Pavel P. Kuksa
Pavel P. Kuksa
Institute for Biomedical Informatics, University of Pennsylvania
Verified email at
Cited by
Cited by
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
Systems and methods for semi-supervised relationship extraction
Y Qi, B Bai, X Ning, P Kuksa
US Patent 8,874,432, 2014
Efficient alignment-free DNA barcode analytics
P Kuksa, V Pavlovic
BMC bioinformatics 10 (14), 1-18, 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
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
Scalable algorithms for string kernels with inexact matching
P Kuksa, PH Huang, V Pavlovic
Advances in neural information processing systems 21, 881-888, 2008
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
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
Efficient motif finding algorithms for large-alphabet inputs
PP Kuksa, V Pavlovic
BMC bioinformatics 11 (8), 1-10, 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
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
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
A geometric approach to device-free motion localization using signal strength
R Moore, R Howard, P Kuksa, RP Martin
Spatial representation for efficient sequence classification
PP Kuksa, V Pavlovic
2010 20th International Conference on Pattern Recognition, 3320-3323, 2010
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
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
New insights on the genetic etiology of Alzheimer’s and related dementia
C Bellenguez, F Küçükali, I Jansen, V Andrade, S Moreno-Grau, N Amin, ...
MedRxiv, 2020
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
A fast, large-scale learning method for protein sequence classification
P Kuksa, PH Huang, V Pavlovic
8th Int. Workshop on Data Mining in Bioinformatics, 29-37, 2008
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
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