JF, Liu T, Cody S, Antonacci-Fulton L, Huang Y, Liu J, Montgomery MT, Zeiberg D, Jain S, Pejaver V, Bergquist T, Chen Y, Radivojac P, Gersbach CA, Sherpa RN, Castro CP, Boyle AP, Starita LM, Fowler DM, Ahituv N, Dey KK, Majoros WH, Reddy TE, Craven M, Sinha R, Sverchkov Y, Cai X, Nzima MZ, Calderwood MA, Rozowsky J, Gerstein M, Ma J, Yue F, Cherry JM, Love MI, Engreitz JM, Hitz BC, Wang T. The IGVF catalog-from genetic variation to function. Nucleic Acids Res. (2026) 54(D1): D1437-D1445. PDF PubMed 
• Mathur S, Singh R, Skinner M, Radivojac P, Haas DM, Raman L, Natarajan S. LLMs for causal reasoning in medicine? A call for caution. Proceedings of the 13th ACM IKDD International Conference on Data Science, CODS 2025, pp. 164-172, Pune, India. PDF ACM 
• De Paolis Kaluza MC, Tholeti T, Chen Y, Baeza-Yates R, Radivojac P, Jain S. Are your fairness metrics accurate? A semi-supervised approach to improving fairness estimates under sample selection bias. Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, KDD 2025, pp. 439-450, Toronto, Canada. PDF ACM 
• Bergquist T, Stenton SL, Nadeau EAW, Byrne AB, Greenblatt MS, Harrison SM, Tavtigian SV, O'Donnell-Luria A, Biesecker LG, Radivojac P, Brenner SE, Pejaver V, ClinGen Sequence Variant Interpretation Working Group. Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria. Genet. Med. (2025) 27(6): 101402. PDF PubMed Supp 
• Rastogi R, Chung R, Li S, Li C, Lee K, Woo J, Kim DW, Keum C, Babbi G, Martelli PL, Savojardo C, Casadio R, Chennen K, Weber T, Poch O, Ancien F, Cia G, Pucci F, Raimondi D, Vranken W, Rooman M, Marquet C, Olenyi T, Rost B, Andreoletti G, Kamandula A, Peng Y, Bakolitsa C, Mort M, Cooper DN, Bergquist T, Pejaver V, Liu X, Radivojac P, Brenner SE, Ioannidis NM. Critical assessment of missense variant effect predictors on disease-relevant variant data. Hum. Genet. (2025) 144(2-3): 281-293. PDF PubMed   
• Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, Calici SZ, Cedillo LR, Berardelli S, Ozden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, Ozkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafmuller A, Barron LTJ, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT. Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A. Hum. Genet. (2025) 144(2-3): 295-308. PDF PubMed  
• Turina P, Petrosino M, Enriquez Sandoval CA, Novak L, Pasquo A, Alexov E, Alladin MA, Ascher DB, Babbi G, Bakolitsa C, Casadio R, Cheng J, Fariselli P, Folkman L, Kamandula A, Katsonis P, Li M, Li D, Lichtarge O, Mahmud S, Martelli PL, Pal D, Panday SK, Pires DEV, Portelli S, Pucci F, Rodrigues CHM, Rooman M, Savojardo C, Schwersensky M, Shen Y, Strokach AV, Sun Y, Woo J, Radivojac P, Brenner SE, Chiaraluce R, Consalvi V, Capriotti E. Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges. Hum. Genet. (2025) 144(2-3): 265-280. PDF PubMed 
• Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O'Donnell-Luria A, Mooney, SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. Hum. Genet. (2025) 144(2-3):127-142. PDF PubMed
• Turina P, Dal Cortivo G, Enriquez Sandoval CA, Alexov E, Ascher DB, Babbi G, Bakolitsa C, Casadio R, Fariselli P, Folkman L, Kamandula A, Katsonis P, Li D, Lichtarge O, Martelli PL, Panday SK, Pires DEV, Portelli S, Pucci F, Rodrigues CHM, Rooman M, Savojardo C, Schwersensky M, Shen Y, Strokach AV, Sun Y, Woo J, Radivojac P, Brenner SE, Dell'Orco D, Capriotti E. Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges. Hum. Genet. (2025) 144(2-3): 113-125. PDF PubMed 
• Zhang J, Kinch L, Katsonis P, Lichtarge O, Jagota M, Song YS, Sun Y, Shen Y, Kuru N, Dereli O, Adebali O, Alladin MA, Pal D, Capriotti E, Turina MP, Savojardo C, Martelli PL, Babbi G, Casadio R Hu Z, Pucci F, Rooman M, Cia G, Tsishyn M, Strokach A, van Loggerenberg W, Roth FP, Radivojac P, Brenner SE, Cong Q, Grishin NV. Assessing predictions on fitness effects of missense variants in HMBS in CAGI6. Hum. Genet. (2025) 144(2-3): 173-189. PDF PubMed 
