| Title | Nonlinear physics opens a new paradigm for accurate transcription start site prediction |
|---|---|
| Authors | Barbero-Aparicio J.A. , Cuesta-Lopez S. , García-Osorio C.I. , PÉREZ RODRÍGUEZ, JAVIER, García-Pedrajas N. |
| External publication | No |
| Means | BMC Bioinformatics |
| Scope | Article |
| Nature | Científica |
| JCR Quartile | 2 |
| SJR Quartile | 1 |
| JCR Impact | 3 |
| SJR Impact | 1.1 |
| Web | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85145346819&doi=10.1186%2fs12859-022-05129-4&partnerID=40&md5=e9d8e285d65ceec8777de3351dceb7f0 |
| Publication date | 30/12/2022 |
| ISI | 000906191700001 |
| Scopus Id | 2-s2.0-85145346819 |
| DOI | 10.1186/s12859-022-05129-4 |
| Abstract | 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 learning (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. © 2022, The Author(s). |
| Keywords | Forecasting; Machine learning; Statistical mechanics; DNA breathing; DNA modeling; Machine learning models; Machine-learning; Nonlinear physics; Physical modelling; String Kernel; SVM; Transcription start site; Transcription start site prediction; DNA; article; bioinformatics; breathing; kernel method; machine learning; physical model; physics; prediction; transcription initiation site; validity; biology; procedures; promoter region; transcription initiation site; DNA; Computational Biology; DNA; Promoter Regions, Genetic; Transcription Initiation Site |
| Universidad Loyola members |
|