Predrag Radivojac

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 42

Top Topics

Incomplete Knowledge

Mass Spectrometry

Protein Families

Top Venues

PLoS Comput. Biol.

Publications

Saurabh Mathur, 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. AIME (1) (2024)
Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang
Learning Tree-Structured Composition of Data Augmentation. Trans. Mach. Learn. Res. 2024 (2024)
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. CoRR (2023)
Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac, Sriraam Natarajan
Active feature elicitation: An unified framework. Frontiers Artif. Intell. 6 (2023)
Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
Leveraging Structure for Improved Classification of Grouped Biased Data. AAAI (2023)
Athresh Karanam, Saurabh Mathur, Predrag Radivojac, David M. Haas, Kristian Kersting, Sriraam Natarajan
Explaining Deep Tractable Probabilistic Models: The sum-product network case. PGM (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan 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 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. Database J. Biol. Databases Curation 2022 (2022) (2022)
Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
Leveraging Structure for Improved Classification of Grouped Biased Data. CoRR (2022)
Athresh Karanam, Saurabh Mathur, Predrag Radivojac, Kristian Kersting, Sriraam Natarajan
Explaining Deep Tractable Probabilistic Models: The sum-product network case. CoRR (2021)
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. AIME (2021)
Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac
Classification in biological networks with hypergraphlet kernels. Bioinform. 37 (7) (2021)
Jayvardan S. Naidu, Justin Delano, Scott Mathews, Predrag Radivojac
An examination of citation-based impact of the computational biology conferences. Bioinform. 36 (9) (2020)
Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting. AAAI (2020)
Lukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker
Session Introduction. PSB (2020)
Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinform. 36 (Supplement-1) (2020)
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti
Session Introduction. PSB (2020)
Shantanu Jain, Justin Delano, Himanshu Sharma, Predrag Radivojac
Class Prior Estimation with Biased Positives and Unlabeled Examples. AAAI (2020)
Rashika Ramola, Shantanu Jain, Predrag Radivojac
Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. PSB (2019)
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac
Session introduction. PSB (2019)
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. PLoS Comput. Biol. 15 (6) (2019)
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. Data Min. Knowl. Discov. 33 (4) (2019)
Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac
ISMB/ECCB 2019 Proceedings. Bioinform. 35 (14) (2019)
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, Yi Chang
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Trans. Knowl. Data Eng. 30 (7) (2018)
Yisu Peng, Yuxiang Jiang, Predrag Radivojac
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. Bioinform. 34 (13) (2018)
Sriraam Natarajan, Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac
On Whom Should I Perform this Lab Test Next? An Active Feature Elicitation Approach. IJCAI (2018)
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. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Yana Bromberg, Predrag Radivojac
ISMB 2018 proceedings. Bioinform. 34 (13) (2018)
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. Bioinform. 33 (14) (2017)
Shantanu Jain, Martha White, Predrag Radivojac
Recovering True Classifier Performance in Positive-Unlabeled Learning. AAAI (2017)
Yana Bromberg, Matthew W. Hahn, Predrag Radivojac
Session Introduction. PSB (2017)
Yisu Peng, Yuxiang Jiang, Predrag Radivojac
Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies. CoRR (2017)
Jose Lugo-Martinez, Predrag Radivojac
Classification in biological networks with hypergraphlet kernels. CoRR (2017)
Shantanu Jain, Martha White, Predrag Radivojac
Recovering True Classifier Performance in Positive-Unlabeled Learning. CoRR (2017)
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). PLoS Comput. Biol. 12 (5) (2016)
Shantanu Jain, Martha White, Predrag Radivojac
Estimating the class prior and posterior from noisy positives and unlabeled data. NIPS (2016)
Shantanu Jain, Martha White, Predrag Radivojac
Estimating the class prior and posterior from noisy positives and unlabeled data. CoRR (2016)
Shantanu Jain, Martha White, Michael W. Trosset, Predrag Radivojac
Nonparametric semi-supervised learning of class proportions. CoRR (2016)
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. PLoS Comput. Biol. 12 (8) (2016)
Youngsang Shin, Steven A. Myers, Minaxi Gupta, Predrag Radivojac
A link graph-based approach to identify forum spam. Secur. Commun. Networks 8 (2) (2015)
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. BCB (2015)
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. Pacific Symposium on Biocomputing (2015)
Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
Ten Simple Rules for a Community Computational Challenge. PLoS Comput. Biol. 11 (4) (2015)
