Barcelona skyline with the Sagrada Família, Torre Glòries and the Mediterranean Sea
Portrait of Francesco Craighero

Francesco Craighero

Senior Computational BiologistCNAG, Barcelona

I am a Senior Computational Biologist in Holger Heyn’s Single Cell Genomics Group at CNAG, Barcelona, working on interpretable machine learning for computational biology.

Before joining CNAG, I was at EPFL, working with the Signal Processing Laboratory 2 (LTS2) and the Naef Lab. I obtained my PhD in Computer Science at the University of Milano-Bicocca. During my PhD, I spent six months as a visiting researcher at IBM Research Zurich.

news

“BIO-Distiller: Boosting Supervised Baselines by Distilling Biological Foundation Models” was presented at the MLGenX workshop at ICLR 2026.
Our inflammation atlas is out in Nature Medicine
“Conditional deep learning model reveals translation elongation determinants during amino acid deprivation” has been accepted by Communications Biology.
archive (2)
“Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations” has been accepted as a Spotlight poster at the MLCB conference, held in Seattle.
“Beyond fine-tuning: LoRA modules boost near-OOD detection and LLM security” won the Best Extended Abstract Award at DLSP 2024, held in San Francisco.

selected publications

  1. Nat. Med.

    Interpretable inflammation landscape of circulating immune cells

    Laura Jiménez-Gracia, Davide Maspero, Sergio Aguilar-Fernández, Francesco Craighero, Maria Boulougouri, Max Ruiz, Domenica Marchese, Ginevra Caratù, Jose Liñares-Blanco, Miren Berasategi, Ricardo O. Ramirez Flores, Angela Sanzo-Machuca, Ana M. Corraliza, Hoang A. Tran, Rachelly Normand, Jacquelyn Nestor, Yourae Hong, Tessa Kole, Petra Van Der Velde, Frederique Alleblas, Flaminia Pedretti, Adrià Aterido, Martin Banchero, German Soriano, Eva Román, Maarten Van Den Berge, Azucena Salas, Jose Manuel Carrascosa, Antonio Fernández Nebro, Eugeni Domènech, Juan D. Cañete, Jesús Tornero, Javier P. Gisbert, Ernest Choy, Giampiero Girolomoni, Britta Siegmund, Antonio Julià, Violeta Serra, Roberto Elosua, Sabine Tejpar, Silvia Vidal, Martijn C. Nawijn, Ivo Gut, Julio Saez-Rodriguez, Sara Marsal, Alexandra-Chloé Villani, Juan C. Nieto, and Holger Heyn
    Nature Medicine, 2026
    HTML DOI 
    @article{jimenez2026interpretable,
  title = {Interpretable inflammation landscape of circulating immune cells},
  author = {Jim{\'e}nez-Gracia, Laura and Maspero, Davide and Aguilar-Fern{\'a}ndez, Sergio and Craighero, Francesco and Boulougouri, Maria and Ruiz, Max and Marchese, Domenica and Carat{\`u}, Ginevra and Li{\~n}ares-Blanco, Jose and Berasategi, Miren and Ramirez Flores, Ricardo O. and Sanzo-Machuca, Angela and Corraliza, Ana M. and Tran, Hoang A. and Normand, Rachelly and Nestor, Jacquelyn and Hong, Yourae and Kole, Tessa and Van Der Velde, Petra and Alleblas, Frederique and Pedretti, Flaminia and Aterido, Adri{\`a} and Banchero, Martin and Soriano, German and Rom{\'a}n, Eva and Van Den Berge, Maarten and Salas, Azucena and Carrascosa, Jose Manuel and Fern{\'a}ndez Nebro, Antonio and Dom{\`e}nech, Eugeni and Ca{\~n}ete, Juan D. and Tornero, Jes{\'u}s and Gisbert, Javier P. and Choy, Ernest and Girolomoni, Giampiero and Siegmund, Britta and Juli{\`a}, Antonio and Serra, Violeta and Elosua, Roberto and Tejpar, Sabine and Vidal, Silvia and Nawijn, Martijn C. and Gut, Ivo and Saez-Rodriguez, Julio and Marsal, Sara and Villani, Alexandra-Chlo{\'e} and Nieto, Juan C. and Heyn, Holger},
  journal = {Nature Medicine},
  volume = {32},
  number = {2},
  pages = {633--644},
  year = {2026},
  month = feb,
  publisher = {Nature Publishing Group US},
  doi = {10.1038/s41591-025-04126-3}
}