Author

Mari Kojima

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· 3 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:benchmark study· 2 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1

Frequent Co-Authors

Bjoern PetersiD· 4 shared Lisa WillemseniD· 4 shared Minori Aoki· 4 shared Pramod S. ShindeiD· 4 shared Shelby Orfield· 4 shared Barry J. GrantiD· 3 shared Brendan Ha· 3 shared Ferhat AyiD· 3 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersImmunology

Bjoern PetersORCID

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Author profile →

4 papers

Recent·Most cited

An Open Benchmark for Systems Vaccinology: Insights from the CMI-PB Challenges

Pramod S. Shinde, Lisa Willemsen, Jiyeun Lee, Shelby Orfield, Ziyuan Ren, Minori Aoki, Nicola Thrupp, Aanya Gupta, Cheng-Chang Wu, Liran Mao, Chuxuan Li, Yuhao Tan, Tram Anh Nguyen, Nou Chang, Philipp S. L. Schäfer, , Bjoern Peters

The paper benchmarks computational models predicting B. pertussis booster vaccine responses using multi-omics data from three cohorts, identifying key predictors of immunity and establishing a community resource for systems vaccinology.

bioRxiv · Aug 28, 2026 · PreprintImmunology

Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop

Lisa Willemsen, Jiyeun Lee, Pramod S. Shinde, Ferran Soldevila, Minori Aoki, Shelby Orfield, Mari Kojima, Ricardo da Silva Antunes, Alessandro Sette, Bjoern Peters

This study compares immune responses to whole-cell and acellular pertussis vaccines, finding that Th1 polarization is maintained through an early interferon response in whole-cell vaccine recipients.

Nature Communications · Apr 1, 2025Peer-reviewedImmunology

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