Gundogdu P, Payá-Milans M, Alamo-Alvarez I, Nepomuceno-Chamorro IA, Dopazo J, Loucera C. Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder. Cham: Springer Nature Switzerland; 2023:62 - 77. doi:10.1007/978-3-031-42697-110.1007/978-3-031-42697-1_5.

Gundogdu P, Alamo I, Nepomuceno-Chamorro IA, Dopazo J, Loucera C. SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types. Biology (Basel). 2023;12(4). doi:10.3390/biology12040579.

Gundogdu P, Loucera C, Alamo-Alvarez I, Dopazo J, Nepomuceno I. Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. BioData Min. 2022;15(1):1. doi:10.1186/s13040-021-00285-4.