Calibration of variant effect predictors for in-frame indels for clinical variant classification.

Predrag Radivojac

Haneen Abderrazzaq Mugdha Singh Timothy Bergquist Vikas Pejaver Anne H. O'Donnell-Luria Predrag Radivojac Calibration of variant effect predictors for in-frame indels for clinical variant classification. 2025 41- 26 Briefings Bioinform. Supplement_1 https://doi.org/10.1093/bib/bbaf631.073 db/journals/bib/bib26.html#AbderrazzaqSBPOR25 streams/journals/bib

M. Clara De Paolis Kaluza Thulasi Tholeti Yile Chen 0006 Ricardo Baeza-Yates Predrag Radivojac Shantanu Jain Are Your Fairness Metrics Accurate? A Semi-Supervised Approach to Improving Fairness Estimates Under Sample Selection Bias. 439-450 2025 KDD (2) https://doi.org/10.1145/3711896.3736846 conf/kdd/2025-2 db/conf/kdd/kdd2025-2.html#KaluzaTCBRJ25

Yisu Peng Shantanu Jain Predrag Radivojac An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics. i428-i436 2024 40 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btae233 db/journals/bioinformatics/bioinformatics40.html#PengJR24

Dongyue Li Kailai Chen Predrag Radivojac Hongyang R. Zhang Learning Tree-Structured Composition of Data Augmentation. 2024 2024 Trans. Mach. Learn. Res. https://openreview.net/forum?id=lmgf03HeqV db/journals/tmlr/tmlr2024.html#LiCRZ24

Saurabh Mathur 0002 Veerendra P. Gadekar Rashika Ramola Peixin Wang Ramachandran Thiruvengadam David M. Haas Shinjini Bhatnagar Nitya Wadhwa Garbhini Study Group Predrag Radivojac Himanshu Sinha Kristian Kersting Sriraam Natarajan Modeling Multiple Adverse Pregnancy Outcomes: Learning from Diverse Data Sources. 293-302 2024 AIME (1) https://doi.org/10.1007/978-3-031-66538-7_29 conf/aime/2024-1 db/conf/aime/aime2024-1.html#MathurGRWTHBWGRSKN24 streams/conf/aime

Dongyue Li Kailai Chen Predrag Radivojac Hongyang R. Zhang Learning Tree-Structured Composition of Data Augmentation. 2024 abs/2408.14381 CoRR https://doi.org/10.48550/arXiv.2408.14381 db/journals/corr/corr2408.html#abs-2408-14381 streams/journals/corr

Srijita Das 0001 Nandini Ramanan Gautam Kunapuli Predrag Radivojac Sriraam Natarajan Active feature elicitation: An unified framework. 2023 February 6 Frontiers Artif. Intell. https://doi.org/10.3389/frai.2023.1029943 db/journals/frai/frai6.html#DasRKRN23

Daniel Zeiberg Shantanu Jain Predrag Radivojac Leveraging Structure for Improved Classification of Grouped Biased Data. 11113-11120 2023 AAAI https://doi.org/10.1609/aaai.v37i9.26316 conf/aaai/2023 db/conf/aaai/aaai2023.html#ZeibergJR23

Damiano Piovesan Davide Zago Parnal Joshi M. Clara De Paolis Kaluza Alexander Miguel Monzon Walter Reade Iddo Friedberg Predrag Radivojac Silvio C. E. Tosatto CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. 2023 abs/2310.06881 CoRR https://doi.org/10.48550/arXiv.2310.06881 db/journals/corr/corr2310.html#abs-2310-06881

Valérie de Crécy-Lagard Rocio Amorin de Hegedus Cecilia N. Arighi Jill Babor Alex Bateman Ian Blaby Crysten Blaby-Haas Alan J. Bridge Stephen K. Burley Stacey Cleveland Lucy J. Colwell Ana Conesa Christian Dallago Antoine Danchin Anita de Waard Adam Deutschbauer Raquel Dias Yousong Ding Gang Fang Iddo Friedberg John Gerlt Joshua Goldford Mark Gorelik Benjamin M. Gyori Christopher S. Henry Geoffrey Hutinet Marshall Jaroch Peter D. Karp Liudmyla Kondratova Zhiyong Lu Aron Marchler-Bauer Maria Jesus Martin Claire D. McWhite Gaurav D. Moghe Paul Monaghan Anne Morgat Christopher J. Mungall Darren A. Natale William C. Nelson Seán I. O'Donoghue Christine A. Orengo Katherine H. O'Toole Predrag Radivojac Colbie Reed Richard J. Roberts Dmitri Rodionov Irina A. Rodionova Jeffrey DePons Lana Saleh Gloria M. Sheynkman Françoise Thibaud-Nissen Paul D. Thomas Peter Uetz David Vallenet Erica Watson Carter Peter Weigele Valerie Wood Elisha M. Wood-Charlson Jin Xu A roadmap for the functional annotation of protein families: a community perspective. 2022 2022 Database J. Biol. Databases Curation 2022 https://doi.org/10.1093/database/baac062 db/journals/biodb/biodb2022.html#Crecy-LagardHAB22

