2026-06-01T15:46:08Zhttps://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 819 500 0000-0002-3269-0806 Cuesta López, Santiago 133 600 0000-0002-7401-3889 García Osorio, César 212 600 0000-0002-1206-1084 Pérez-Rodríguez, Javier 8947c154-0779-4026-afe0-763d5303e772 600 García-Pedrajas, Nicolás 54c5f778-92ea-4204-a74a-dd5efd6c35d3 600 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 THUMBNAIL Barbero-bmcb_2022.pdf.jpg Barbero-bmcb_2022.pdf.jpg IM Thumbnail image/jpeg 4810 https://riubu.ubu.es/bitstream/10259/7337/4/Barbero-bmcb_2022.pdf.jpg 8bbb22ad5a12732d68f52835aa0d09bd MD5 4 LICENSE license.txt license.txt text/plain; charset=utf-8 999 https://riubu.ubu.es/bitstream/10259/7337/3/license.txt b295bcbce42e2caabeb0c623d3860c06 MD5 3 CC-LICENSE license_rdf license_rdf application/rdf+xml; charset=utf-8 908 https://riubu.ubu.es/bitstream/10259/7337/2/license_rdf 0175ea4a2d4caec4bbcc37e300941108 MD5 2 ORIGINAL Barbero-bmcb_2022.pdf Barbero-bmcb_2022.pdf application/pdf 2279393 https://riubu.ubu.es/bitstream/10259/7337/1/Barbero-bmcb_2022.pdf 000df28d180fa9d150235f98102a5087 MD5 1 10259/7337 oai:riubu.ubu.es:10259/7337 2023-03-21 10:16:00.126 Repositorio Institucional de la Universidad de Burgos bubrep@ubu.es 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