CRAFT/CITATION.cff at master · KarchinLab/CRAFT · GitHub

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cff-version: 1.2.0
message: "If you use CRAFT in your research, please cite the manuscript below."
title: "A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling"
type: software
license: MIT
repository-code: "https://github.com/KarchinLab/CRAFT"
doi: 10.5281/zenodo.19891746
url: "https://doi.org/10.5281/zenodo.19891746"
authors:
  - family-names: Balan
    given-names: Archana
    affiliation: "Institute for Computational Medicine, Johns Hopkins University; Department of Biomedical Engineering, Johns Hopkins University; Department of Oncology, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine"
  - family-names: Elhanati
    given-names: Yuval
    affiliation: "Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center"
  - family-names: Meza Landeros
    given-names: Kevin E.
    affiliation: "Institute for Computational Medicine, Johns Hopkins University; Department of Biomedical Engineering, Johns Hopkins University"
  - family-names: De Almeida Mendes
    given-names: Marcus
    affiliation: "Institute for Computational Medicine, Johns Hopkins University; Department of Oncology, Johns Hopkins University School of Medicine"
  - family-names: Lai
    given-names: Jiaying
    affiliation: "Institute for Computational Medicine, Johns Hopkins University"
  - family-names: Ali Zaidi
    given-names: Syed Shujaat
    affiliation: "Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center"
  - family-names: Unal
    given-names: Mesut
    affiliation: "Department of Neurosurgery Research, The University of Texas MD Anderson Cancer Center"
  - family-names: Kim
    given-names: Betty Y.S.
    affiliation: "James P. Allison Institute, The University of Texas MD Anderson Cancer Center; Department of Neurosurgery, The University of Texas MD Anderson Cancer Center"
  - family-names: Lucas
    given-names: Calixto-Hope G.
    affiliation: "Department of Pathology, Johns Hopkins University School of Medicine"
  - family-names: Runco
    given-names: Emerenziana
    affiliation: "Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School"
  - family-names: Puduvalli
    given-names: Vinay K.
    affiliation: "Department of Neuro-Oncology, Center for Neurosciences of Cancer, The University of Texas MD Anderson Cancer Center"
  - family-names: Gantchev
    given-names: Jennifer
    affiliation: "Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School"
  - family-names: Whittaker
    given-names: Charles A.
    affiliation: "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology"
  - family-names: Sharma
    given-names: Pratibha
    affiliation: "Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center"
  - family-names: Tabar
    given-names: Viviane
    affiliation: "Department of Neurosurgery, Memorial Sloan Kettering Cancer Center"
  - family-names: Cima
    given-names: Michael J.
    affiliation: "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology"
  - family-names: Baquer
    given-names: Gerard
    affiliation: "Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School"
  - family-names: Reardon
    given-names: David A.
    affiliation: "Center for Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School"
  - family-names: Stortchevoi
    given-names: Alexei
    affiliation: "Department of Biology, Massachusetts Institute of Technology"
  - family-names: Boire
    given-names: Adrienne
    affiliation: "Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center"
  - family-names: Wang
    given-names: Linghua
    affiliation: "Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center"
  - family-names: White
    given-names: Forest M.
    affiliation: "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology"
  - family-names: Sidiropoulos
    given-names: Dimitrios N.
    affiliation: "Department of Oncology, Johns Hopkins University School of Medicine"
  - family-names: Yu
    given-names: Kenny Kwok Hei
    affiliation: "Department of Neurosurgery, Memorial Sloan Kettering Cancer Center"
  - family-names: Chiocca
    given-names: E. Antonio
    affiliation: "Department of Neurosurgery, Mass General Brigham"
  - family-names: Anagnostou
    given-names: Valsamo
    affiliation: "Department of Oncology, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine"
  - name: "Data Science Teamlab"
  - name: "Accelerating GBM Therapies TeamLab"
  - family-names: Karchin
    given-names: Rachel
    email: karchin@jhu.edu
    affiliation: "Institute for Computational Medicine, Johns Hopkins University; Department of Biomedical Engineering, Johns Hopkins University; Department of Oncology, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine"
preferred-citation:
  type: article
  title: "A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling"
  authors:
    - family-names: Balan
      given-names: Archana
    - family-names: Karchin
      given-names: Rachel
  # journal: "Nature Methods"
  # year: 2026
  # doi: 10.XXXX/XXXXXX  # FILL IN after Nature Methods accession is minted
  # url: "https://doi.org/10.XXXX/XXXXXX"
  # Preprint (bioRxiv): FILL IN after preprint deposition.