Athresh Karanam Saurabh Mathur 0002 Predrag Radivojac David M. Haas Kristian Kersting Sriraam Natarajan Explaining Deep Tractable Probabilistic Models: The sum-product network case. 325-336 2022 PGM https://proceedings.mlr.press/v186/karanam22a.html conf/pgm/2022 db/conf/pgm/pgm2022.html#KaranamMRHKN22

Daniel Zeiberg Shantanu Jain Predrag Radivojac Leveraging Structure for Improved Classification of Grouped Biased Data. 2022 abs/2212.03697 CoRR https://doi.org/10.48550/arXiv.2212.03697 db/journals/corr/corr2212.html#abs-2212-03697

Jose Lugo-Martinez Daniel Zeiberg Thomas Gaudelet Noël Malod-Dognin Natasa Przulj Predrag Radivojac Classification in biological networks with hypergraphlet kernels. 1000-1007 2021 37 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btaa768 https://www.wikidata.org/entity/Q98949385 db/journals/bioinformatics/bioinformatics37.html#Lugo-MartinezZG21

Athresh Karanam Alexander L. Hayes Harsha Kokel David M. Haas Predrag Radivojac Sriraam Natarajan A Probabilistic Approach to Extract Qualitative Knowledge for Early Prediction of Gestational Diabetes. 497-502 2021 AIME https://doi.org/10.1007/978-3-030-77211-6_59 conf/aime/2021 db/conf/aime/aime2021.html#KaranamHKHRN21

Athresh Karanam Saurabh Mathur 0002 Predrag Radivojac Kristian Kersting Sriraam Natarajan Explaining Deep Tractable Probabilistic Models: The sum-product network case. 2021 abs/2110.09778 CoRR https://arxiv.org/abs/2110.09778 db/journals/corr/corr2110.html#abs-2110-09778

Jayvardan S. Naidu Justin Delano Scott Mathews Predrag Radivojac An examination of citation-based impact of the computational biology conferences. 2958-2962 2020 36 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btaa071 https://www.wikidata.org/entity/Q89521900 db/journals/bioinformatics/bioinformatics36.html#NaiduDMR20

Moses Stamboulian Rafael F. Guerrero Matthew W. Hahn Predrag Radivojac The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. i219-i226 2020 36 Bioinform. Supplement-1 https://doi.org/10.1093/bioinformatics/btaa468 https://www.wikidata.org/entity/Q97542285 db/journals/bioinformatics/bioinformatics36.html#StamboulianGHR20

Yisu Peng Shantanu Jain Yong Fuga Li Michal Gregus Alexander R. Ivanov Olga Vitek Predrag Radivojac New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics. i745-i761 2020 36 Bioinform. Supplement-2 https://doi.org/10.1093/bioinformatics/btaa807 https://www.wikidata.org/entity/Q104681777 db/journals/bioinformatics/bioinformatics36.html#PengJLGIVR20

Shantanu Jain Justin Delano Himanshu Sharma Predrag Radivojac Class Prior Estimation with Biased Positives and Unlabeled Examples. 4255-4263 2020 AAAI https://doi.org/10.1609/aaai.v34i04.5848 conf/aaai/2020 db/conf/aaai/aaai2020.html#JainDSR20 Daniel Zeiberg Shantanu Jain Predrag Radivojac Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting. 6729-6736 2020 AAAI https://doi.org/10.1609/aaai.v34i04.6151 conf/aaai/2020 db/conf/aaai/aaai2020.html#ZeibergJR20 Lukasz A. Kurgan Predrag Radivojac Joel L. Sussman A. Keith Dunker Session Introduction. 149-158 2020 PSB https://psb.stanford.edu/psb-online/proceedings/psb20/Intro_IDPS.pdf conf/psb/2020 db/conf/psb/psb2020.html#KurganRSD20 Steven E. Brenner Martha L. Bulyk Dana C. Crawford Alexander A. Morgan Predrag Radivojac Nicholas P. Tatonetti Session Introduction. 547-550 2020 PSB https://psb.stanford.edu/psb-online/proceedings/psb20/Intro_PrecisionMed.pdf conf/psb/2020 db/conf/psb/psb2020.html#BrennerBCMRT20

Yana Bromberg Nadia El-Mabrouk Predrag Radivojac ISMB/ECCB 2019 Proceedings. i1-i2 2019 35 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btz439 https://www.wikidata.org/entity/Q90065027 db/journals/bioinformatics/bioinformatics35.html#BrombergER19

