{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:03:03Z","timestamp":1775325783748,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,4,6]],"date-time":"2018-04-06T00:00:00Z","timestamp":1522972800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Convolutional neural networks (CNNs) have been shown to perform exceptionally well in a variety of tasks, including biological sequence classification. Available implementations, however, are usually optimized for a particular task and difficult to reuse. To enable researchers to utilize these networks more easily, we implemented pysster, a Python package for training CNNs on biological sequence data. Sequences are classified by learning sequence and structure motifs and the package offers an automated hyper-parameter optimization procedure and options to visualize learned motifs along with information about their positional and class enrichment. The package runs seamlessly on CPU and GPU and provides a simple interface to train and evaluate a network with a handful lines of code. Using an RNA A-to-I editing dataset and cross-linking immunoprecipitation (CLIP)-seq binding site sequences, we demonstrate that pysster classifies sequences with higher accuracy than previous methods, such as GraphProt or ssHMM, and is able to recover known sequence and structure motifs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>pysster is freely available at https:\/\/github.com\/budach\/pysster.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty222","type":"journal-article","created":{"date-parts":[[2018,4,5]],"date-time":"2018-04-05T07:10:19Z","timestamp":1522912219000},"page":"3035-3037","source":"Crossref","is-referenced-by-count":95,"title":["pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks"],"prefix":"10.1093","volume":"34","author":[{"given":"Stefan","family":"Budach","sequence":"first","affiliation":[{"name":"Otto-Warburg-Laboratory, RNA Bioinformatics, Max Planck Institute for Molecular Genetics, Berlin, Germany"}]},{"given":"Annalisa","family":"Marsico","sequence":"additional","affiliation":[{"name":"Otto-Warburg-Laboratory, RNA Bioinformatics, Max Planck Institute for Molecular Genetics, Berlin, Germany"},{"name":"Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,4,6]]},"reference":[{"key":"2023061313381352500_bty222-B1","author":"Abadi","year":"2016"},{"key":"2023061313381352500_bty222-B2","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. 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