Author

Brendan Ha

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

Click to filter author papers

Immunology· 2 Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

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

Frequent Co-Authors

Bjoern PetersiD· 4 shared Barry J. GrantiD· 3 shared Ferhat AyiD· 3 shared James A. OvertoniD· 3 shared Jason A GreenbaumiD· 3 shared Jeremy P. GygiiD· 3 shared Joaquin ReynaiD· 3 shared Leying GuaniD· 3 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

4 shared papersImmunology

Bjoern PetersORCID

Mutual co-authors in cluster

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

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

Uncovering the cell type specificity of blood sample derived gene signatures using RNA expression data

Mikhail Pomaznoy, Brendan Ha, Bjoern Peters

The paper develops a web tool to quantify and visualize gene signature expression in blood cell types using RNA data.

bioRxiv · Jun 27, 2019 · PreprintBioinformatics