Ruiyu Yang Yuxiang Jiang Scott Mathews Elizabeth A. Housworth Matthew W. Hahn Predrag Radivojac A new class of metrics for learning on real-valued and structured data. 995-1016 2019 33 Data Min. Knowl. Discov. 4 https://doi.org/10.1007/s10618-019-00622-6 https://www.wikidata.org/entity/Q114690139 db/journals/datamine/datamine33.html#YangJMHHR19

Kymberleigh A. Pagel Danny Antaki Aojie Lian Matthew E. Mort David N. Cooper Jonathan Sebat Lilia M. Iakoucheva Sean D. Mooney Predrag Radivojac Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. 2019 15 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1007112 https://www.wikidata.org/entity/Q92751178 db/journals/ploscb/ploscb15.html#PagelALMCSIMR19

Rashika Ramola Shantanu Jain Predrag Radivojac Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. 124-135 2019 PSB http://psb.stanford.edu/psb-online/proceedings/psb19/ramola.pdf conf/psb/2019 db/conf/psb/psb2019.html#RamolaJR19 Steven E. Brenner Martha L. Bulyk Dana C. Crawford Jill P. Mesirov Alexander A. Morgan Predrag Radivojac Session introduction. 220-223 2019 PSB http://psb.stanford.edu/psb-online/proceedings/psb19/intro-pm.pdf conf/psb/2019 db/conf/psb/psb2019.html#BrennerBCMMR19

Yana Bromberg Predrag Radivojac ISMB 2018 proceedings. i2-i3 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty413 https://www.wikidata.org/entity/Q55416410 db/journals/bioinformatics/bioinformatics34.html#BrombergR18

Yisu Peng Yuxiang Jiang Predrag Radivojac Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. i313-i322 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty268 https://www.wikidata.org/entity/Q55438932 db/journals/bioinformatics/bioinformatics34.html#PengJR18

Rodrigo F. Ramalho Sujun Li Predrag Radivojac Matthew W. Hahn Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse. 1284-1289 2018 15 IEEE ACM Trans. Comput. Biol. Bioinform. 4 https://doi.org/10.1109/TCBB.2015.2480068 https://doi.ieeecomputersociety.org/10.1109/TCBB.2015.2480068 https://dl.acm.org/doi/10.1109/TCBB.2015.2480068 https://www.wikidata.org/entity/Q40514157 db/journals/tcbb/tcbb15.html#RamalhoLRH18

Makoto Yamada Jiliang Tang Jose Lugo-Martinez Ermin Hodzic Raunak Shrestha Avishek Saha Hua Ouyang Dawei Yin 0001 Hiroshi Mamitsuka Süleyman Cenk Sahinalp Predrag Radivojac Filippo Menczer Yi Chang 0001 Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. 1352-1365 2018 30 IEEE Trans. Knowl. Data Eng. 7 https://doi.org/10.1109/TKDE.2018.2789451 http://doi.ieeecomputersociety.org/10.1109/TKDE.2018.2789451 db/journals/tkde/tkde30.html#YamadaTLHSSOYMS18

Sriraam Natarajan Srijita Das 0001 Nandini Ramanan Gautam Kunapuli Predrag Radivojac On Whom Should I Perform this Lab Test Next? An Active Feature Elicitation Approach. 3498-3505 2018 IJCAI https://doi.org/10.24963/ijcai.2018/486 conf/ijcai/2018 db/conf/ijcai/ijcai2018.html#NatarajanDRKR18

Kymberleigh A. Pagel Vikas Pejaver Guan Ning Lin Hyun-Jun Nam Matthew E. Mort David N. Cooper Jonathan Sebat Lilia M. Iakoucheva Sean D. Mooney Predrag Radivojac When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. i389-i398 2017 33 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btx272 https://www.wikidata.org/entity/Q45945798 db/journals/bioinformatics/bioinformatics33.html#PagelPLNMCSIMR17

Shantanu Jain Martha White Predrag Radivojac Recovering True Classifier Performance in Positive-Unlabeled Learning. 2066-2072 2017 AAAI https://doi.org/10.1609/aaai.v31i1.10937 conf/aaai/2017 db/conf/aaai/aaai2017.html#JainWR17 Yana Bromberg Matthew W. Hahn Predrag Radivojac Session Introduction. 1-2 2017 PSB http://psb.stanford.edu/psb-online/proceedings/psb17/intro-comp.pdf conf/psb/2017 db/conf/psb/psb2017.html#BrombergHR17

Shantanu Jain Martha White Predrag Radivojac Recovering True Classifier Performance in Positive-Unlabeled Learning. 2017 abs/1702.00518 CoRR http://arxiv.org/abs/1702.00518 db/journals/corr/corr1702.html#JainWR17