• Lord J, Jaramillo Oquendo C, Wai HA, Douglas AGL, Bunyan DJ, Wang Y, Hu Z, Zeng Z, Danis D, Katsonis P, Williams A, Lichtarge O, Chang Y, Bagnall RD, Mount SM, Matthiasardottir B, Lin C, van Overeem Hansen T, Leman R, Martins A, Houdayer  C, Krieger S, Bakolitsa C, Peng Y, Kamandula A, Radivojac P, Baralle D. Predicting the impact of rare variants on RNA splicing in CAGI6. Hum. Genet. (2025) 144(2-3): 243-251. PDF PubMed 
• IGVF Consortium. Deciphering the impact of genomic variation on function. Nature (2024) 633(8028): 47-57. PDF PubMed 
• Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Current and future directions in network biology. Bioinform. Adv. (2024) 4(1): vbae099. PDF PubMed 
• Haas DM, Faysal H, Grecu M, Flannery KM, Schmidt H, Aamir M, Guerrero R, Chung CF, Scordalakes C, Fitzpatrick B, Dowden S, Barnes S, Guise D, Kotarski AJ, Saha C, Radivojac P, Scifres C, Connelly K. Early pregnancy associations with Gestational Diabetes: methods and cohort results of the Hoosier Moms Cohort. North Am Proc Gynecol Obstet (2024) 3(3). PDF DOI 
• Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau E, Greenblatt MS, Harrison SM, Tavtigian SV, Radivojac P, Brenner SE, O’Donnell-Luria A, ClinGen Sequence Variant Interpretation Working Group. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. Genet. Med. (2024) 26(11): 101213. PDF PubMed  
• Karchin R, Radivojac P, O’Donnell-Luria A, Greenblatt MS, Tolstorukov MY, Sonkin D. Improving transparency of computational tools for variant effect prediction. Nat. Genet. (2024) 56(7): 1324-1326. PDF PubMed 
• Peng Y, Jain S, Radivojac P. An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics. Bioinformatics (2024) 40(Supplement_1): i428-i436. PDF PubMed Supp 
• Li D, Chen K, Radivojac P, Zhang HR. Learning tree-structured composition of data augmentation. Trans. Mach. Learn. Res. (2024) 06. PDF OpenReview  
• Khan RR, Guerrero RF, Wapner RJ, Hahn MW, Raja A, Salleb-Aouissi A, Grobman WA, Simhan H, Silver RM, Chung JH, Reddy UM, Radivojac P, Pe’er I, Haas DM. Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas. Sci. Rep. (2024) 14(1): 10514. PDF PubMed Supp 
• Mathur S, Gadekar VP, Ramola R, Wang P, Thiruvengadam R, Haas DM, Bhatnagar S, Wadhwa N, Garbhini Study Group, Radivojac P, Sinha H, Kersting K, Natarajan S. Modeling multiple adverse pregnancy outcomes: learning from diverse data sources. Proceedings of the 22nd International Conference on Artificial Intelligence in Medicine, AIME 2024, pp. 293-302, Salt Lake City, UT, U.S.A., July 2024. PDF 
• Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. Hum. Genomics (2024) 18(1): 44. PDF PubMed 
• Piovesan D, Zago D, Joshi P, De Paolis Kaluza MC, Mehdiabadi M, Ramola R, Monzon AM, Reade W, Friedberg I, Radivojac P, Tosatto SCE. CAFA-evaluator: a Python tool for benchmarking ontological classification methods. Bioinform. Adv. (2024) 4(1): vbae043. PDF PubMed  
• The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. (2024) 25(1): 53. PDF PubMed Web  
• Mahlich Y, Zhu C, Chung H, Velaga PK, De Paolis Kaluza MC, Radivojac P, Friedberg I, Bromberg Y. Learning from the unknown: exploring the range of bacterial functionality. Nucleic Acids Res. (2023) 51(19): 10162-10175. PDF PubMed 
• Yan Q, Guerrero RF, Khan RR, Surujnarine AA, Wapner RJ, Hahn MW, Raja A, Salleb-Aouissi A, Grobman WA, Simhan H, Blue NR, Silver R, Chung JH, Reddy UM, Radivojac P, Pe’er I, Haas DM. Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b. Genetics (2023) 225(2): iyad151. PDF PubMed 
• Zeiberg D, Jain S, Radivojac P. Leveraging structure for improved classification of grouped biased data. AAAI Conference on Artificial Intelligence, AAAI 2023, pp. 11113-11120, Washington, DC, U.S.A., February 2023. PDF Supp AAAI 
• Das S, Ramanan N, Kunapuli G, Radivojac P, Natarajan S. Active feature elicitation: a unified framework. Front. Artif. Intell. (2023) 6: 1029943. PDF PubMed 
• Misal SA, Ovhal SD, Li S, Karty JA, Tang H, Radivojac P, Reilly JP. Non-specific signal peptidase processing of extracellular proteins in Staphylococcus aureus N315. Proteomes (2023) 11(1): 8. PDF PubMed 
