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1

Transcriptome-wide measurement of plant RNA secondary structure

Foley, Shawn W, Vandivier, Lee E, Kuksa, Pavel P, Gregory, Brian D

Journal:

Current Opinion in Plant Biology

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

2

Efficient alignment-free DNA barcode analytics

Pavel Kuksa, Vladimir Pavlovic

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.79 MB

english, 2009

3

Efficient use of unlabeled data for protein sequence classification: a comparative study

Pavel Kuksa, Pai-Hsi Huang, Vladimir Pavlovic

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 488 KB

english, 2009

4

Efficient motif finding algorithms for large-alphabet inputs

Pavel P Kuksa, Vladimir Pavlovic

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 894 KB

english, 2010

5

[IEEE 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Washington, D.C., USA (2009.11.1-2009.11.4)] 2009 IEEE International Conference on Bioinformatics and Biomedicine - Fast Motif Selection for Biological Sequences

Kuksa, Pavel, Pavlovic, Vladimir

Year:

2009

Language:

english

File:

PDF, 231 KB

english, 2009

6

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - On the Role of Local Matching for Efficient Semi-supervised Protein Sequence Classification

Kuksa, Pavel, Huang, Pai-Hsi, Pavlovic, Vladimir

Year:

2008

Language:

english

File:

PDF, 196 KB

english, 2008

7

Biological Sequence Classification with Multivariate String Kernels

Kuksa, Pavel P.

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.13 MB

english, 2013

8

[IEEE 2010 20th International Conference on Pattern Recognition (ICPR) - Istanbul, Turkey (2010.08.23-2010.08.26)] 2010 20th International Conference on Pattern Recognition - Spatial Representation for Efficient Sequence Classification

Kuksa, Pavel P., Pavlovic, Vladimir

Year:

2010

Language:

english

File:

PDF, 213 KB

english, 2010

9

[IEEE 2009 Ninth IEEE International Conference on Data Mining (ICDM) - Miami Beach, FL, USA (2009.12.6-2009.12.9)] 2009 Ninth IEEE International Conference on Data Mining - Semi-Supervised Sequence Labeling with Self-Learned Features

Qi, Yanjun, Kuksa, Pavel, Collobert, Ronan, Sadamasa, Kunihiko, Kavukcuoglu, Koray, Weston, Jason

Year:

2009

Language:

english

File:

PDF, 293 KB

english, 2009

10

[IEEE 2008 19th International Conference on Pattern Recognition (ICPR) - Tampa, FL, USA (2008.12.8-2008.12.11)] 2008 19th International Conference on Pattern Recognition - Fast protein homology and fold detection with sparse spatial sample kernels

Kuksa, Pavel, Pai-Hsi Huang,, Pavlovic, Vladimir

Year:

2008

Language:

english

File:

PDF, 129 KB

english, 2008

11

High-order neural networks and kernel methods for peptide-MHC binding prediction

Kuksa, Pavel P., Min, Martin Renqiang, Dugar, Rishabh, Gerstein, Mark

Journal:

Year:

2015

Language:

english

File:

PDF, 389 KB

english, 2015

12

[ACM Press the 18th ACM SIGKDD international conference - Beijing, China (2012.08.12-2012.08.16)] Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '12 - Efficient evaluation of large sequence kernels

Kuksa, Pavel P., Pavlovic, Vladimir

Year:

2012

Language:

english

File:

PDF, 456 KB

english, 2012

13

[ACM Press the 11th International Workshop - Beijing, China (2012.08.12-2012.08.12)] Proceedings of the 11th International Workshop on Data Mining in Bioinformatics - BIOKDD '12 - 2D similarity kernels for biological sequence classification

Kuksa, Pavel P.

Year:

2012

Language:

english

File:

PDF, 843 KB

english, 2012

14

[ACM Press Proceeding of the 18th ACM conference - Hong Kong, China (2009.11.02-2009.11.06)] Proceeding of the 18th ACM conference on Information and knowledge management - CIKM '09 - Combining labeled and unlabeled data with word-class distribution learning

Qi, Yanjun, Collobert, Ronan, Kuksa, Pavel, Kavukcuoglu, Koray, Weston, Jason

Year:

2009

Language:

english

File:

PDF, 324 KB

english, 2009

15

Prediction of late-onset Alzheimer’s disease-associated enhancer elements

Tang, Mitchell, Kramer, Christian, Xu, George, Hawk, Michele, Hwang, Yih-Chii, Lin, Chiao-Feng, Kuksa, Pavel, Wang, Weixin, Dombroski, Beth A., Naj, Adam C., Wang, Li-San, Schellenberg, Gerald D.

Journal:

Alzheimer's & Dementia

Year:

2015

Language:

english

File:

PDF, 107 KB

english, 2015

16

SPAR: small RNA-seq portal for analysis of sequencing experiments

Kuksa, Pavel P, Amlie-Wolf, Alexandre, Katanić, Živadin, Valladares, Otto, Wang, Li-San, Leung, Yuk Yee

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 1.84 MB

english, 2018

17

INFERNO: inferring the molecular mechanisms of noncoding genetic variants

Amlie-Wolf, Alexandre, Tang, Mitchell, Mlynarski, Elisabeth E, Kuksa, Pavel P, Valladares, Otto, Katanic, Zivadin, Tsuang, Debby, Brown, Christopher D, Schellenberg, Gerard D, Wang, Li-San

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 817 KB

english, 2018

18

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

Kuksa, Pavel P, Amlie-Wolf, Alexandre, Katanić, Živadin, Valladares, Otto, Wang, Li-San, Leung, Yuk Yee, Kelso, Janet

Journal:

Year:

2018

Language:

english

File:

PDF, 1.17 MB

english, 2018

19

Optical and Electronic properties of amorphous Silicon Dioxide by single and double electron spectroscopy

Astašauskas, Vytautas, Bellissimo, Alessandra, Kuksa, Pavel, Tomastik, Christian, Kalbe, Henryk, Werner, Wolfgang S.M.

Journal:

Journal of Electron Spectroscopy and Related Phenomena

Year:

2019

Language:

english

File:

PDF, 1.13 MB

english, 2019

20

[Society for Industrial and Applied Mathematics Proceedings of the 2012 SIAM International Conference on Data Mining - ()] Proceedings of the 2012 SIAM International Conference on Data Mining - Generalized Similarity Kernels for Efficient Sequence Classification

P. Kuksa, Pavel, Khan, Imdadullah, Pavlovic, Vladimir

Language:

english

File:

PDF, 497 KB

english

21

HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

Kuksa, Pavel P, Amlie-Wolf, Alexandre, Hwang, Yih-Chii, Valladares, Otto, Gregory, Brian D, Wang, Li-San

Journal:

NAR Genomics and Bioinformatics

Year:

2020

File:

PDF, 3.20 MB

2020

22

HiPR: High-throughput Probabilistic RNA structure inference

Kuksa, Pavel P., Li, Fan, Kannan, Sampath, Gregory, Brian D., Yee Leung, Yuk, Wang, Li-San

Journal:

Computational and Structural Biotechnology Journal

Year:

2020

File:

PDF, 1.09 MB

2020

23

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants

Kuksa, Pavel P, Lee, Chien-Yueh, Amlie-Wolf, Alexandre, Gangadharan, Prabhakaran, Mlynarski, Elizabeth E, Chou, Yi-Fan, Lin, Han-Jen, Issen, Heather, Greenfest-Allen, Emily, Valladares, Otto, Leung, Y

Journal:

Year:

2020

File:

PDF, 191 KB

2020