Author

Marcus Fabiano de Almeida Mendes

La Jolla Institute for ImmunologyORCID 0000-0002-2183-0121Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:drug response / drug discovery· 1 Approach:machine learning (classical)· 1 Assay:protein sequence· 1

Frequent Co-Authors

Bjoern PetersiD· 2 shared Eve RichardsoniD· 2 shared Jarjapu MahitaiD· 2 shared Jason A GreenbaumiD· 2 shared Aidan Dunleavy· 1 shared Aidan NeheriD· 1 shared Aixin Li· 1 shared Alessandro SetteiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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2 shared papersBioinformatics

Bjoern PetersORCID

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2 papers

Recent·Most cited

Characterizing antibodies binding to the same epitope reveals limited contribution by heavy chain CDR3 sequences relative to other CDRs

Jarjapu Mahita, Haeuk Kim, Marcus Fabiano de Almeida Mendes, Eve Richardson, Jason Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters

The paper identifies that CDR1 and CDR2 sequence identities are more predictive of epitope similarity than CDR3, and develops BCRMatch to predict epitope binding based on antibody sequences.

bioRxiv · May 24, 2025 · PreprintBioinformatics

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

Pramod S. Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G. Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A Greenbaum, , Bjoern Peters

The paper benchmarks 49 algorithms for predicting B. pertussis vaccination outcomes, finding that purpose-built models outperform literature-based ones due to better handling of nonlinearities and data preprocessing.

PLoS Computational Biology · Mar 31, 2025Peer-reviewedImmunology