Author

Mark Edward M. Gonzales

De La Salle UniversityORCID 0000-0001-5050-3157Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Research Focus:protein structure prediction· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:protein design· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Anish Man Singh ShresthaiD· 2 shared Jennifer C. UretaiD· 2 shared

Activity by Year

2023-2024 · peak 1/yr

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2 top collaborators · 1 mutual co-author link

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2 shared papersBioinformatics

Anish Man Singh ShresthaORCID

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2 papers

Recent·Most cited

BioinformaticsBioinformaticsPeer-reviewedDec 26, 2024

PHIStruct: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

Mark Edward M. Gonzales, Jennifer C. Ureta, Anish Man Singh Shrestha

PHIStruct improves phage-host interaction prediction by using structure-aware embeddings, achieving better precision and recall than sequence-only methods, especially at low sequence similarity.

23 citationstop 3%

protein sequencedeep learning

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BioinformaticsPLoS ONEPeer-reviewedJul 24, 2023

Protein embeddings improve phage-host interaction prediction

Mark Edward M. Gonzales, Jennifer C. Ureta, Anish Man Singh Shrestha

The paper uses protein embeddings to predict phage-host interactions, showing improved performance over handcrafted features with ProtT5 achieving higher F1 scores.

27 citationstop 5%

protein sequencetransformer / foundation model

𝕏 PostBluesky