• De Paolis Kaluza MC, Jain S, Radivojac P. An approach to identifying and quantifying bias in biomedical data. Pac. Symp. Biocomput. (2023) 28: 311-322. PDF PubMed 
• Chu H, Ramola R, Jain S, Haas DM, Natarajan S, Radivojac P. Using association rules to understand the risk of adverse pregnancy outcomes in a diverse population. Pac. Symp. Biocomput. (2023) 28: 209-220. PDF  PubMed 
• Chen Y, Jain S, Zeiberg D, Iakoucheva LM, Mooney SD, Radivojac P, Pejaver V. Multi-objective prioritization of genes for high-throughput functional assays towards improved clinical variant interpretation. Pac. Symp. Biocomput. (2023) 28: 323-334. PDF PubMed 
• Mathur S, Karanam A, Radivojac P, Haas DM, Kersting K, Natarajan S. Exploiting domain knowledge as causal independencies in modeling gestational diabetes. Pac. Symp. Biocomput. (2023) 28: 359-370. PDF PubMed 
• Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O’Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE, ClinGen Sequence Variant Interpretation Working Group. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am. J. Hum. Genet. (2022) 109(12): 2163-2177. PDF PubMed 
• Karanam A, Mathur S, Radivojac P, Haas DM, Kersting K, Natarajan S. Explaining deep tractable probabilistic models: the sum-product network case. International Conference on Probabilistic Graphical Models, PGM 2022, pp. 325-336, Almería, Spain, October 2022. PDF 
• Pagel KA, Chu H, Ramola R, Guerrero RF, Chung JH, Parry S, Reddy UM, Silver RM, Steller JG, Yee LM, Wapner RJ, Hahn MW, Natarajan S, Haas DM, Radivojac P. Association of genetic predisposition and physical activity with risk of gestational diabetes in nulliparous women. JAMA Netw. Open (2022) 5(8): e2229158. PDF PubMed Supp 
• Coverage in Medscape 
• Bromberg Y, Radivojac P. Computational interpretation of human genetic variation. Hum. Genet. (2022) 141(10): 1545-1548. PDF PubMed 
• 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. (2022) 141(10): 1595-1613. PDF PubMed 
• de Crecy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O’Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (2022) 2022: baac062. PDF PubMed 
• Ramola R, Friedberg I, Radivojac P. The field of protein function prediction as viewed by different domain scientists. Bioinform. Adv. (2022) 2(1): vbac057. PDF Supp PubMed   
• Radivojac P. Advancing remote homology detection: a step toward understanding and accurately predicting protein function. Cell Syst. (2022) 13(6): 435-437. PDF PubMed  
• 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 
• 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 Code/Data 
• 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 
• 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
• 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
• 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 Supp 
• 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
• 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
• 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
• 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
• 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 
• 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 
• 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
• 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
• 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 
• 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 
• Bromberg Y, El-Mabrouk N, Radivojac P. ISMB/ECCB 2019 proceedings. Bioinformatics (2019) 35(14): i1-i2. PDF PubMed
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Bromberg Y, Radivojac P. ISMB 2018 proceedings. Bioinformatics (2018) 34(13): i2-i3. PDF PubMed
• 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 
• 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
• 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
• 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
• 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.
