{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T08:14:51Z","timestamp":1774599291484,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,4,25]],"date-time":"2025-04-25T00:00:00Z","timestamp":1745539200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Differentiable folding is an emerging paradigm for RNA design in which a probabilistic sequence representation is optimized via gradient descent. However, given the significant memory overhead of differentiating the expected partition function over all RNA sequences, the existing proof-of-concept algorithm only scales to \u226450 nucleotides. We present JAX-RNAfold, an open-source software package for our drastically improved differentiable folding algorithm that scales to 1,250 nucleotides on a single GPU. Our software permits the natural inclusion of differentiable folding as a module in larger deep learning pipelines, as well as complex RNA design procedures such as mRNA design with flexible objective functions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>JAX-RNAfold is hosted on GitHub (https:\/\/github.com\/rkruegs123\/jax-rnafold) and can be installed locally as a Python package. All source code is also archived on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.15003072).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf203","type":"journal-article","created":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T06:46:24Z","timestamp":1745477184000},"source":"Crossref","is-referenced-by-count":8,"title":["JAX-RNAfold: scalable differentiable folding"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6856-0248","authenticated-orcid":false,"given":"Ryan K","family":"Krueger","sequence":"first","affiliation":[{"name":"School of Engineering and Applied Sciences, Harvard University , Cambridge, MA 02138,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9114-7339","authenticated-orcid":false,"given":"Max","family":"Ward","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Software Engineering, The University of Western Australia , Crawley, WA 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