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29 results on '"Hoinka, Jan"'

1. AptaBlocks Online - A web-based toolkit for the in-silico assembly of RNA complexes

Author

Hoinka, Jan, Wang, Yijie, and Przytycka, Teresa M.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Summary: The AptaBlocks Web Interface is focused on providing graphical, intuitive, and platform independent access to AptaBlocks, an experimentally validated algorithmic approach for the in-silico design of oligonucleotide sticky bridges. The availability of AptaBlocks online to the nucleic acid research community at large makes this software a highly effective tool for accelerating the design and development of novel oligonucleotide based drugs and other biotechnologies. Availability: The AptaBlocks Web Interface is freely available at www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi\#aptablocks

Published
2019

3. AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments

Author

Dao, Phuong, Hoinka, Jan, Wang, Yijie, Takahashi, Mayumi, Zhou, Jiehua, Costa, Fabrizio, Rossi, John, Burnett, John, Backofen, Rolf, and Przytycka, Teresa M.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science
Abstract

Aptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identified in vitro via the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol. SELEX selects binders through an iterative process that, starting from a pool of random ssDNA/RNA sequences, amplifies target-affine species through a series of selection cycles. HT-SELEX, which combines SELEX with high throughput sequencing, has recently transformed aptamer development and has opened the field to even more applications. HT-SELEX is capable of generating over half a billion data points, challenging computational scientists with the task of identifying aptamer properties such as sequence structure motifs that determine binding. While currently available motif finding approaches suggest partial solutions to this question, none possess the generality or scalability required for HT-SELEX data, and they do not take advantage of important properties of the experimental procedure. We present AptaTRACE, a novel approach for the identification of sequence-structure binding motifs in HT-SELEX derived aptamers. Our approach leverages the experimental design of the SELEX protocol and identifies sequence-structure motifs that show a signature of selection. Because of its unique approach, AptaTRACE can uncover motifs even when these are present in only a minuscule fraction of the pool. Due to these features, our method can help to reduce the number of selection cycles required to produce aptamers with the desired properties, thus reducing cost and time of this rather expensive procedure. The performance of the method on simulated and real data indicates that AptaTRACE can detect sequence-structure motifs even in highly challenging data., Comment: This paper was selected for oral presentation at RECOMB 2016 and an abstract is published in the conference proceedings

Published
2016

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

Author

Dao, Phuong, Hoinka, Jan, Takahashi, Mayumi, Zhou, Jiehua, Ho, Michelle, Wang, Yijie, Costa, Fabrizio, Rossi, John J, Backofen, Rolf, Burnett, John, and Przytycka, Teresa M

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Bioengineering, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Aptamers, Nucleotide, Nucleotide Motifs, RNA, SELEX Aptamer Technique, Sequence Analysis, RNA, Biochemistry and cell biology
Abstract

Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX), but scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that, because of this, it could lower HT-SELEX cost and time by reducing the number of selection cycles required.

Published
2016

5. AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application

Author

Hoinka, Jan, Berezhnoy, Alexey, Sauna, Zuben E., Gilboa, Eli, Przytycka, Teresa M., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, and Sharan, Roded, editor

Published
2014
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8. Immunotherapy using IgE or CAR T cells for cancers expressing the tumor antigen SLC3A2

Author

Pellizzari, Giulia, primary, Martinez, Olivier, additional, Crescioli, Silvia, additional, Page, Robert, additional, Di Meo, Ashley, additional, Mele, Silvia, additional, Chiaruttini, Giulia, additional, Hoinka, Jan, additional, Batruch, Ihor, additional, Prassas, Ioannis, additional, Grandits, Melanie, additional, López-Abente, Jacobo, additional, Bugallo-Blanco, Eva, additional, Ward, Malcolm, additional, Bax, Heather J, additional, French, Elise, additional, Cheung, Anthony, additional, Lombardi, Sara, additional, Figini, Mariangela, additional, Lacy, Katie E, additional, Diamandis, Eleftherios P, additional, Josephs, Debra H, additional, Spicer, James, additional, Papa, Sophie, additional, and Karagiannis, Sophia N, additional

Published
2021
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9. DNA Aptamers for Early Detection of Ebolavirus

Author

Banerjee, Soma, primary, Hoinka, Jan, additional, Gosai, Agnivo, additional, Zhu, Zhichen, additional, Devarakonda, Sivaranjani, additional, Geekiyanage, Charith, additional, Shubham, Shambhavi, additional, Lennemann, Nicholas, additional, Dillard, Jake, additional, Ruggio, Natalie, additional, Przytycka, Teresa, additional, Maury, Wendy, additional, Shrotriya, Pranav, additional, and Nilsen‐Hamilton, Marit, additional

Published
2021
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28. Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides viamRNA Display

Author

Hacker, David E., Hoinka, Jan, Iqbal, Emil S., Przytycka, Teresa M., and Hartman, Matthew C. T.

Abstract

Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitroselections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin). Both selections resulted in peptides with mid-nanomolar affinity, and the bicyclic selection yielded a peptide with remarkable protease resistance.

Published
2017
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29. The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE.

Author

Hoinka J and Przytycka TM

Subjects
Computational Biology methods, High-Throughput Nucleotide Sequencing, Software, Aptamers, Nucleotide genetics, Aptamers, Nucleotide metabolism, SELEX Aptamer Technique methods
Abstract

Next-generation systematic evolution of ligands by exponential enrichment approaches consistently combine the experimental protocol with high-throughput sequencing after each round of selection. This extension, known as HT-SELEX, results in a vast amount of raw sequencing data that requires tailored bioinformatics approaches to efficiently process and analyze these reads. Here, we present a step-by-step walkthrough of AptaSUITE, a previously published, open-source, and platform-independent software collection of peer-reviewed bioinformatics tools for HT-SELEX data, integrated into a convenient and efficient graphical user interface. We highlight AptaSUITE's main components and illustrate their utility for a variety of usage scenarios. These include, but are not limited to, computational solutions for data preprocessing such as demultiplexing and quality control, aptamer candidate identification, as well as binding motif elucidation. Taken together, AptaSUITE comprises a complete bioinformatics solution for HT-SELEX data analysis while providing real-time, intuitive, and graphical access to the aptamer information., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2023
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