Preprints

• Sweetwater: An interpretable and adaptive autoencoder for efficient tissue deconvolution
  Under review at Nucleic Acid Research, 2023
  Jesús de la Fuente^*, Naroa Legarra^*, Aintzane Diaz-Mazkiaran, Guillermo Serrano, Irene Marín-Goñi, Markel Benito Sendin, Ana García Osta, Krishna R. Kalari, Carlos Fernandez-Granda, Idoia Ochoa, Mikel Hernaez

• Characterization of Transcriptional Alterations Leading to Aberrant Myeloid Differentiation in Myelodysplastic Syndromes
  ASH conference, Blood, 2022
  Aintzane Diaz-Mazkiaran, Jesús De la Fuente, Guillermo Serrano, Paula Garcia-Olloqui, Nerea Berastegui, Marina Ainciburu, Ana Alfonso Pierola, Amaia Vilas-Zornoza, Patxi San Martin-Uriz, Jose Maria Lamo De Espinosa, Mikel San Julián, Pamela Acha, Francesc Solé, Tamara Jimenez, Félix López Cadenas, Maria Diez-Campelo, Antonieta Molero, Maria Julia Montoro, David Valcarcel, Teresa Ezponda, Mikel Hernáez, Felipe Prosper

Publications

• Interpretable Causal Representation Learning for Biological Data in the Pathway Space
  ICLR 2025, Poster
  Jesús de la Fuente Cedeño, Robert Lehmann, Carlos Ruiz-Arenas, Irene Marín-Goñi, Jan Voges, Xabier Martinez de Morentin, David Gomez-Cabrero, Idoia Ochoa, Jesper Tegnér, Vincenzo Lagani, Mikel Hernaez

• Towards a more inductive world for drug repurposing approaches
  Nature Machine Intelligence, 2024
  Jesús de la Fuente^*, Guillermo Serrano^*, Uxía Veleiro^*, Mikel Casals, Laura Vera, Marija Pizurica, Nuria Gómez-Cebrián, Leonor Puchades-Carrasco, Antonio Pineda-Lucena, Idoia Ochoa, Silve Vicent, Olivier Gevaert, Mikel Hernaez

• Application of graph models to the identification of transcriptomic oncometabolic pathways in human hepatocellular carcinoma
  Biomolecules, 2024
  Sergio Barace, Eva Santamaria, Stefany Infante, Sara Arcelus, Jesus De La Fuente, Enrique Goni, Ibon Tamayo, Idoia Ochoa, Miguel Sogbe, Bruno Sangro, Mikel Hernaez, Matias A Avila, Josepmaria Argemi

• GeNNius: An ultrafast drug–target interaction inference method based on graph neural networks
  Bioinformatics, 2024
  Uxía Veleiro, Jesús de la Fuente, Guillermo Serrano, Marija Pizurica, Mikel Casals, Antonio Pineda-Lucena, Idoia Ochoa, Olivier Gevaert, Mikel Hernaez

• Bayesian machine learning enables transcriptional rewiring
  Cancer Research, 2023
  Charles Blatti^*, Jesús de la Fuente^*, Huanyao Gao, Irene Marín-Goñi, Zikun Chen, Sihai D Zhao, Winston Tan, Richard Weinshilboum, Krishna R Kalari, Liewei Wang, Mikel Hernaez

• Suitability of machine learning for atrophy and fibrosis development in neovascular age-related macular degeneration
  Acta Ophthalmologica, 2023
  Jesús de la Fuente, Sara Llorente-Gonzalez, Patricia Fernandez-Robredo, Maria Hernandez, Alfredo Garcia-Layana, Idoia Ochoa, Sergio Recalde, Spanish AMD Group