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Items: 10

1.

INFERNO: inferring the molecular mechanisms of noncoding genetic variants.

Amlie-Wolf A, Tang M, Mlynarski EE, Kuksa PP, Valladares O, Katanic Z, Tsuang D, Brown CD, Schellenberg GD, Wang LS.

Nucleic Acids Res. 2018 Sep 28;46(17):8740-8753. doi: 10.1093/nar/gky686.

2.

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

Kuksa PP, Amlie-Wolf A, Katanic Ž, Valladares O, Wang LS, Leung YY.

Nucleic Acids Res. 2018 Jul 2;46(W1):W36-W42. doi: 10.1093/nar/gky330.

3.

In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR.

Kuksa PP, Leung YY, Vandivier LE, Anderson Z, Gregory BD, Wang LS.

Methods Mol Biol. 2017;1562:211-229. doi: 10.1007/978-1-4939-6807-7_14.

PMID:
28349463
4.

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis.

Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang LS, Gregory BD.

Plant Cell. 2015 Nov;27(11):3024-37. doi: 10.1105/tpc.15.00591. Epub 2015 Nov 11.

5.

DASHR: database of small human noncoding RNAs.

Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS.

Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. doi: 10.1093/nar/gkv1188. Epub 2015 Nov 8.

6.

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

Kuksa PP, Min MR, Dugar R, Gerstein M.

Bioinformatics. 2015 Nov 15;31(22):3600-7. doi: 10.1093/bioinformatics/btv371. Epub 2015 Jul 23.

PMID:
26206306
7.

Transcriptome-wide measurement of plant RNA secondary structure.

Foley SW, Vandivier LE, Kuksa PP, Gregory BD.

Curr Opin Plant Biol. 2015 Oct;27:36-43. doi: 10.1016/j.pbi.2015.05.021. Epub 2015 Jun 26. Review.

8.

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS.

Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4.

9.

Biological sequence classification with multivariate string kernels.

Kuksa PP.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1201-10. doi: 10.1109/TCBB.2013.15.

PMID:
24384708
10.

Efficient motif finding algorithms for large-alphabet inputs.

Kuksa PP, Pavlovic V.

BMC Bioinformatics. 2010 Oct 26;11 Suppl 8:S1. doi: 10.1186/1471-2105-11-S8-S1.

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