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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 - [i10]Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang:
Learning Tree-Structured Composition of Data Augmentation. CoRR abs/2408.14381 (2024) - 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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