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Items: 11

1.

A 2'FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein.

Shubham S, Hoinka J, Banerjee S, Swanson E, Dillard JA, Lennemann NJ, Przytycka TM, Maury W, Nilsen-Hamilton M.

Sci Rep. 2018 Aug 17;8(1):12373. doi: 10.1038/s41598-018-30590-8.

2.

AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.

Wang Y, Hoinka J, Liang Y, Adamus T, Swiderski P, Przytycka TM.

Nucleic Acids Res. 2018 Sep 19;46(16):8133-8142. doi: 10.1093/nar/gky577.

3.

AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments.

Hoinka J, Backofen R, Przytycka TM.

Mol Ther Nucleic Acids. 2018 Jun 1;11:515-517. doi: 10.1016/j.omtn.2018.04.006. Epub 2018 Apr 22. No abstract available.

4.

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display.

Hacker DE, Hoinka J, Iqbal ES, Przytycka TM, Hartman MC.

ACS Chem Biol. 2017 Mar 17;12(3):795-804. doi: 10.1021/acschembio.6b01006. Epub 2017 Feb 1.

5.

AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.

Dao P, Hoinka J, Takahashi M, Zhou J, Ho M, Wang Y, Costa F, Rossi JJ, Backofen R, Burnett J, Przytycka TM.

Cell Syst. 2016 Jul;3(1):62-70. doi: 10.1016/j.cels.2016.07.003.

6.

AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data.

Hoinka J, Przytycka T.

Methods. 2016 Aug 15;106:82-5. doi: 10.1016/j.ymeth.2016.04.011. Epub 2016 Apr 11.

PMID:
27080809
7.

AptaGUI-A Graphical User Interface for the Efficient Analysis of HT-SELEX Data.

Hoinka J, Dao P, Przytycka TM.

Mol Ther Nucleic Acids. 2015 Oct 13;4:e257. doi: 10.1038/mtna.2015.26. No abstract available.

8.

Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment.

Levay A, Brenneman R, Hoinka J, Sant D, Cardone M, Trinchieri G, Przytycka TM, Berezhnoy A.

Nucleic Acids Res. 2015 Jul 13;43(12):e82. doi: 10.1093/nar/gkv534. Epub 2015 May 24.

9.

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.

Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM.

Nucleic Acids Res. 2015 Jul 13;43(12):5699-707. doi: 10.1093/nar/gkv308. Epub 2015 Apr 13.

10.

AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application.

Hoinka J, Berezhnoy A, Sauna ZE, Gilboa E, Przytycka TM.

Res Comput Mol Biol. 2014;8394:115-128.

11.

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.

Hoinka J, Zotenko E, Friedman A, Sauna ZE, Przytycka TM.

Bioinformatics. 2012 Jun 15;28(12):i215-23. doi: 10.1093/bioinformatics/bts210.

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