Pavel P. Kuksa

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 5

Top Topics

Sequence Classification

Biological Knowledge

Functional Genomics

Top Venues

Nucleic Acids Res.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung
hipFG: high-throughput harmonization and integration pipeline for functional genomics data. Bioinform. 39 (11) (2023)
Pavel P. Kuksa, Chien-Yueh Lee, Alexandre Amlie-Wolf, Prabhakaran Gangadharan, Elizabeth E. Mlynarski, Yi-Fan Chou, Han-Jen Lin, Heather Issen, Emily Greenfest-Allen, Otto Valladares, Yuk Yee Leung, Li-San Wang
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. Bioinform. 36 (12) (2020)
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinform. 35 (6) (2019)
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang
DASHR: database of small human noncoding RNAs. Nucleic Acids Res. 44 (Database-Issue) (2016)
Pavel P. Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein
High-order neural networks and kernel methods for peptide-MHC binding prediction. Bioinform. 31 (22) (2015)
Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. Bioinform. 31 (8) (2015)
Pavel P. Kuksa
Efficient multivariate sequence classification. CoRR (2014)
Pavel P. Kuksa
Biological Sequence Classification with Multivariate String Kernels. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Pavel P. Kuksa, Imdadullah Khan, Vladimir Pavlovic
Generalized Similarity Kernels for Efficient Sequence Classification. SDM (2012)
Pavel P. Kuksa
2D similarity kernels for biological sequence classification. BIOKDD (2012)
Pavel P. Kuksa, Vladimir Pavlovic
Efficient evaluation of large sequence kernels. KDD (2012)
Ronan Collobert, Jason Weston, Léon Bottou, Michael Karlen, Koray Kavukcuoglu, Pavel P. Kuksa
Natural Language Processing (Almost) from Scratch. J. Mach. Learn. Res. 12 (2011)
Ronan Collobert, Jason Weston, Léon Bottou, Michael Karlen, Koray Kavukcuoglu, Pavel P. Kuksa
Natural Language Processing (almost) from Scratch CoRR (2011)
Pavel P. Kuksa, Yanjun Qi, Bing Bai, Ronan Collobert, Jason Weston, Vladimir Pavlovic, Xia Ning
Semi-supervised Abstraction-Augmented String Kernel for Multi-level Bio-Relation Extraction. ECML/PKDD (2) (2010)
Pavel P. Kuksa, Vladimir Pavlovic
Spatial Representation for Efficient Sequence Classification. ICPR (2010)
Pavel P. Kuksa, Yanjun Qi
Semi-supervised Bio-named Entity Recognition with Word-Codebook Learning. SDM (2010)
Pavel P. Kuksa, Vladimir Pavlovic
Efficient motif finding algorithms for large-alphabet inputs. BMC Bioinform. 11 (S-8) (2010)
Pavel P. Kuksa, Vladimir Pavlovic
Efficient alignment-free DNA barcode analytics. BMC Bioinform. 10 (S-14) (2009)
Yanjun Qi, Ronan Collobert, Pavel P. Kuksa, Koray Kavukcuoglu, Jason Weston
Combining labeled and unlabeled data with word-class distribution learning. CIKM (2009)
Pavel P. Kuksa, Vladimir Pavlovic
Fast Motif Selection for Biological Sequences. BIBM (2009)
Yanjun Qi, Pavel P. Kuksa, Ronan Collobert, Kunihiko Sadamasa, Koray Kavukcuoglu, Jason Weston
Semi-Supervised Sequence Labeling with Self-Learned Features. ICDM (2009)
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
Efficient use of unlabeled data for protein sequence classification: a comparative study. BMC Bioinform. 10 (S-4) (2009)
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
Scalable Algorithms for String Kernels with Inexact Matching. NIPS (2008)
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
Fast protein homology and fold detection with sparse spatial sample kernels. ICPR (2008)
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
On the Role of Local Matching for Efficient Semi-supervised Protein Sequence Classification. BIBM (2008)
Pavel P. Kuksa, Vladimir Pavlovic
Fast Kernel Methods for SVM Sequence Classifiers. WABI (2007)