Introduction to Machine Learning for Pharmacology (Videos):

Tutorial Feature Selection in Gene Expression Omnibus Dataset

Github:

Tutorial GSE

Key Group Publications:

Rojas-Velazquez, D., Kidwai, S., Kraneveld, A. D., Tonda, A., Oberski, D., Garssen, J., & Lopez-Rincon, A. (2024). Methodology for biomarker discovery with reproducibility in microbiome data using machine learning. BMC Bioinformatics, 25(1). https://doi.org/10.1186/s12859-024-05639-3

Peralta-Marzal, L. N., Rojas-Velazquez, D., Rigters, D., Prince, N., Garssen, J., Kraneveld, A. D., Perez-Pardo, P., & Lopez-Rincon, A. (2024). A robust microbiome signature for autism spectrum disorder across different studies using machine learning. Scientific Reports, 14(1), 814. https://doi.org/10.1038/s41598-023-50601-7

Kidwai, S., Barbiero, P., Meijerman, I., Tonda, A., Perez-Pardo, P., Lio, P., van der Maitland-Zee, A. H., Oberski, D. L., Kraneveld, A. D., & Lopez-Rincon, A. (2023). A robust mRNA signature obtained via recursive ensemble feature selection predicts the responsiveness of omalizumab in moderate-to-severe asthma. Clinical and Translational Allergy, 13(11), e12306. Article e12306. https://doi.org/10.1002/clt2.12306

Lopez-Rincon, A., Tonda, A., Elati, M., Schwander, O., Piwowarski, B., & Gallinari, P. (2018). Evolutionary optimization of convolutional neural networks for cancer miRNA biomarkers classification. Applied Soft Computing Journal, 65, 91-100. https://doi.org/10.1016/j.asoc.2017.12.036

Lopez-Rincon, A., Martinez-Archundia, M., Martinez-Ruiz, G. U., Schoenhuth, A., & Tonda, A. (2019). Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics, 20(1), Article 480. https://doi.org/10.1186/s12859-019-3050-8

Lopez-Rincon, A., Mendoza-Maldonado, L., Martinez-Archundia, M., Schönhuth, A., Kraneveld, A. D., Garssen, J., & Tonda, A. (2020). Machine learning-based ensemble recursive feature selection of circulating mirnas for cancer tumor classification. Cancers, 12(7), 1-27. Article 1785. https://doi.org/10.3390/cancers12071785

Metselaar, P. I., Mendoza-Maldonado, L., Li Yim, A. Y. F., Abarkan, I., Henneman, P., te Velde, A. A., Schönhuth, A., Bosch, J. A., Kraneveld, A. D., & Lopez-Rincon, A. (2021). Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. Scientific Reports, 11(1), 1-11. Article 4541. https://doi.org/10.1038/s41598-021-83660-9