Jose Lugo-Martinez Predrag Radivojac Classification in biological networks with hypergraphlet kernels. 2017 abs/1703.04823 CoRR http://arxiv.org/abs/1703.04823 db/journals/corr/corr1703.html#Lugo-MartinezR17

Yisu Peng Yuxiang Jiang Predrag Radivojac Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies. 2017 abs/1712.09679 CoRR http://arxiv.org/abs/1712.09679 db/journals/corr/corr1712.html#abs-1712-09679

Lonnie R. Welch Cath Brooksbank Russell Schwartz Sarah L. Morgan Bruno A. Gaëta Alastair M. Kilpatrick Daniel Mietchen Benjamin L. Moore Nicola J. Mulder Mark A. Pauley William R. Pearson Predrag Radivojac Naomi Rosenberg Anne G. Rosenwald Gabriella Rustici Tandy J. Warnow Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). 2016 12 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1004943 https://www.wikidata.org/entity/Q24288781 db/journals/ploscb/ploscb12.html#WelchBSMGKMMMPP16

Jose Lugo-Martinez Vikas Pejaver Kymberleigh A. Pagel Shantanu Jain Matthew E. Mort David N. Cooper Sean D. Mooney Predrag Radivojac The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. 2016 12 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1005091 https://www.wikidata.org/entity/Q36114159 db/journals/ploscb/ploscb12.html#Lugo-MartinezPP16

Shantanu Jain Martha White Predrag Radivojac Estimating the class prior and posterior from noisy positives and unlabeled data. 2685-2693 2016 NIPS https://proceedings.neurips.cc/paper/2016/hash/79a49b3e3762632813f9e35f4ba53d6c-Abstract.html http://papers.nips.cc/paper/6168-estimating-the-class-prior-and-posterior-from-noisy-positives-and-unlabeled-data conf/nips/2016 db/conf/nips/nips2016.html#JainWR16

Shantanu Jain Martha White Michael W. Trosset Predrag Radivojac Nonparametric semi-supervised learning of class proportions. 2016 abs/1601.01944 CoRR http://arxiv.org/abs/1601.01944 db/journals/corr/corr1601.html#JainWTR16

Shantanu Jain Martha White Predrag Radivojac Estimating the class prior and posterior from noisy positives and unlabeled data. 2016 abs/1606.08561 CoRR http://arxiv.org/abs/1606.08561 db/journals/corr/corr1606.html#JainWR16

Iddo Friedberg Mark N. Wass Sean D. Mooney Predrag Radivojac Ten Simple Rules for a Community Computational Challenge. 2015 11 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1004150 https://www.wikidata.org/entity/Q28974681 db/journals/ploscb/ploscb11.html#FriedbergWMR15

Youngsang Shin Steven A. Myers Minaxi Gupta 0001 Predrag Radivojac A link graph-based approach to identify forum spam. 176-188 2015 8 Secur. Commun. Networks 2 https://doi.org/10.1002/sec.970 db/journals/scn/scn8.html#ShinMGR15

Chao Ji Yong Fuga Li Earl P. Bellinger Sujun Li Randy J. Arnold Predrag Radivojac Haixu Tang A maximum-likelihood approach to absolute protein quantification in mass spectrometry. 296-305 2015 BCB https://doi.org/10.1145/2808719.2808750 https://www.wikidata.org/entity/Q62688585 conf/bcb/2015 db/conf/bcb/bcb2015.html#JiLBLART15 Kristine A. Pattin Anna C. Greene Russ B. Altman Kevin Bretonnel Cohen Elizabeth Wethington Carsten Görg Lawrence E. Hunter Spencer V. Muse Predrag Radivojac Jason H. Moore Training the Next Generation of Quantitative Biologists in the Era of Big Data. 488-492 2015 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb15/wkshop-bioinfo.pdf conf/psb/2015 db/conf/psb/psb2015.html#PattinGACWGHMRM15

Mark N. Wass Sean D. Mooney Michal Linial Predrag Radivojac Iddo Friedberg The automated function prediction SIG looks back at 2013 and prepares for 2014. 2091-2092 2014 30 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btu117 https://www.wikidata.org/entity/Q42719524 db/journals/bioinformatics/bioinformatics30.html#WassMLRF14

Yuxiang Jiang Wyatt T. Clark Iddo Friedberg Predrag Radivojac The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. 609-616 2014 30 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btu472 https://www.wikidata.org/entity/Q34103226 db/journals/bioinformatics/bioinformatics30.html#JiangCFR14

Jose Lugo-Martinez Predrag Radivojac Generalized graphlet kernels for probabilistic inference in sparse graphs. 254-276 2014 2 Netw. Sci. 2 https://doi.org/10.1017/nws.2014.14 db/journals/netsci/netsci2.html#Lugo-MartinezR14

