Publications by authors named "Jan Hoinka"

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The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE.
Jan Hoinka, Teresa M Przytycka

Methods Mol Biol· September 2022

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RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer.
Damian Wojtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka

Cell Syst· October 2021

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Immunotherapy using IgE or CAR T cells for cancers expressing the tumor antigen SLC3A2.
Giulia Pellizzari, Olivier Martinez, Silvia Crescioli, Robert Page, Ashley Di Meo, Jan Hoinka

J Immunother Cancer· June 2021

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Direct, Competitive Comparison of Linear, Monocyclic, and Bicyclic Libraries Using mRNA Display.
David E Hacker, Nicolas A Abrigo, Jan Hoinka, Stacie L Richardson, Teresa M Przytycka

ACS Comb Sci· June 2020

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AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges.
Jan Hoinka, Yijie Wang, Teresa M Przytycka

J Comput Biol· March 2020

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Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.
Soumitra Pal, Jan Hoinka, Teresa M Przytycka

Nucleic Acids Res· July 2019

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Subpopulation Detection and Their Comparative Analysis across Single-Cell Experiments with scPopCorn.
Yijie Wang, Jan Hoinka, Teresa M Przytycka

Cell Syst· June 2019

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AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.
Yijie Wang, Jan Hoinka, Yong Liang, Tomasz Adamus, Piotr Swiderski

Nucleic Acids Res· September 2018

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A 2'FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein.
Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A Dillard

Sci Rep· August 2018

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AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments.
Jan Hoinka, Rolf Backofen, Teresa M Przytycka

Mol Ther Nucleic Acids· June 2018

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Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display.
David E Hacker, Jan Hoinka, Emil S Iqbal, Teresa M Przytycka, Matthew C T Hartman

ACS Chem Biol· March 2017

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AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data.
Jan Hoinka, Teresa Przytycka

Methods· August 2016

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AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.
Phuong Dao, Jan Hoinka, Mayumi Takahashi, Jiehua Zhou, Michelle Ho

Cell Syst· July 2016

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AptaGUI-A Graphical User Interface for the Efficient Analysis of HT-SELEX Data.
Jan Hoinka, Phuong Dao, Teresa M Przytycka

Mol Ther Nucleic Acids· October 2015

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Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.
Jan Hoinka, Alexey Berezhnoy, Phuong Dao, Zuben E Sauna, Eli Gilboa

Nucleic Acids Res· July 2015

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Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment.
Agata Levay, Randall Brenneman, Jan Hoinka, David Sant, Marco Cardone

Nucleic Acids Res· July 2015

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AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application.
Jan Hoinka, Alexey Berezhnoy, Zuben E Sauna, Eli Gilboa, Teresa M Przytycka

Res Comput Mol Biol· January 2014

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Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.
Jan Hoinka, Elena Zotenko, Adam Friedman, Zuben E Sauna, Teresa M Przytycka

Bioinformatics· June 2012

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