| Natural language processing (almost) from scratch R Collobert, J Weston, L Bottou, M Karlen, K Kavukcuoglu, P Kuksa Journal of machine learning research 12 (ARTICLE), 2493− 2537, 2011 | 6856 | 2011 |
| Systems and methods for semi-supervised relationship extraction Y Qi, B Bai, X Ning, P Kuksa US Patent 8,874,432, 2014 | 177 | 2014 |
| Efficient alignment-free DNA barcode analytics P Kuksa, V Pavlovic BMC bioinformatics 10 (S14), S9, 2009 | 71 | 2009 |
| DASHR: database of small human noncoding RNAs YY Leung, PP Kuksa, A Amlie-Wolf, O Valladares, LH Ungar, S Kannan, ... Nucleic acids research 44 (D1), D216-D222, 2016 | 59 | 2016 |
| HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements YC Hwang, CF Lin, O Valladares, J Malamon, PP Kuksa, Q Zheng, ... Bioinformatics 31 (8), 1290-1292, 2015 | 50 | 2015 |
| Scalable algorithms for string kernels with inexact matching P Kuksa, PH Huang, V Pavlovic Advances in neural information processing systems 21, 881-888, 2008 | 47 | 2008 |
| High-order neural networks and kernel methods for peptide-MHC binding prediction PP Kuksa, MR Min, R Dugar, M Gerstein Bioinformatics 31 (22), 3600-3607, 2015 | 32 | 2015 |
| Efficient motif finding algorithms for large-alphabet inputs PP Kuksa, V Pavlovic BMC bioinformatics 11 (S8), S1, 2010 | 30 | 2010 |
| Chemical modifications mark alternatively spliced and uncapped messenger RNAs in Arabidopsis LE Vandivier, R Campos, PP Kuksa, IM Silverman, LS Wang, BD Gregory The Plant Cell 27 (11), 3024-3037, 2015 | 27 | 2015 |
| A geometric approach to device-free motion localization using signal strength R Moore, R Howard, P Kuksa, RP Martin | 27 | 2010 |
| Semi-supervised sequence labeling with self-learned features Y Qi, P Kuksa, R Collobert, K Sadamasa, K Kavukcuoglu, J Weston 2009 Ninth IEEE International Conference on Data Mining, 428-437, 2009 | 27 | 2009 |
| DASHR 2.0: integrated database of human small non-coding RNA genes and mature products PP Kuksa, A Amlie-Wolf, Ž Katanić, O Valladares, LS Wang, YY Leung Bioinformatics 35 (6), 1033-1039, 2019 | 26 | 2019 |
| Spatial representation for efficient sequence classification PP Kuksa, V Pavlovic 2010 20th International Conference on Pattern Recognition, 3320-3323, 2010 | 24 | 2010 |
| INFERNO: inferring the molecular mechanisms of noncoding genetic variants A Amlie-Wolf, M Tang, EE Mlynarski, PP Kuksa, O Valladares, Z Katanic, ... Nucleic acids research 46 (17), 8740-8753, 2018 | 19 | 2018 |
| Semi-supervised bio-named entity recognition with word-codebook learning PP Kuksa, Y Qi Proceedings of the 2010 SIAM International Conference on Data Mining, 25-36, 2010 | 18 | 2010 |
| Combining labeled and unlabeled data with word-class distribution learning Y Qi, R Collobert, P Kuksa, K Kavukcuoglu, J Weston Proceedings of the 18th ACM conference on Information and knowledge …, 2009 | 17 | 2009 |
| Fast protein homology and fold detection with sparse spatial sample kernels P Kuksa, PH Huang, V Pavlovic 2008 19th International Conference on Pattern Recognition, 1-4, 2008 | 16 | 2008 |
| Fast kernel methods for SVM sequence classifiers P Kuksa, V Pavlovic International Workshop on Algorithms in Bioinformatics, 228-239, 2007 | 15 | 2007 |
| Transcriptome-wide measurement of plant RNA secondary structure SW Foley, LE Vandivier, PP Kuksa, BD Gregory Current opinion in plant biology 27, 36-43, 2015 | 14 | 2015 |
| Efficient use of unlabeled data for protein sequence classification: a comparative study P Kuksa, PH Huang, V Pavlovic BMC bioinformatics 10 (S4), S2, 2009 | 14 | 2009 |
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