2026-06-19T12:25:07Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/73372023-03-21T09:16:00Zcom_10259_4219com_10259_5086com_10259_2604col_10259_4220

Barbero Aparicio, José Antonio Cuesta López, Santiago García Osorio, César Pérez-Rodríguez, Javier García-Pedrajas, Nicolás 2023-01-26T12:32:03Z 2023-01-26T12:32:03Z 2022-12 http://hdl.handle.net/10259/7337 10.1186/s12859-022-05129-4 1471-2105 There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learn‑ ing (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors. This work has been supported by the Junta de Andalucia under project UCO1264182 and by the Ministry of Science, Innovation and Universities under project PID2019-109481GB-I00/AEI/q10.13039/501100011033, in both cases co-financed through European Union FEDER funds. José A. Barbero-Aparicio is founded through a predoctoral grant from the University of Burgos. application/pdf eng Springer Nature BMC Bioinformatics. 2022, V. 23, n. 1, 565 https://doi.org/10.1186/s12859-022-05129-4 info:eu-repo/grantAgreement/Junta de Andalucía//UCO-1264182/ info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-109481GB-I00/ES/NUEVA APROXIMACION A LA CONSTRUCCION DE ENJAMBRES PARA APRENDIZAJE MULTI-ETIQUETA: APLICACION A LA QUEMINFORMATICA Y LA BIOINFORMATICA/ Atribución 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess DNA modelling DNA breathing Machine learning TSS prediction SVM String kernels Informática Computer science Nonlinear physics opens a new paradigm for accurate transcription start site prediction info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion BMC Bioinformatics 23 1