Kuksa PP - Search Results

1

DASHR: database of small human noncoding RNAs.

Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. Leung YY, et al. Among authors: kuksa pp. Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. doi: 10.1093/nar/gkv1188. Epub 2015 Nov 8. Nucleic Acids Res. 2016. PMID: 26553799 Free PMC article.

2

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. Hwang YC, et al. Among authors: kuksa pp. Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4. Bioinformatics. 2015. PMID: 25480377 Free PMC article.

3

Transcriptome-wide measurement of plant RNA secondary structure.

Foley SW, Vandivier LE, Kuksa PP, Gregory BD. Foley SW, et al. Among authors: kuksa pp. Curr Opin Plant Biol. 2015 Oct;27:36-43. doi: 10.1016/j.pbi.2015.05.021. Epub 2015 Jun 26. Curr Opin Plant Biol. 2015. PMID: 26119389 Free PMC article. Review.

4

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

Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang LS, Gregory BD. Vandivier LE, et al. Among authors: kuksa pp. Plant Cell. 2015 Nov;27(11):3024-37. doi: 10.1105/tpc.15.00591. Epub 2015 Nov 11. Plant Cell. 2015. PMID: 26561561 Free PMC article.

5

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. Kuksa PP, et al. Methods Mol Biol. 2017;1562:211-229. doi: 10.1007/978-1-4939-6807-7_14. Methods Mol Biol. 2017. PMID: 28349463 Free PMC article.

6

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

Kuksa PP, Amlie-Wolf A, Katanic Ž, Valladares O, Wang LS, Leung YY. Kuksa PP, et al. Nucleic Acids Res. 2018 Jul 2;46(W1):W36-W42. doi: 10.1093/nar/gky330. Nucleic Acids Res. 2018. PMID: 29733404 Free PMC article.

7

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. Amlie-Wolf A, et al. Among authors: kuksa pp. Nucleic Acids Res. 2018 Sep 28;46(17):8740-8753. doi: 10.1093/nar/gky686. Nucleic Acids Res. 2018. PMID: 30113658 Free PMC article.

8

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

Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang LS, Leung YY. Kuksa PP, et al. Bioinformatics. 2019 Mar 15;35(6):1033-1039. doi: 10.1093/bioinformatics/bty709. Bioinformatics. 2019. PMID: 30668832 Free PMC article.

9

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

Kuksa PP, Amlie-Wolf A, Hwang YC, Valladares O, Gregory BD, Wang LS. Kuksa PP, et al. NAR Genom Bioinform. 2020 Jun;2(2):lqaa022. doi: 10.1093/nargab/lqaa022. Epub 2020 Mar 31. NAR Genom Bioinform. 2020. PMID: 32270138 Free PMC article.

10

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

Kuksa PP, Lee CY, Amlie-Wolf A, Gangadharan P, Mlynarski EE, Chou YF, Lin HJ, Issen H, Greenfest-Allen E, Valladares O, Leung YY, Wang LS. Kuksa PP, et al. Bioinformatics. 2020 Jun 1;36(12):3879-3881. doi: 10.1093/bioinformatics/btaa246. Bioinformatics. 2020. PMID: 32330239 Free PMC article.

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