Improving Sequence Alignments For Intrinsically Disordered Proteins. - Predrag Radivojac; Zoran Obradovic; Celeste J. Brown; A. Keith Dunker (Pacific Symposium on Biocomputing, 2002)

Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions. - Predrag Radivojac; Zoran Obradovic; Celeste J. Brown; A. Keith Dunker (Pacific Symposium on Biocomputing, 2003)

Feature Selection Filters Based on the Permutation Test. - Predrag Radivojac; Zoran Obradovic; A. Keith Dunker; Slobodan Vucetic (ECML, 2004)

Classification and knowledge discovery in protein databases. - Predrag Radivojac; Nitesh V. Chawla; A. Keith Dunker; Zoran Obradovic (J. Biomed. Informatics, 2004)

Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. - Kenneth Daily; Predrag Radivojac; A. Keith Dunker (CIBCB, 2005)

DisProt: a database of protein disorder. - 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 (Bioinform., 2005)

Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. - Kang Peng; Slobodan Vucetic; Predrag Radivojac; Celeste J. Brown; A. Keith Dunker; Zoran Obradovic (J. Bioinform. Comput. Biol., 2005)

A computational approach toward label-free protein quantification using predicted peptide detectability. - Haixu Tang; Randy J. Arnold; Pedro Alves; Zhiyin Xun; David E. Clemmer; Milos V. Novotny; James P. Reilly; Predrag Radivojac (ISMB (Supplement of Bioinformatics), 2006)

A Machine Learning Approach to Predicting Peptide Fragmentation Spectra. - Randy J. Arnold; Narmada Jayasankar; Divya Aggarwal; Haixu Tang; Predrag Radivojac (Pacific Symposium on Biocomputing, 2006)

Session Introduction. - Maricel G. Kann; Yanay Ofran; Marco Punta; Predrag Radivojac (Pacific Symposium on Biocomputing, 2006)

Using Compression to Identify Classes of Inauthentic Texts. - Mehmet M. Dalkilic; Wyatt T. Clark; James C. Costello; Predrag Radivojac (SDM, 2006)

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. - Vladimir Vacic; Lilia M. Iakoucheva; Predrag Radivojac (Bioinform., 2006)

Length-dependent prediction of protein intrinsic disorder. - Kang Peng; Predrag Radivojac; Slobodan Vucetic; A. Keith Dunker; Zoran Obradovic (BMC Bioinform., 2006)

Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. - Sourav Roy; Santiago Schnell; Predrag Radivojac (Comput. Biol. Chem., 2006)

Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes. - Chad Haynes; Christopher J. Oldfield; Fei Ji; Niels Klitgord; Michael E. Cusick; Predrag Radivojac; Vladimir N. Uversky; Marc Vidal; Lilia M. Iakoucheva (PLoS Comput. Biol., 2006)

Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability. - Pedro Alves; Randy J. Arnold; Milos V. Novotny; Predrag Radivojac; James P. Reilly; Haixu Tang (Pacific Symposium on Biocomputing, 2007)

Gain and loss of phosphorylation sites in human cancer. - Predrag Radivojac; Peter H. Baenziger; Maricel G. Kann; Matthew E. Mort; Matthew W. Hahn; Sean D. Mooney (ECCB, 2008)

Session Introduction. - Yves A. Lussier; Younghee Lee; Predrag Radivojac; Yanay Ofran; Marco Punta; Atul J. Butte; Maricel G. Kann (Pacific Symposium on Biocomputing, 2008)

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. - Pedro Alves; Randy J. Arnold; David E. Clemmer; Yixue Li; James P. Reilly; Quanhu Sheng; Haixu Tang; Zhiyin Xun; Rong Zeng; Predrag Radivojac (Bioinform., 2008)

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks - Alaa Abi-Haidar; Jasleen Kaur 002; Ana Gabriela Maguitman; Predrag Radivojac; Andreas Rechtsteiner; Karin Verspoor; Zhiping Wang; Luis M. Rocha (CoRR, 2008)

MutDB: update on development of tools for the biochemical analysis of genetic variation. - Arti Singh; Adebayo Olowoyeye; Peter H. Baenziger; Jessica Dantzer; Maricel G. Kann; Predrag Radivojac; Randy W. Heiland; Sean D. Mooney (Nucleic Acids Res., 2008)

Session Introduction. - Yves A. Lussier; Younghee Lee; Predrag Radivojac; Yanay Ofran; Atul J. Butte; Maricel G. Kann (Pacific Symposium on Biocomputing, 2009)

Automated inference of molecular mechanisms of disease from amino acid substitutions. - Biao Li; Vidhya G. Krishnan; Matthew E. Mort; Fuxiao Xin; Kishore K. Kamati; David N. Cooper; Sean D. Mooney; Predrag Radivojac (Bioinform., 2009)

Analysis of AML genes in dysregulated molecular networks. - Eunjung Lee; Hyunchul Jung; Predrag Radivojac; Jong-Won Kim 001; Doheon Lee (BMC Bioinform., 2009)

