Author

Ruben Emilio Jimenez Franco

Fundação Getulio VargasORCID 0000-0001-8577-351XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Research Focus:drug response / drug discovery· 1 Approach:machine learning (classical)· 1 Research Focus:perturbation response prediction· 1 Research Focus:protein design· 1 Assay:protein sequence· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Alberto PaccanaroiD· 2 shared Aldo GaleanoiD· 1 shared Dario MalchiodiiD· 1 shared Elena CasiraghiiD· 1 shared Emanuele CavalleriiD· 1 shared Emanuele SaittoiD· 1 shared Giorgio ValentiniiD· 1 shared M. NicoliniiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

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10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Alberto PaccanaroORCID

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2 papers

Recent·Most cited

BioinformaticsPLoS Computational BiologyPeer-reviewedOct 5, 2026

Robust prediction of drug combination side effects in realistic settings

Ruben Emilio Jimenez Franco, Alberto Paccanaro

DCSE predicts drug combination side effects using a deep learning model, outperforming existing methods in realistic settings with limited data.

DOI 10.1371/journal.pcbi.1013619

deep learningmachine learning (classical)

𝕏 PostBluesky

BioinformaticsbioRxivPreprintAug 10, 2024

Fine-tuning of conditional Transformers for the generation of functionally characterized enzymes

M. Nicolini, Emanuele Saitto, Ruben Emilio Jimenez Franco…·Giorgio Valentini

This paper introduces Finenzyme, a Protein Language Model that improves EC category prediction through fine-tuning, generating functionally similar enzymes with preserved structure and function.

1 citation

protein sequencedeep learning

𝕏 PostBluesky