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Pavel P. Kuksa
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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
86542011
Systems and methods for semi-supervised relationship extraction
Y Qi, B Bai, X Ning, P Kuksa
US Patent 8,874,432, 2014
2792014
Efficient alignment-free DNA barcode analytics
P Kuksa, V Pavlovic
BMC bioinformatics 10 (14), 1-18, 2009
782009
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
752016
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
592015
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
552020
Scalable algorithms for string kernels with inexact matching
P Kuksa, PH Huang, V Pavlovic
Advances in neural information processing systems 21, 2008
542008
New insights into the genetic etiology of Alzheimer’s disease and related dementias
C Bellenguez, F Küçükali, IE Jansen, L Kleineidam, S Moreno-Grau, ...
Nature genetics 54 (4), 412-436, 2022
452022
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
432019
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
412018
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
372015
Efficient motif finding algorithms for large-alphabet inputs
PP Kuksa, V Pavlovic
BMC bioinformatics 11 (8), 1-10, 2010
352010
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
342015
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
302009
A geometric approach to device-free motion localization using signal strength
R Moore, R Howard, P Kuksa, RP Martin
Rutgers University, 2010
292010
Spatial representation for efficient sequence classification
PP Kuksa, V Pavlovic
2010 20th International Conference on Pattern Recognition, 3320-3323, 2010
262010
Generalized similarity kernels for efficient sequence classification
P P. Kuksa, I Khan, V Pavlovic
Proceedings of the 2012 SIAM International Conference on Data Mining, 873-882, 2012
232012
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
232010
Large meta-analysis of genome-wide association studies expands knowledge of the genetic etiology of Alzheimer’s disease and highlights potential translational opportunities
C Bellenguez, F Küçükali, I Jansen, V Andrade, S Morenau-Grau, N Amin, ...
MedRxiv 17 (10), 2020
202020
SPAR: small RNA-seq portal for analysis of sequencing experiments
PP Kuksa, A Amlie-Wolf, Ž Katanić, O Valladares, LS Wang, YY Leung
Nucleic acids research 46 (W1), W36-W42, 2018
192018
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Articles 1–20