Pavel P. Kuksa

28 papers A* 2A 3B 2C 1Journal 15Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets.
Bioinform.
Pavel P. Kuksa, Matei Ionita, Luke Carter, Jeffrey Cifello, Prabhakaran Gangadharan, Kaylyn Clark, Otto Valladares, Yuk Yee Leung, Li-San Wang
2023 J jnl
hipFG: high-throughput harmonization and integration pipeline for functional genomics data.
Bioinform.
Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung
2020 J jnl
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.
Bioinform.
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
2019 J jnl
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.
Bioinform.
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
2018 J jnl
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Nucleic Acids Res.
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
2016 J jnl
DASHR: database of small human noncoding RNAs.
Nucleic Acids Res.
Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang
2015 J jnl
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
Bioinform.
Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang
2015 J jnl
High-order neural networks and kernel methods for peptide-MHC binding prediction.
Bioinform.
Pavel P. Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein
2014 J jnl
Efficient multivariate sequence classification.
CoRR
Pavel P. Kuksa
2013 J jnl
Biological Sequence Classification with Multivariate String Kernels.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pavel P. Kuksa
2012 — conf
2D similarity kernels for biological sequence classification.
BIOKDD
Pavel P. Kuksa
2012 A* conf
Efficient evaluation of large sequence kernels.
KDD
Pavel P. Kuksa, Vladimir Pavlovic
2012 A conf
Generalized Similarity Kernels for Efficient Sequence Classification.
SDM
Pavel P. Kuksa, Imdadullah Khan, Vladimir Pavlovic
2011 J jnl
Natural Language Processing (Almost) from Scratch.
J. Mach. Learn. Res.
Ronan Collobert, Jason Weston, Léon Bottou, Michael Karlen, Koray Kavukcuoglu, Pavel P. Kuksa
2011 J jnl
Natural Language Processing (almost) from Scratch
CoRR
Ronan Collobert, Jason Weston, Léon Bottou, Michael Karlen, Koray Kavukcuoglu, Pavel P. Kuksa
2010 J jnl
Efficient motif finding algorithms for large-alphabet inputs.
BMC Bioinform.
Pavel P. Kuksa, Vladimir Pavlovic
2010 — conf
Semi-supervised Abstraction-Augmented String Kernel for Multi-level Bio-Relation Extraction.
ECML/PKDD (2)
Pavel P. Kuksa, Yanjun Qi, Bing Bai, Ronan Collobert, Jason Weston, Vladimir Pavlovic, Xia Ning
2010 A conf
Semi-supervised Bio-named Entity Recognition with Word-Codebook Learning.
SDM
Pavel P. Kuksa, Yanjun Qi
2010 B conf
Spatial Representation for Efficient Sequence Classification.
ICPR
Pavel P. Kuksa, Vladimir Pavlovic
2009 A conf
Combining labeled and unlabeled data with word-class distribution learning.
CIKM
Yanjun Qi, Ronan Collobert, Pavel P. Kuksa, Koray Kavukcuoglu, Jason Weston
2009 J jnl
Efficient alignment-free DNA barcode analytics.
BMC Bioinform.
Pavel P. Kuksa, Vladimir Pavlovic
2009 J jnl
Efficient use of unlabeled data for protein sequence classification: a comparative study.
BMC Bioinform.
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
2009 — conf
Fast Motif Selection for Biological Sequences.
BIBM
Pavel P. Kuksa, Vladimir Pavlovic
2009 A* conf
Semi-Supervised Sequence Labeling with Self-Learned Features.
ICDM
Yanjun Qi, Pavel P. Kuksa, Ronan Collobert, Kunihiko Sadamasa, Koray Kavukcuoglu, Jason Weston
2008 B conf
Fast protein homology and fold detection with sparse spatial sample kernels.
ICPR
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
2008 — conf
On the Role of Local Matching for Efficient Semi-supervised Protein Sequence Classification.
BIBM
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
2008 — conf
Scalable Algorithms for String Kernels with Inexact Matching.
NIPS
Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
2007 C conf
Fast Kernel Methods for SVM Sequence Classifiers.
WABI
Pavel P. Kuksa, Vladimir Pavlovic