Lonnie R. Welch Fran Lewitter Russell Schwartz Catherine Brooksbank Predrag Radivojac Bruno A. Gaëta Maria Victoria Schneider Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. 2014 10 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1003496 https://www.wikidata.org/entity/Q24810391 db/journals/ploscb/ploscb10.html#WelchLSBRGS14

Wyatt T. Clark Predrag Radivojac Vector Quantization Kernels for the Classification of Protein Sequences and Structures. 316-327 2014 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb14/clark.pdf conf/psb/2014 db/conf/psb/psb2014.html#ClarkR14

Wyatt T. Clark Predrag Radivojac Information-theoretic evaluation of predicted ontological annotations. 53-61 2013 29 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btt228 https://www.wikidata.org/entity/Q36960725 db/journals/bioinformatics/bioinformatics29.html#ClarkR13

Alex Bateman Janet Kelso Daniel Mietchen Geoff MacIntyre Tomás Di Domenico Thomas Abeel Darren W. Logan Predrag Radivojac Burkhard Rost ISCB Computational Biology Wikipedia Competition. 2013 9 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1003242 https://www.wikidata.org/entity/Q21092516 db/journals/ploscb/ploscb9.html#BatemanKMMDALRR13

Sujun Li Randy J. Arnold Haixu Tang Predrag Radivojac Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. 316 2013 BCB https://doi.org/10.1145/2506583.2506634 conf/bcb/2013 db/conf/bcb/bcb2013.html#LiATR13

Fuxiao Xin Predrag Radivojac Post-translational modifications induce significant yet not extreme changes to protein structure. 2905-2913 2012 28 Bioinform. 22 https://doi.org/10.1093/bioinformatics/bts541 https://www.wikidata.org/entity/Q30420946 db/journals/bioinformatics/bioinformatics28.html#XinR12

Yong Fuga Li Predrag Radivojac Computational approaches to protein inference in shotgun proteomics. S4 2012 13 BMC Bioinform. S-16 https://doi.org/10.1186/1471-2105-13-S16-S4 https://www.wikidata.org/entity/Q34486852 db/journals/bmcbi/bmcbi13S.html#LiR12

Idit Kosti Predrag Radivojac Yael Mandel-Gutfreund An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. 2012 8 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1002603 https://www.wikidata.org/entity/Q36119908 db/journals/ploscb/ploscb8.html#KostiRM12

Nathan L. Nehrt Wyatt T. Clark Predrag Radivojac Matthew W. Hahn Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. 2011 7 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1002073 https://www.wikidata.org/entity/Q21145323 db/journals/ploscb/ploscb7.html#NehrtCRH11

Fuxiao Xin Steven A. Myers Yong Fuga Li David N. Cooper Sean D. Mooney Predrag Radivojac Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. 1975-1982 2010 26 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btq319 https://www.wikidata.org/entity/Q34046936 db/journals/bioinformatics/bioinformatics26.html#XinMLCMR10

Fuxiao Xin Steven A. Myers Yong Fuga Li David N. Cooper Sean D. Mooney Predrag Radivojac Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. O4 2010 11 BMC Bioinform. S-10 https://doi.org/10.1186/1471-2105-11-S10-O4 db/journals/bmcbi/bmcbi11S.html#XinMLCMR10

Vladimir Vacic Lilia M. Iakoucheva Stefano Lonardi Predrag Radivojac Graphlet Kernels for Prediction of Functional Residues in Protein Structures. 55-72 2010 17 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2009.0029 https://www.wikidata.org/entity/Q42272603 db/journals/jcb/jcb17.html#VacicILR10

Shuyan Li Lilia M. Iakoucheva Sean D. Mooney Predrag Radivojac Loss of Post-Translational Modification Sites in Disease. 337-347 2010 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb10/li_s.pdf conf/psb/2010 db/conf/psb/psb2010.html#LiIMR10

Biao Li Vidhya G. Krishnan Matthew E. Mort Fuxiao Xin Kishore K. Kamati David N. Cooper Sean D. Mooney Predrag Radivojac Automated inference of molecular mechanisms of disease from amino acid substitutions. 2744-2750 2009 25 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btp528 https://www.wikidata.org/entity/Q30380440 db/journals/bioinformatics/bioinformatics25.html#LiKMXKCMR09

Eunjung Lee Hyunchul Jung Predrag Radivojac Jong-Won Kim 0001 Doheon Lee Analysis of AML genes in dysregulated molecular networks. 2 2009 10 BMC Bioinform. S-9 https://doi.org/10.1186/1471-2105-10-S9-S2 https://www.wikidata.org/entity/Q33504376 db/journals/bmcbi/bmcbi10S.html#LeeJRKL09