Jose Lugo-Martinez, Predrag Radivojac
Generalized graphlet kernels for probabilistic inference in sparse graphs. Netw. Sci. 2 (2) (2014)
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. Bioinform. 30 (17) (2014)
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. PLoS Comput. Biol. 10 (3) (2014)
Wyatt T. Clark, Predrag Radivojac
Vector Quantization Kernels for the Classification of Protein Sequences and Structures. Pacific Symposium on Biocomputing (2014)
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. Bioinform. 30 (14) (2014)
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. PLoS Comput. Biol. 9 (9) (2013)
Wyatt T. Clark, Predrag Radivojac
Information-theoretic evaluation of predicted ontological annotations. Bioinform. 29 (13) (2013)
Sujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac
Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. BCB (2013)
Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. PLoS Comput. Biol. 8 (7) (2012)
Fuxiao Xin, Predrag Radivojac
Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinform. 28 (22) (2012)
Yong Fuga Li, Predrag Radivojac
Computational approaches to protein inference in shotgun proteomics. BMC Bioinform. 13 (S-16) (2012)
Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. PLoS Comput. Biol. 7 (6) (2011)
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. Bioinform. 26 (16) (2010)
Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac
Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. 17 (1) (2010)
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. BMC Bioinform. 11 (S-10) (2010)
Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
Loss of Post-Translational Modification Sites in Disease. Pacific Symposium on Biocomputing (2010)
Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac
Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins. PLoS Comput. Biol. 5 (9) (2009)
Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee
Analysis of AML genes in dysregulated molecular networks. BMC Bioinform. 10 (S-9) (2009)
Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann
Session Introduction. Pacific Symposium on Biocomputing (2009)
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. Bioinform. 25 (21) (2009)
Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. J. Comput. Biol. 16 (8) (2009)
Alaa Abi-Haidar, Jasleen Kaur, Ana Gabriela Maguitman, Predrag Radivojac, Andreas Rechtsteiner, Karin Verspoor, Zhiping Wang, Luis Mateus Rocha
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks CoRR (2008)
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. ECCB (2008)
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. Bioinform. 24 (1) (2008)
Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann
Session Introduction. Pacific Symposium on Biocomputing (2008)
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. Nucleic Acids Res. 36 (Database-Issue) (2008)
Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. RECOMB (2008)
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. Pacific Symposium on Biocomputing (2007)
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
Session Introduction. Pacific Symposium on Biocomputing (2007)
Mehmet M. Dalkilic, Wyatt T. Clark, James C. Costello, Predrag Radivojac
Using Compression to Identify Classes of Inauthentic Texts. SDM (2006)
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. PLoS Comput. Biol. 2 (8) (2006)
Kang Peng, Predrag Radivojac, Slobodan Vucetic, A. Keith Dunker, Zoran Obradovic
Length-dependent prediction of protein intrinsic disorder. BMC Bioinform. 7 (2006)
Sourav Roy, Santiago Schnell, Predrag Radivojac
Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. Comput. Biol. Chem. 30 (4) (2006)
Vladimir Vacic, Lilia M. Iakoucheva, Predrag Radivojac
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinform. 22 (12) (2006)
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
Session Introduction. Pacific Symposium on Biocomputing (2006)
Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, Predrag Radivojac
A Machine Learning Approach to Predicting Peptide Fragmentation Spectra. Pacific Symposium on Biocomputing (2006)
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. ISMB (Supplement of Bioinformatics) (2006)
Kang Peng, Slobodan Vucetic, Predrag Radivojac, Celeste J. Brown, A. Keith Dunker, Zoran Obradovic
Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. J. Bioinform. Comput. Biol. 3 (1) (2005)
Kenneth Daily, Predrag Radivojac, A. Keith Dunker
Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. CIBCB (2005)
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. Bioinform. 21 (1) (2005)
Predrag Radivojac, Zoran Obradovic, A. Keith Dunker, Slobodan Vucetic
Feature Selection Filters Based on the Permutation Test. ECML (2004)
Predrag Radivojac, Nitesh V. Chawla, A. Keith Dunker, Zoran Obradovic
Classification and knowledge discovery in protein databases. J. Biomed. Informatics 37 (4) (2004)
Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions. Pacific Symposium on Biocomputing (2003)
Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker
Improving Sequence Alignments For Intrinsically Disordered Proteins. Pacific Symposium on Biocomputing (2002)