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. - Yong Fuga Li; Randy J. Arnold; Yixue Li; Predrag Radivojac; Quanhu Sheng; Haixu Tang (J. Comput. Biol., 2009)

Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins. - Amrita Mohan; Vladimir N. Uversky; Predrag Radivojac (PLoS Comput. Biol., 2009)

Loss of Post-Translational Modification Sites in Disease. - Shuyan Li; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (Pacific Symposium on Biocomputing, 2010)

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. - Fuxiao Xin; Steven A. Myers; Yong Fuga Li; David N. Cooper; Sean D. Mooney; Predrag Radivojac (BMC Bioinform., 2010)

Graphlet Kernels for Prediction of Functional Residues in Protein Structures. - Vladimir Vacic; Lilia M. Iakoucheva; Stefano Lonardi; Predrag Radivojac (J. Comput. Biol., 2010)

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. - Nathan L. Nehrt; Wyatt T. Clark; Predrag Radivojac; Matthew W. Hahn (PLoS Comput. Biol., 2011)

Post-translational modifications induce significant yet not extreme changes to protein structure. - Fuxiao Xin; Predrag Radivojac (Bioinform., 2012)

Computational approaches to protein inference in shotgun proteomics. - Yong Fuga Li; Predrag Radivojac (BMC Bioinform., 2012)

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. - Idit Kosti; Predrag Radivojac; Yael Mandel-Gutfreund (PLoS Comput. Biol., 2012)

Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. - Sujun Li; Randy J. Arnold; Haixu Tang; Predrag Radivojac (BCB, 2013)

Information-theoretic evaluation of predicted ontological annotations. - Wyatt T. Clark; Predrag Radivojac (Bioinform., 2013)

ISCB Computational Biology Wikipedia Competition. - Alex Bateman; Janet Kelso; Daniel Mietchen; Geoff MacIntyre; Tomás Di Domenico; Thomas Abeel; Darren W. Logan; Predrag Radivojac; Burkhard Rost (PLoS Comput. Biol., 2013)

Vector Quantization Kernels for the Classification of Protein Sequences and Structures. - Wyatt T. Clark; Predrag Radivojac (Pacific Symposium on Biocomputing, 2014)

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. - Yuxiang Jiang; Wyatt T. Clark; Iddo Friedberg; Predrag Radivojac (Bioinform., 2014)

The automated function prediction SIG looks back at 2013 and prepares for 2014. - Mark N. Wass; Sean D. Mooney; Michal Linial; Predrag Radivojac; Iddo Friedberg (Bioinform., 2014)

Generalized graphlet kernels for probabilistic inference in sparse graphs. - Jose Lugo-Martinez; Predrag Radivojac (Netw. Sci., 2014)

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. - Lonnie R. Welch; Fran Lewitter; Russell Schwartz; Catherine Brooksbank; Predrag Radivojac; Bruno A. Gaëta; Maria Victoria Schneider (PLoS Comput. Biol., 2014)

A maximum-likelihood approach to absolute protein quantification in mass spectrometry. - Chao Ji; Yong Fuga Li; Earl P. Bellinger; Sujun Li; Randy J. Arnold; Predrag Radivojac; Haixu Tang (BCB, 2015)

Training the Next Generation of Quantitative Biologists in the Era of Big Data. - 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 (Pacific Symposium on Biocomputing, 2015)

Ten Simple Rules for a Community Computational Challenge. - Iddo Friedberg; Mark N. Wass; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2015)

A link graph-based approach to identify forum spam. - Youngsang Shin; Steven A. Myers; Minaxi Gupta; Predrag Radivojac (Secur. Commun. Networks, 2015)

Estimating the class prior and posterior from noisy positives and unlabeled data. - Shantanu Jain; Martha White; Predrag Radivojac (NIPS, 2016)

Nonparametric semi-supervised learning of class proportions. - Shantanu Jain; Martha White; Michael W. Trosset; Predrag Radivojac (CoRR, 2016)

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. - Jose Lugo-Martinez; Vikas Pejaver; Kymberleigh A. Pagel; Shantanu Jain; Matthew E. Mort; David N. Cooper; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2016)

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). - 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; et al. (PLoS Comput. Biol., 2016)

Recovering True Classifier Performance in Positive-Unlabeled Learning. - Shantanu Jain; Martha White; Predrag Radivojac (AAAI, 2017)

Session Introduction. - Yana Bromberg; Matthew W. Hahn; Predrag Radivojac (PSB, 2017)

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. - 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 (Bioinform., 2017)

Classification in biological networks with hypergraphlet kernels. - Jose Lugo-Martinez; Predrag Radivojac (CoRR, 2017)

Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies. - Yisu Peng; Yuxiang Jiang; Predrag Radivojac (CoRR, 2017)

On Whom Should I Perform this Lab Test Next? An Active Feature Elicitation Approach. - Sriraam Natarajan; Srijita Das 001; Nandini Ramanan; Gautam Kunapuli; Predrag Radivojac (IJCAI, 2018)