Yong Fuga Li Randy J. Arnold Yixue Li Predrag Radivojac Quanhu Sheng Haixu Tang A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. 1183-1193 2009 16 J. Comput. Biol. 8 https://doi.org/10.1089/cmb.2009.0018 https://www.wikidata.org/entity/Q41879344 db/journals/jcb/jcb16.html#LiALRST09

Amrita Mohan Vladimir N. Uversky Predrag Radivojac Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins. 2009 5 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1000497 https://www.wikidata.org/entity/Q30380392 db/journals/ploscb/ploscb5.html#MohanUR09

Yves A. Lussier Younghee Lee Predrag Radivojac Yanay Ofran Atul J. Butte Maricel G. Kann Session Introduction. 464-466 2009 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb09/intro-bioinfo.pdf conf/psb/2009 db/conf/psb/psb2009.html#LussierLROBK09

Pedro Alves Randy J. Arnold David E. Clemmer Yixue Li James P. Reilly Quanhu Sheng Haixu Tang Zhiyin Xun Rong Zeng Predrag Radivojac Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. 102-109 2008 24 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btm545 https://www.wikidata.org/entity/Q48373928 db/journals/bioinformatics/bioinformatics24.html#AlvesACLRSTXZR08

Arti Singh Adebayo Olowoyeye Peter H. Baenziger Jessica Dantzer Maricel G. Kann Predrag Radivojac Randy W. Heiland Sean D. Mooney MutDB: update on development of tools for the biochemical analysis of genetic variation. 815-819 2008 36 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkm659 https://www.wikidata.org/entity/Q36454309 db/journals/nar/nar36.html#SinghOBDKRHM08

Predrag Radivojac Peter H. Baenziger Maricel G. Kann Matthew E. Mort Matthew W. Hahn Sean D. Mooney Gain and loss of phosphorylation sites in human cancer. 241-247 2008 ECCB https://doi.org/10.1093/bioinformatics/btn267 https://www.wikidata.org/entity/Q43063740 conf/eccb/2008 db/conf/eccb/eccb2008.html#RadivojacBKMHM08 Yves A. Lussier Younghee Lee Predrag Radivojac Yanay Ofran Marco Punta Atul J. Butte Maricel G. Kann Session Introduction. 228-230 2008 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb08/bioinfo.pdf conf/psb/2008 db/conf/psb/psb2008.html#LussierLROPBK08 Yong Fuga Li Randy J. Arnold Yixue Li Predrag Radivojac Quanhu Sheng Haixu Tang A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. 167-180 2008 RECOMB https://doi.org/10.1007/978-3-540-78839-3_15 conf/recomb/2008 db/conf/recomb/recomb2008.html#LiALRST08

Alaa Abi-Haidar Jasleen Kaur 0002 Ana Gabriela Maguitman Predrag Radivojac Andreas Rechtsteiner Karin Verspoor Zhiping Wang Luis M. Rocha Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks http://arxiv.org/abs/0812.1029 2008 CoRR abs/0812.1029 db/journals/corr/corr0812.html#abs-0812-1029

Maricel G. Kann Yanay Ofran Marco Punta Predrag Radivojac Session Introduction. 1-3 2007 conf/psb/2007 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb07/intro-protein.pdf db/conf/psb/psb2007.html#KannOPR07 Pedro Alves Randy J. Arnold Milos V. Novotny Predrag Radivojac James P. Reilly Haixu Tang Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability. 409-420 2007 conf/psb/2007 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb07/alves.pdf db/conf/psb/psb2007.html#AlvesANRRT07

Vladimir Vacic Lilia M. Iakoucheva Predrag Radivojac Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. 1536-1537 2006 22 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btl151 https://www.wikidata.org/entity/Q42683783 db/journals/bioinformatics/bioinformatics22.html#VacicIR06

Kang Peng Predrag Radivojac Slobodan Vucetic A. Keith Dunker Zoran Obradovic Length-dependent prediction of protein intrinsic disorder. 208 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-208 https://www.wikidata.org/entity/Q30353929 db/journals/bmcbi/bmcbi7.html#PengRVDO06

Sourav Roy Santiago Schnell Predrag Radivojac Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. 241-248 2006 30 Comput. Biol. Chem. 4 https://doi.org/10.1016/j.compbiolchem.2006.04.005 https://www.wikidata.org/entity/Q41492486 db/journals/candc/candc30.html#RoySR06

Chad Haynes Christopher J. Oldfield Fei Ji Niels Klitgord Michael E. Cusick Predrag Radivojac Vladimir N. Uversky Marc Vidal Lilia M. Iakoucheva Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes. 2006 2 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.0020100 https://www.wikidata.org/entity/Q33252616 db/journals/ploscb/ploscb2.html#HaynesOJKCRUVI06

