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Predrag Radivojac
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2020 – today
- 2024
- [j44]Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang:
Learning Tree-Structured Composition of Data Augmentation. Trans. Mach. Learn. Res. 2024 (2024) - [c33]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: 293-302 - 2023
- [j43]Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac, Sriraam Natarajan:
Active feature elicitation: An unified framework. Frontiers Artif. Intell. 6 (2023) - [c32]Daniel Zeiberg, Shantanu Jain, Predrag Radivojac:
Leveraging Structure for Improved Classification of Grouped Biased Data. AAAI 2023: 11113-11120 - [i9]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 abs/2310.06881 (2023) - 2022
- [j42]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. Database J. Biol. Databases Curation 2022(2022) (2022) - [c31]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: 325-336 - [i8]Daniel Zeiberg, Shantanu Jain, Predrag Radivojac:
Leveraging Structure for Improved Classification of Grouped Biased Data. CoRR abs/2212.03697 (2022) - 2021
- [j41]Jose Lugo-Martinez
, Daniel Zeiberg
, Thomas Gaudelet, Noël Malod-Dognin
, Natasa Przulj
, Predrag Radivojac
:
Classification in biological networks with hypergraphlet kernels. Bioinform. 37(7): 1000-1007 (2021) - [c30]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: 497-502 - [i7]Athresh Karanam, Saurabh Mathur, Predrag Radivojac, Kristian Kersting, Sriraam Natarajan:
Explaining Deep Tractable Probabilistic Models: The sum-product network case. CoRR abs/2110.09778 (2021) - 2020
- [j40]Jayvardan S. Naidu, Justin Delano
, Scott Mathews, Predrag Radivojac
:
An examination of citation-based impact of the computational biology conferences. Bioinform. 36(9): 2958-2962 (2020) - [j39]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): i219-i226 (2020) - [c29]Shantanu Jain, Justin Delano, Himanshu Sharma, Predrag Radivojac:
Class Prior Estimation with Biased Positives and Unlabeled Examples. AAAI 2020: 4255-4263 - [c28]Daniel Zeiberg
, Shantanu Jain, Predrag Radivojac:
Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting. AAAI 2020: 6729-6736 - [c27]Lukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker:
Session Introduction. PSB 2020: 149-158 - [c26]Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti:
Session Introduction. PSB 2020: 547-550
2010 – 2019
- 2019
- [j38]Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac:
ISMB/ECCB 2019 Proceedings. Bioinform. 35(14): i1-i2 (2019) - [j37]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): 995-1016 (2019) - [j36]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) - [c25]Rashika Ramola, Shantanu Jain, Predrag Radivojac:
Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. PSB 2019: 124-135 - [c24]Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac:
Session introduction. PSB 2019: 220-223 - 2018
- [j35]Yana Bromberg
, Predrag Radivojac:
ISMB 2018 proceedings. Bioinform. 34(13): i2-i3 (2018) - [j34]Yisu Peng, Yuxiang Jiang, Predrag Radivojac:
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. Bioinform. 34(13): i313-i322 (2018) - [j33]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): 1284-1289 (2018) - [j32]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): 1352-1365 (2018) - [c23]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: 3498-3505 - 2017
- [j31]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): i389-i398 (2017) - [c22]Shantanu Jain, Martha White, Predrag Radivojac:
Recovering True Classifier Performance in Positive-Unlabeled Learning. AAAI 2017: 2066-2072 - [c21]Yana Bromberg, Matthew W. Hahn, Predrag Radivojac:
Session Introduction. PSB 2017: 1-2 - [i6]Shantanu Jain, Martha White, Predrag Radivojac:
Recovering True Classifier Performance in Positive-Unlabeled Learning. CoRR abs/1702.00518 (2017) - [i5]Jose Lugo-Martinez, Predrag Radivojac:
Classification in biological networks with hypergraphlet kernels. CoRR abs/1703.04823 (2017) - [i4]Yisu Peng, Yuxiang Jiang, Predrag Radivojac:
Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies. CoRR abs/1712.09679 (2017) - 2016
- [j30]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) - [j29]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) - [c20]Shantanu Jain, Martha White, Predrag Radivojac:
Estimating the class prior and posterior from noisy positives and unlabeled data. NIPS 2016: 2685-2693 - [i3]Shantanu Jain, Martha White, Michael W. Trosset, Predrag Radivojac:
Nonparametric semi-supervised learning of class proportions. CoRR abs/1601.01944 (2016) - [i2]Shantanu Jain, Martha White, Predrag Radivojac:
Estimating the class prior and posterior from noisy positives and unlabeled data. CoRR abs/1606.08561 (2016) - 2015
- [j28]Iddo Friedberg
, Mark N. Wass
, Sean D. Mooney
, Predrag Radivojac:
Ten Simple Rules for a Community Computational Challenge. PLoS Comput. Biol. 11(4) (2015) - [j27]Youngsang Shin, Steven A. Myers, Minaxi Gupta, Predrag Radivojac:
