Jan Hoinka
Jan Hoinka
National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda MD 20894
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Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery
J Hoinka, A Berezhnoy, P Dao, ZE Sauna, E Gilboa, TM Przytycka
Nucleic acids research 43 (12), 5699-5707, 2015
Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers
J Hoinka, E Zotenko, A Friedman, ZE Sauna, TM Przytycka
Bioinformatics 28 (12), i215-i223, 2012
Aptacluster–a method to cluster ht-selex aptamer pools and lessons from its application
J Hoinka, A Berezhnoy, ZE Sauna, E Gilboa, TM Przytycka
Research in Computational Molecular Biology: 18th Annual International …, 2014
Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment
A Levay, R Brenneman, J Hoinka, D Sant, M Cardone, G Trinchieri, ...
Nucleic acids research 43 (12), e82-e82, 2015
AptaSUITE: a full-featured bioinformatics framework for the comprehensive analysis of aptamers from HT-SELEX experiments
J Hoinka, R Backofen, TM Przytycka
Molecular Therapy-Nucleic Acids 11, 515-517, 2018
AptaTRACE elucidates RNA sequence-structure motifs from selection trends in HT-SELEX experiments
P Dao, J Hoinka, M Takahashi, J Zhou, M Ho, Y Wang, F Costa, JJ Rossi, ...
Cell systems 3 (1), 62-70, 2016
Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display
DE Hacker, J Hoinka, ES Iqbal, TM Przytycka, MCT Hartman
ACS chemical biology 12 (3), 795-804, 2017
A 2′ FY-RNA motif defines an aptamer for Ebolavirus secreted protein
S Shubham, J Hoinka, S Banerjee, E Swanson, JA Dillard, ...
Scientific reports 8 (1), 12373, 2018
AptaPLEX–A dedicated, multithreaded demultiplexer for HT-SELEX data
J Hoinka, T Przytycka
Methods 106, 82-85, 2016
Direct, competitive comparison of linear, monocyclic, and bicyclic libraries using mRNA display
DE Hacker, NA Abrigo, J Hoinka, SL Richardson, TM Przytycka, ...
ACS Combinatorial Science 22 (6), 306-310, 2020
AptaGUI—a graphical user interface for the efficient analysis of HT-SELEX data
J Hoinka, P Dao, TM Przytycka
Molecular Therapy-Nucleic Acids 4, 2015
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro
S Pal, J Hoinka, TM Przytycka
Nucleic acids research 47 (13), 6632-6641, 2019
Subpopulation detection and their comparative analysis across single-cell experiments with scPopCorn
Y Wang, J Hoinka, TM Przytycka
Cell systems 8 (6), 506-513. e5, 2019
AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems
Y Wang, J Hoinka, Y Liang, T Adamus, P Swiderski, TM Przytycka
Nucleic acids research 46 (16), 8133-8142, 2018
RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer
D Wojtowicz, J Hoinka, B Amgalan, YA Kim, TM Przytycka
Cell Systems 12 (10), 994-1003. e4, 2021
The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE
J Hoinka, TM Przytycka
Nucleic Acid Aptamers: Selection, Characterization, and Application, 73-83, 2022
DNA aptamers for early detection of ebolavirus
S Banerjee, J Hoinka, A Gosai, Z Zhu, S Devarakonda, C Geekiyanage, ...
The FASEB Journal 35, 2021
Embedding gene sets in low-dimensional space
J Hoinka, TM Przytycka
Nature Machine Intelligence 2 (7), 367-368, 2020
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro
S Pal, J Hoinka, TM Przytycka
BioRxiv, 413922, 2018
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
P Dao, J Hoinka, Y Wang, M Takahashi, J Zhou, F Costa, J Rossi, ...
arXiv preprint arXiv:1604.03081, 2016
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