ArticleBioinformatics (Oxford, England)2023
ePlatypus: an ecosystem for computational analysis of immunogenomics data.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- IL-12-secreting CAR-T cells reprogram the tumor microenvironment and improve efficacy against heterogeneous models of glioblastoma.Journal for immunotherapy of cancer · 2026Article
- Stability and progressive differentiation of TNature immunology · 2026Article
- Adenophages are an atypical macrophage population in exocrine glands sustained by ILC2-derived GM-CSF.Nature immunology · 2026Article
- Tumor-infiltrating B cells produce tumor-specific antibodies and may contribute to suppressing tumor in head and neck squamous cell carcinoma.Oncoimmunology · 2025Article
- The co-inhibitory receptor TIGIT promotes tissue-protective functions in T cells.Nature immunology · 2025Article
- Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution.Briefings in bioinformatics · 2025Article
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Authors and funding
32 authors.
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Abstract
motivationThe maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner.
resultsHere, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand-receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science. AVAILABILITY AND IMPLEMENTATION: Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.