Haixu Tang Randy J. Arnold Pedro Alves Zhiyin Xun David E. Clemmer Milos V. Novotny James P. Reilly Predrag Radivojac A computational approach toward label-free protein quantification using predicted peptide detectability. 481-488 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl237 https://www.wikidata.org/entity/Q45965839 db/conf/ismb/ismb2006.html#TangAAXCNRR06 Randy J. Arnold Narmada Jayasankar Divya Aggarwal Haixu Tang Predrag Radivojac A Machine Learning Approach to Predicting Peptide Fragmentation Spectra. 219-230 2006 conf/psb/2006 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb06/arnold.pdf db/conf/psb/psb2006.html#ArnoldJATR06 Maricel G. Kann Yanay Ofran Marco Punta Predrag Radivojac Session Introduction. 351-353 2006 conf/psb/2006 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb06/intro-protein.pdf db/conf/psb/psb2006.html#KannOPR06 Mehmet M. Dalkilic Wyatt T. Clark James C. Costello Predrag Radivojac Using Compression to Identify Classes of Inauthentic Texts. 2006 conf/sdm/2006 SDM https://doi.org/10.1137/1.9781611972764.69 db/conf/sdm/sdm2006.html#DalkilicCCR06 604-608

Slobodan Vucetic Zoran Obradovic Vladimir Vacic Predrag Radivojac Kang Peng Lilia M. Iakoucheva Marc S. Cortese J. David Lawson Celeste J. Brown Jason G. Sikes Crystal D. Newton A. Keith Dunker DisProt: a database of protein disorder. 137-140 2005 21 Bioinform. 1 https://doi.org/10.1093/bioinformatics/bth476 https://www.wikidata.org/entity/Q34341031 db/journals/bioinformatics/bioinformatics21.html#VuceticOVRPICLBSND05

Kang Peng Slobodan Vucetic Predrag Radivojac Celeste J. Brown A. Keith Dunker Zoran Obradovic Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. 35-60 2005 3 J. Bioinform. Comput. Biol. 1 https://doi.org/10.1142/S0219720005000886 https://www.wikidata.org/entity/Q81484824 db/journals/jbcb/jbcb3.html#PengVRBDO05

Kenneth Daily Predrag Radivojac A. Keith Dunker Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. 475-481 2005 conf/cibcb/2005 CIBCB db/conf/cibcb/cibcb2005.html#DailyRD05

Predrag Radivojac Nitesh V. Chawla A. Keith Dunker Zoran Obradovic Classification and knowledge discovery in protein databases. 224-239 2004 37 J. Biomed. Informatics 4 https://doi.org/10.1016/j.jbi.2004.07.008 https://www.wikidata.org/entity/Q45966633 db/journals/jbi/jbi37.html#RadivojacCDO04

