{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T03:25:39Z","timestamp":1782962739443,"version":"3.54.5"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG013876"],"award-info":[{"award-number":["HG013876"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Nanopore sequencing measures ionic current as native DNA or RNA molecules move through a biological pore. The resulting ionic current changes are inferred into sequence by Oxford Nanopore Technologies\u2019 Dorado basecaller. These data permit direct analysis of nucleotide sequences and modifications. The Dorado basecaller also outputs a move-table that contains approximate mappings between ionic current signal and basecalled sequence. This ionic current information can be visualized at specific positions given the alignment between a read sequence and a reference sequence. We present CurrentView, a fast and user-friendly toolkit for reference-guided visualization of nanopore ionic current signals. CurrentView uses conventional sequence alignment and move-table information from BAM files and signal information from ONT POD5 files to extract and visualize ionic current traces at specific positions. The toolkit supports simultaneous comparison across multiple experimental conditions, computes summary statistics through kernel density estimation and histograms, and enables visual analysis of signal patterns associated with modifications or sequence context. Notably, CurrentView can visualize and analyze more than two conditions at once. It supports UMAP dimensionality reduction and Gaussian Mixture Model (GMM) clustering, enabling the identification of distinct signal populations across experimental groups. CurrentView is available as both a Python API and an exploratory interactive web application, allowing researchers to rapidly inspect ionic current patterns and compare conditions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CurrentView is fully open-source and available on GitHub https:\/\/github.com\/genometechlab\/currentview. The repository includes full documentation, an installation guide, usage instructions, and an example Jupyter notebook showing typical use cases similar to the one presented in the manuscript.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag161","type":"journal-article","created":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T11:42:15Z","timestamp":1775734935000},"source":"Crossref","is-referenced-by-count":4,"title":["CurrentView: a tool for visualization and comparison of nanopore ionic current signals"],"prefix":"10.1093","volume":"42","author":[{"given":"Pooria","family":"Daneshvar Kakhaki","sequence":"first","affiliation":[{"name":"Northeastern University, Department of Electrical & Computer Engineering, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neda","family":"Ghohabi Esfahani","sequence":"additional","affiliation":[{"name":"Northeastern University, Department of Bioengineering, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart","family":"Akeson","sequence":"additional","affiliation":[{"name":"Northeastern University, Department of Bioengineering, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4571-3982","authenticated-orcid":false,"given":"Miten","family":"Jain","sequence":"additional","affiliation":[{"name":"Northeastern University, Department of Bioengineering, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]},{"name":"Northeastern University, Department of Physics, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]},{"name":"Northeastern University, Khoury College of Computer Sciences, 360 Huntington Ave, Boston, MA 02115,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,10]]},"reference":[{"key":"2026042409463024300_btag161-B1","author":"Akeson","year":"2025"},{"key":"2026042409463024300_btag161-B2","author":"Esfahani","year":"2025"},{"key":"2026042409463024300_btag161-B3","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1186\/s12859-020-03697-x","article-title":"GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis","volume":"21","author":"Gamaarachchi","year":"2020","journal-title":"BMC Bioinf"},{"key":"2026042409463024300_btag161-B4","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat Methods"},{"key":"2026042409463024300_btag161-B5","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1038\/s41592-022-01666-1","article-title":"Detection of m6A from direct RNA sequencing using a multiple instance learning framework","volume":"19","author":"Hendra","year":"2022","journal-title":"Nat Methods"},{"key":"2026042409463024300_btag161-B6","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/s41592-022-01633-w","article-title":"Advances in nanopore direct RNA sequencing","volume":"19","author":"Jain","year":"2022","journal-title":"Nat Methods"},{"key":"2026042409463024300_btag161-B7","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nbt.2950","article-title":"Decoding long nanopore sequencing reads of natural DNA","volume":"32","author":"Laszlo","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2026042409463024300_btag161-B8","doi-asserted-by":"crossref","first-page":"7198","DOI":"10.1038\/s41467-021-27393-3","article-title":"RNA modifications detection by comparative nanopore direct RNA sequencing","volume":"12","author":"Leger","year":"2021","journal-title":"Nat Commun"},{"key":"2026042409463024300_btag161-B9","article-title":"Leveraging basecaller\u2019s move table to generate a lightweight k-mer model for nanopore sequencing analysis","volume":"41","author":"Samarakoon","year":"2025","journal-title":"Bioinf"},{"key":"2026042409463024300_btag161-B10","author":"Tzadikario","year":"2025"},{"key":"2026042409463024300_btag161-B11","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2026042409463024300_btag161-B12","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1038\/s41592-019-0617-2","article-title":"Nanopore native RNA sequencing of a human poly(A) transcriptome","volume":"16","author":"Workman","year":"2019","journal-title":"Nat Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag161\/68024725\/btag161.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/4\/btag161\/68024725\/btag161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/4\/btag161\/68024725\/btag161.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T13:46:38Z","timestamp":1777038398000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag161\/8651103"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,4]]},"references-count":12,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag161","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,4]]},"published":{"date-parts":[[2026,4]]},"article-number":"btag161"}}