{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T12:09:14Z","timestamp":1761566954462,"version":"build-2065373602"},"reference-count":70,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T00:00:00Z","timestamp":1758931200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Singapore Ministry of Education through the Academic Research Fund Tier 1","award":["RG140\/22"],"award-info":[{"award-number":["RG140\/22"]}]},{"name":"Academic Research Fund Tier 2","award":["MOE-T2EP50223-0014"],"award-info":[{"award-number":["MOE-T2EP50223-0014"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>G-quadruplexes (G4s) are non-canonical nucleic acid structures formed in guanine-rich regions that modulate gene regulation and genomic stability. The thermodynamic stability of G4s directly influences their biological functions and potential as therapeutic targets. However, current quantitative frameworks for predicting G4 stability rely on predetermined structural features, limiting their effectiveness for diverse G4 topologies, and fail to account for environmental factors such as ion concentration and pH that significantly modulate G4 stability in cellular contexts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present G4STAB, a multi-input deep learning neural network that accurately predicts DNA G4 melting temperatures based on sequence features, salt concentration, and pH. Trained on 2382 diverse DNA G4 sequences, our model achieves high accuracy (R\u20022=0.8) without relying on predetermined G4 structural features. G4STAB successfully captures established G4 stability determinants and proposes previously unobserved sequence\u2013stability relationships. Analysis of 391\u00a0502 experimentally validated G4s reveals that cancer-like ionic environments alter G4 stability profiles, with a 13.5-fold increase in the number of structures exhibiting physiological melting temperatures (36\u201342\u00b0C). These findings suggest systematic genomic patterns in G4 stability responses across chromosomes and gene types.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>G4STAB is available at https:\/\/github.com\/donn-liew\/G4STAB; G4STAB web database interface is available at https:\/\/donn-liew.github.io\/g4stab-web-database\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf545","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T12:04:54Z","timestamp":1758801894000},"source":"Crossref","is-referenced-by-count":0,"title":["G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration"],"prefix":"10.1093","volume":"41","author":[{"given":"Donn","family":"Liew","sequence":"first","affiliation":[{"name":"Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371,","place":["Singapore"]}]},{"given":"Akesha Dinuli","family":"Dharmatilleke","sequence":"additional","affiliation":[{"name":"Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371,","place":["Singapore"]}]},{"given":"Edwin","family":"See","sequence":"additional","affiliation":[{"name":"Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371,","place":["Singapore"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4583-4071","authenticated-orcid":false,"given":"Ee Hou","family":"Yong","sequence":"additional","affiliation":[{"name":"Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 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