A link graph-based approach to identify forum spam. Secur. Commun. Networks 8(2): 176-188 (2015) - [c19]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: 296-305 - [c18]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: 488-492 - 2014
- [j26]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): 2091-2092 (2014) - [j25]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): 609-616 (2014) - [j24]Jose Lugo-Martinez
, Predrag Radivojac:
Generalized graphlet kernels for probabilistic inference in sparse graphs. Netw. Sci. 2(2): 254-276 (2014) - [j23]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) - [c17]Wyatt T. Clark, Predrag Radivojac:
Vector Quantization Kernels for the Classification of Protein Sequences and Structures. Pacific Symposium on Biocomputing 2014: 316-327 - 2013
- [j22]Wyatt T. Clark, Predrag Radivojac:
Information-theoretic evaluation of predicted ontological annotations. Bioinform. 29(13): 53-61 (2013) - [j21]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) - [c16]Sujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac:
Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. BCB 2013: 316 - 2012
- [j20]Fuxiao Xin, Predrag Radivojac:
Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinform. 28(22): 2905-2913 (2012) - [j19]Yong Fuga Li, Predrag Radivojac:
Computational approaches to protein inference in shotgun proteomics. BMC Bioinform. 13(S-16): S4 (2012) - [j18]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) - 2011
- [j17]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) - 2010
- [j16]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): 1975-1982 (2010) - [j15]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): O4 (2010) - [j14]Vladimir Vacic
, Lilia M. Iakoucheva
, Stefano Lonardi
, Predrag Radivojac:
Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. 17(1): 55-72 (2010) - [c15]Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac:
Loss of Post-Translational Modification Sites in Disease. Pacific Symposium on Biocomputing 2010: 337-347
2000 – 2009
- 2009
- [j13]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): 2744-2750 (2009) - [j12]Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee
:
Analysis of AML genes in dysregulated molecular networks. BMC Bioinform. 10(S-9): 2 (2009) - [j11]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): 1183-1193 (2009) - [j10]Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac:
Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins. PLoS Comput. Biol. 5(9) (2009) - [c14]Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann:
Session Introduction. Pacific Symposium on Biocomputing 2009: 464-466 - 2008
- [j9]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): 102-109 (2008) - [j8]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): 815-819 (2008) - [c13]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: 241-247 - [c12]Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann:
Session Introduction. Pacific Symposium on Biocomputing 2008: 228-230 - [c11]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: 167-180 - [i1]Alaa Abi-Haidar, Jasleen Kaur, 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. CoRR abs/0812.1029 (2008) - 2007
- [c10]Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac:
Session Introduction. Pacific Symposium on Biocomputing 2007: 1-3 - [c9]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: 409-420 - 2006
- [j7]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): 1536-1537 (2006) - [j6]Kang Peng, Predrag Radivojac, Slobodan Vucetic, A. Keith Dunker, Zoran Obradovic:
Length-dependent prediction of protein intrinsic disorder. BMC Bioinform. 7: 208 (2006) - [j5]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): 241-248 (2006) - [j4]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) - [c8]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: 481-488 - [c7]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: 219-230 - [c6]Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac:
Session Introduction. Pacific Symposium on Biocomputing 2006: 351-353 - [c5]Mehmet M. Dalkilic, Wyatt T. Clark, James C. Costello, Predrag Radivojac:
Using Compression to Identify Classes of Inauthentic Texts. SDM 2006: 604-608 - 2005
- [j3]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): 137-140 (2005) - [j2]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): 35-60 (2005) - [c4]Kenneth Daily, Predrag Radivojac, A. Keith Dunker:
Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. CIBCB 2005: 475-481 - 2004
- [j1]Predrag Radivojac, Nitesh V. Chawla
, A. Keith Dunker, Zoran Obradovic:
Classification and knowledge discovery in protein databases. J. Biomed. Informatics 37(4): 224-239 (2004) - [c3]Predrag Radivojac, Zoran Obradovic, A. Keith Dunker, Slobodan Vucetic:
Feature Selection Filters Based on the Permutation Test. ECML 2004: 334-346 - 2003
- [c2]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: 216-227 - 2002
- [c1]Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker:
Improving Sequence Alignments For Intrinsically Disordered Proteins. Pacific Symposium on Biocomputing 2002: 589-600
Coauthor Index
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