Author

Josep M. Badia

Institut de Recerca Biomèdica Catalunya SudORCID 0000-0002-5704-1124Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:metabolomics· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Research Focus:drug response / drug discovery· 1 Organism:E. coli· 1 Research Focus:protein structure prediction· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Óscar YanesiD· 3 shared Roger GinéiD· 3 shared Alexandra JunzaiD· 2 shared Jordi CapelladesiD· 2 shared María VinaixaiD· 2 shared Maribel Pérez-Ribera· 2 shared Marta Sales‐PardoiD· 2 shared Muhammad Faizan-KhaniD· 2 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Óscar YanesORCID

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3 papers

Recent·Most cited

BioinformaticsBriefings in BioinformaticsPeer-reviewedJan 1, 2026

ChemEmbed: A deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings

Muhammad Faizan-Khan, Roger Giné, Josep M. Badia…·Óscar Yanes

ChemEmbed improves metabolite identification by combining enhanced MS/MS data with multidimensional molecular embeddings, achieving high accuracy in benchmark tests.

11 citationstop 1%

humanmetabolomics

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BioinformaticsBriefings in BioinformaticsPeer-reviewedJul 1, 2025

SingleFrag: A deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation

Maribel Pérez-Ribera, Muhammad Faizan-Khan, Roger Giné…·Roger Guimerà

SingleFrag predicts MS/MS fragments and annotates metabolites using deep learning, outperforming existing tools and identifying three unknown compounds in human samples.

12 citations

humanmetabolomics

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BioinformaticsbioRxivPreprintMar 8, 2021

HERMES: a molecular formula-oriented method to target the metabolome

Roger Giné, Jordi Capellades, Josep M. Badia…·Óscar Yanes

HERMES improves metabolite identification and structural annotation in mass spectrometry by using molecular formulas and avoiding peak detection.

2 citations

E. colihuman

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