Predrag Radivojac Zoran Obradovic A. Keith Dunker Slobodan Vucetic Feature Selection Filters Based on the Permutation Test. 334-346 https://doi.org/10.1007/978-3-540-30115-8_32 2004 conf/ecml/2004 ECML db/conf/ecml/ecml2004.html#RadivojacODV04 Predrag Radivojac Zoran Obradovic Celeste J. Brown A. Keith Dunker Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions. 216-227 2003 conf/psb/2003 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb03/radivojac.pdf db/conf/psb/psb2003.html#RadivojacOBD03 Predrag Radivojac Zoran Obradovic Celeste J. Brown A. Keith Dunker Improving Sequence Alignments For Intrinsically Disordered Proteins. 589-600 2002 conf/psb/2002 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb02/radivojac.pdf db/conf/psb/psb2002.html#RadivojacOBD02 Haneen Abderrazzaq Thomas Abeel Alaa Abi-Haidar Divya Aggarwal Russ B. Altman Pedro Alves Danny Antaki Cecilia N. Arighi Randy J. Arnold Jill Babor Peter H. Baenziger Ricardo Baeza-Yates Alex Bateman Earl P. Bellinger Timothy Bergquist Shinjini Bhatnagar Ian Blaby Crysten Blaby-Haas Steven E. Brenner Alan J. Bridge Yana Bromberg Catherine BrooksbankCath Brooksbank Celeste J. Brown Martha L. Bulyk Stephen K. Burley Atul J. Butte Erica Watson Carter Yi Chang 0001 Nitesh V. Chawla Kailai Chen Yile Chen 0006 Wyatt Travis ClarkWyatt T. Clark David E. Clemmer Stacey Cleveland Kevin Cohen 0001Kevin Bretonnel Cohen Lucy J. Colwell Ana Conesa David N. Cooper Marc S. Cortese James C. Costello Dana C. Crawford Valérie de Crécy-Lagard Michael E. Cusick Kenneth Daily Mehmet M. Dalkilic Christian Dallago Antoine Danchin Jessica Dantzer Srijita Das 0001 Justin Delano Adam Deutschbauer Raquel Dias Yousong Ding Tomás Di Domenico A. Keith Dunker Nadia El-Mabrouk Gang Fang Iddo Friedberg Veerendra P. Gadekar Bruno A. Gaëta Thomas Gaudelet John Gerlt Joshua Goldford Mark Gorelik Carsten Görg Anna C. Greene Michal Gregus Garbhini Study Group Rafael F. Guerrero Minaxi Gupta 0001 Benjamin M. Gyori David M. Haas Matthew W. Hahn Alexander L. Hayes Chad Haynes Rocio Amorin de Hegedus Randy W. Heiland Christopher S. Henry Ermin Hodzic Elizabeth A. Housworth Lawrence HunterLawrence E. Hunter Geoffrey Hutinet Lilia M. Iakoucheva Alexander R. Ivanov Shantanu Jain Marshall Jaroch Narmada Jayasankar Chao Ji Fei Ji Yuxiang Jiang Parnal Joshi Hyunchul Jung M. Clara De Paolis Kaluza Kishore K. Kamati Maricel G. Kann Athresh Karanam Peter D. Karp Jasleen Kaur 0002 Janet Kelso Kristian Kersting Alastair M. Kilpatrick Jong-Won Kim 0001 Niels Klitgord Harsha Kokel Liudmyla Kondratova Idit Kosti Vidhya G. Krishnan Gautam Kunapuli Lukasz A. Kurgan J. David Lawson Doheon Lee Eunjung Lee Younghee Lee Fran Lewitter Biao Li Dongyue Li Shuyan Li Sujun Li Yixue Li Yong Fuga Li Aojie Lian Guan Ning Lin Michal Linial Darren W. Logan Stefano Lonardi Zhiyong Lu Jose Lugo-Martinez Yves A. Lussier Geoff MacIntyre Ana Gabriela Maguitman Noël Malod-Dognin Hiroshi Mamitsuka Yael Mandel-Gutfreund Aron Marchler-Bauer Maria Jesus Martin Scott Mathews Saurabh Mathur 0002 Claire D. McWhite Filippo Menczer Jill P. Mesirov Daniel Mietchen Gaurav D. Moghe Amrita Mohan Paul Monaghan Alexander Miguel Monzon Sean D. Mooney Benjamin L. Moore Jason H. Moore Alexander A. Morgan Sarah L. Morgan Anne Morgat Matthew E. Mort Nicola J. Mulder Chris MungallChristopher J. Mungall Spencer V. Muse Steven MyersSteven A. Myers Jayvardan S. Naidu Hyun-Jun Nam Darren A. Natale Sriraam Natarajan Nathan L. Nehrt William C. Nelson Crystal D. Newton Milos V. Novotny Zoran Obradovic Anne H. O'Donnell-Luria Seán I. O'Donoghue Yanay Ofran Christopher J. Oldfield Adebayo Olowoyeye Christine A. Orengo Katherine H. O'Toole Hua Ouyang Kymberleigh A. Pagel Kristine A. Pattin Mark A. Pauley William R. Pearson Vikas Pejaver Kang Peng Yisu Peng Damiano Piovesan Jeff de PonsJeffrey DePons Natasa Przulj Marco Punta Rodrigo F. Ramalho Nandini Ramanan Rashika Ramola Walter Reade Andreas Rechtsteiner Colbie Reed James P. Reilly Richard J. Roberts Luis M. Rocha Dmitri Rodionov Irina A. Rodionova Naomi Rosenberg Anne G. Rosenwald Burkhard Rost Sourav Roy Gabriella Rustici Avishek Saha Süleyman Cenk Sahinalp Lana Saleh Maria Victoria Schneider Santiago Schnell Russell Schwartz Jonathan Sebat Himanshu Sharma Quanhu Sheng Gloria M. Sheynkman Youngsang Shin Raunak Shrestha Jason G. Sikes Arti Singh Mugdha Singh Himanshu Sinha Moses Stamboulian Joel L. Sussman Haixu Tang Jiliang Tang Nicholas P. Tatonetti Françoise Thibaud-Nissen Ramachandran Thiruvengadam Thulasi Tholeti Paul D. Thomas Silvio C. E. Tosatto Michael W. Trosset Peter Uetz Vladimir N. Uversky Vladimir Vacic David Vallenet Karin Verspoor Marc Vidal Olga Vitek Slobodan Vucetic Anita de Waard Nitya Wadhwa Peixin Wang Zhiping Wang Tandy J. Warnow Mark N. Wass Peter Weigele Lonnie R. Welch Elizabeth Wethington Martha White Valerie Wood Elisha M. Wood-Charlson Fuxiao Xin Jin Xu Zhiyin Xun Makoto Yamada Ruiyu Yang Dawei Yin 0001 Davide Zago Daniel Zeiberg Rong Zeng Hongyang R. Zhang