• 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
• 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
• Bromberg Y, Hahn MW, Radivojac P. Computational approaches to understanding the evolution of molecular function. Pac. Symp. Biocomput. (2017) 22: 1-2. PDF PubMed
• 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
• 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
• 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
• 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
• 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
• 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 
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Glover MS, Bellinger EP, Radivojac P, Clemmer DE. Penultimate proline in neuropeptides. Anal. Chem. (2015) 87(16): 8466-8472. PDF PubMed
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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 
• 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
• Lugo-Martinez J, Radivojac P. Generalized graphlet kernels for probabilistic inference in sparse graphs. Network Science (2014) 2(2): 254-276. PDF Code
• 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
• 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
• Clark WT, Radivojac P. Vector quantization kernels for the classification of protein sequences and structures. Pac. Symp. Biocomput. (2014) 19: 316-327. PDF PubMed
• 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
• 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.
• Lugo-Martinez J, Radivojac P. Vertex classification in graphs. Biomedical Computation Review. p. 25. June 2013. PDF BCR
• 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
• 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
• 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
• 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
• 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
• 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
• Li YF, Radivojac P. Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics (2012) 13(Suppl 16): S4. PDF PubMed
• 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
• Xin F, Radivojac P. Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinformatics (2012) 28(22): 2905-2913. PDF PubMed
• Nussinov R, Tsai CJ, Xin F, Radivojac P. Allosteric post-translational modification codes. Trends Biochem. Sci. (2012) 37(10): 447-455. PDF PubMed
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Clark WT, Radivojac P. Analysis of protein function and its prediction from amino acid sequence. Proteins (2011) 79(7): 2086-2096. PDF Software PubMed
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Lussier YA, Lee Y, Radivojac P, Ofran Y, Butte A, Kann MG. Molecular bioinformatics for disease. Pac. Symp. Biocomput. (2009) 14: 464-466. PDF
• 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
• 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
• 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
• 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
• Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Front. Biosci. (2008) 13: 3391-3407. PDF PubMed
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pac. Symp. Biocomput. (2007) 12: 1-3. PDF
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Kann MG, Ofran Y, Punta M, Radivojac P. Protein interactions and disease. Pac. Symp. Biocomput. (2006) 11: 351-353. PDF
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G. Improved amino acid flexibility parameters. Protein Sci. (2003), 12 (5):1060-1072. PDF PubMed
• 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
• 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
• 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
• Radivojac P, Obradovic Z, Brown CJ, Dunker AK. Improving sequence alignments for intrinsically disordered proteins. Pac. Symp. Biocomput. (2002) 7: 589-600. PDF PubMed
• 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
• 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
• 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
• 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
• 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.
• 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.
• 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
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Radivojac P, Senk V. The generalized Viterbi-T algorithm. Proceedings of XXXIX Yugoslav Conference on ETRAN, Vol. 2, pp. 13-16, Zlatibor, June 1995.
• 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: June 15, 2026