ISMB 2018 proceedings. - Yana Bromberg; Predrag Radivojac (Bioinform., 2018)

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. - Yisu Peng; Yuxiang Jiang; Predrag Radivojac (Bioinform., 2018)

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse. - Rodrigo F. Ramalho; Sujun Li; Predrag Radivojac; Matthew W. Hahn (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. - Makoto Yamada; Jiliang Tang; Jose Lugo-Martinez; Ermin Hodzic; Raunak Shrestha; Avishek Saha; Hua Ouyang; Dawei Yin; Hiroshi Mamitsuka; Süleyman Cenk Sahinalp; Predrag Radivojac; Filippo Menczer; et al. (IEEE Trans. Knowl. Data Eng., 2018)

Session introduction. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Jill P. Mesirov; Alexander A. Morgan; Predrag Radivojac (PSB, 2019)

Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. - Rashika Ramola; Shantanu Jain; Predrag Radivojac (PSB, 2019)

ISMB/ECCB 2019 Proceedings. - Yana Bromberg; Nadia El-Mabrouk; Predrag Radivojac (Bioinform., 2019)

A new class of metrics for learning on real-valued and structured data. - Ruiyu Yang; Yuxiang Jiang; Scott Mathews; Elizabeth A. Housworth; Matthew W. Hahn; Predrag Radivojac (Data Min. Knowl. Discov., 2019)

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. - Kymberleigh A. Pagel; Danny Antaki; Aojie Lian; Matthew E. Mort; David N. Cooper; Jonathan Sebat; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2019)

Class Prior Estimation with Biased Positives and Unlabeled Examples. - Shantanu Jain; Justin Delano; Himanshu Sharma; Predrag Radivojac (AAAI, 2020)

Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting. - Daniel Zeiberg; Shantanu Jain; Predrag Radivojac (AAAI, 2020)

Session Introduction. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Alexander A. Morgan; Predrag Radivojac; Nicholas P. Tatonetti (PSB, 2020)

Session Introduction. - Lukasz A. Kurgan; Predrag Radivojac; Joel L. Sussman; A. Keith Dunker (PSB, 2020)

An examination of citation-based impact of the computational biology conferences. - Jayvardan S. Naidu; Justin Delano; Scott Mathews; Predrag Radivojac (Bioinform., 2020)

New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics. - Yisu Peng; Shantanu Jain; Yong Fuga Li; Michal Gregus; Alexander R. Ivanov; Olga Vitek; Predrag Radivojac (Bioinform., 2020)

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. - Moses Stamboulian; Rafael F. Guerrero; Matthew W. Hahn; Predrag Radivojac (Bioinform., 2020)

A Probabilistic Approach to Extract Qualitative Knowledge for Early Prediction of Gestational Diabetes. - Athresh Karanam; Alexander L. Hayes; Harsha Kokel; David M. Haas; Predrag Radivojac; Sriraam Natarajan (AIME, 2021)

Classification in biological networks with hypergraphlet kernels. - Jose Lugo-Martinez; Daniel Zeiberg; Thomas Gaudelet; Noël Malod-Dognin; Natasa Przulj; Predrag Radivojac (Bioinform., 2021)

Explaining Deep Tractable Probabilistic Models: The sum-product network case. - Athresh Karanam; Saurabh Mathur 002; Predrag Radivojac; Kristian Kersting; Sriraam Natarajan (CoRR, 2021)

Explaining Deep Tractable Probabilistic Models: The sum-product network case. - Athresh Karanam; Saurabh Mathur 002; Predrag Radivojac; David M. Haas; Kristian Kersting; Sriraam Natarajan (PGM, 2022)

A roadmap for the functional annotation of protein families: a community perspective. - 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; et al. (Database J. Biol. Databases Curation, 2022)

Leveraging Structure for Improved Classification of Grouped Biased Data. - Daniel Zeiberg; Shantanu Jain; Predrag Radivojac (AAAI, 2023)

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. - Damiano Piovesan; Davide Zago; Parnal Joshi; M. Clara De Paolis Kaluza; Alexander Miguel Monzon; Walter Reade; Iddo Friedberg; Predrag Radivojac; Silvio C. E. Tosatto (CoRR, 2023)

Active feature elicitation: An unified framework. - Srijita Das 001; Nandini Ramanan; Gautam Kunapuli; Predrag Radivojac; Sriraam Natarajan (Frontiers Artif. Intell., 2023)

Modeling Multiple Adverse Pregnancy Outcomes: Learning from Diverse Data Sources. - Saurabh Mathur 002; 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; et al. (AIME (1), 2024)

An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics. - Yisu Peng; Shantanu Jain; Predrag Radivojac (Bioinform., 2024)

Learning Tree-Structured Composition of Data Augmentation. - Dongyue Li; Kailai Chen; Predrag Radivojac; Hongyang R. Zhang (Trans. Mach. Learn. Res., 2024)