Author

John S. West

Personalis (United States)

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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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Assay:proteomics· 1 Approach:statistical model· 1 Assay:whole-exome sequencing· 1

Frequent Co-Authors

Charles W. AbbottiD· 2 shared Dattatreya MellacheruvuiD· 2 shared Gabor T. Bartha· 2 shared Michael P. SnyderiD· 2 shared Rachel Marty PykeiD· 2 shared Richard CheniD· 2 shared Sean Michael BoyleiD· 2 shared Simo V. ZhangiD· 2 shared

Activity by Year

2021-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Charles W. AbbottORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Validated machine learning algorithm with sub-clonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity

Rachel Marty Pyke, Dattatreya Mellacheruvu, Steven Dea, Charles W. Abbott, Simo V. Zhang, Lee McDaniel, Éric Levy, Gabor T. Bartha, John S. West, Michael P. Snyder, Richard Chen, Sean Michael Boyle

The paper develops DASH, a machine learning algorithm to detect HLA LOH in cancer, showing 18% prevalence across 611 patients and correlations with PD-L1 and MSI.

bioRxiv · May 20, 2021 · PreprintBioinformatics

Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation

Rachel Marty Pyke, Dattatreya Mellacheruvu, Steven Dea, Charles W. Abbott, Simo V. Zhang, Nick A. Phillips, Jason Harris, Gabor T. Bartha, Sejal Desai, Rena McClory, John S. West, Michael P. Snyder, Richard Chen, Sean Michael Boyle

This paper introduces SHERPA, a pan-allelic MHC-peptide prediction algorithm, which improves neoantigen discovery by integrating immunopeptidomics data and composite modeling.

Molecular & Cellular Proteomics · Jan 1, 2021Peer-reviewedBioinformatics