Author

Jiyeun Lee

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

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Organism:human· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Bjoern PetersiD· 3 shared Lisa WillemseniD· 3 shared Mari Kojima· 3 shared Minori Aoki· 3 shared Pramod S. ShindeiD· 3 shared Shelby Orfield· 3 shared Barry J. GrantiD· 2 shared Brendan Ha· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersImmunology

Bjoern PetersORCID

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3 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