Author

Somayeh Nili

La Jolla Institute for Immunology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:benchmark study· 2 Research Focus:benchmarking· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Assay:multiome· 1

Frequent Co-Authors

Anna KonstorumiD· 2 shared Barry J. GrantiD· 2 shared Bjoern PetersiD· 2 shared Brendan Ha· 2 shared Ferhat AyiD· 2 shared James A. OvertoniD· 2 shared Jason A GreenbaumiD· 2 shared Jeremy P. GygiiD· 2 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersImmunology

Anna KonstorumORCID

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2 papers

Recent·Most cited

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

A systems vaccinology resource to develop and test computational models of immunity

Pramod S. Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason Greenbaum, James A. Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P. Gygi, Ricardo da Silva Antunes, , Bjoern Peters

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

bioRxiv · Aug 28, 2023 · PreprintSystems Biology