Please cite the relevant papers for individual methods and the EpiDISH paper for the whole package.

Zheng SC, Breeze CE, Beck S, Teschendorff AE. 2018. Identification of differentially methylated cell-types in Epigenome-Wide Association Studies. Nat Methods 15: 1059-1066.

Zheng SC, Webster AP, Dong D, Feber A, Graham DG, Sullivan R, Jevons S, Lovat LB, Beck S, Widschwendter M, Teschendorff AE. 2018. A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix. Epigenomics 10: 925-940.

Teschendorff AE, Breeze CE, Zheng SC, Beck S. 2017. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. BMC Bioinformatics 18: 105.

Luo Q et al. A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes. Genome Med. 2023 Jul 31;15(1):59.

Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT. 2012. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13: 86.

Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. 2015. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 12: 453-457.

Teschendorff AE, Zheng SC. 2017. Cell-type deconvolution in epigenome-wide association studies: a review and recommendations. Epigenomics 9: 757-768.

Corresponding BibTeX entries:

  @Article{,
    author = {Shijie C. Zheng and Charles E. Breeze and Stephan Beck
      and Andrew E. Teschendorff},
    title = {Identification of differentially methylated cell-types in
      Epigenome-Wide Association Studies},
    journal = {Nature Methods},
    volume = {15},
    number = {12},
    pages = {1059},
    year = {2018},
  }

  @Article{,
    author = {Shijie C. Zheng and Amy P. Webster and Danyue Dong and
      Andy Feber and David G. Graham and Roisin Sullivan and Sarah
      Jevons and Laurence B. Lovat and Stephan Beck and Martin
      Widschwendter and Andrew E. Teschendorff},
    title = {A novel cell-type deconvolution algorithm reveals
      substantial contamination by immune cells in saliva, buccal and
      cervix},
    journal = {Epigenomics},
    year = {2018},
    volume = {10},
    number = {7},
  }

  @Article{,
    author = {Andrew E. Teschendorff and Charles E. Breeze and Shijie
      C. Zheng and Stephan Beck},
    title = {A comparison of reference-based algorithms for correcting
      cell-type heterogeneity in Epigenome-Wide Association Studies},
    journal = {BMC bioinformatics},
    volume = {18},
    number = {1},
    pages = {105},
    year = {2017},
  }

  @Article{,
    author = {Qi Luo and Varun B. Dwaraka and Qingwen Chen and Huige
      Tong and Tianyu Zhu and Kirsten Seale and Joseph M. Raffaele and
      Shijie C. Zheng and Tavis L. Mendez and Yulu Chen and Natalia
      Carreras and Sofina Begum and Kevin Mendez and Sarah Voisin and
      Nir Eynon and Jessica A. Lasky-Su and Ryan Smith and Andrew E.
      Teschendorff},
    title = {A meta-analysis of immune-cell fractions at high
      resolution reveals novel associations with common phenotypes and
      health outcomes},
    journal = {Genome Medicine},
    volume = {15},
    number = {1},
    pages = {59},
    year = {2023},
  }

  @Article{,
    author = {Eugene A. Houseman and William P. Accomando and Devin C.
      Koestler and Brock C. Christensen and Carmen J. Marsit and
      Heather H. Nelson and John K. Wiencke and Karl T. Kelsey},
    title = {DNA methylation arrays as surrogate measures of cell
      mixture distribution},
    journal = {BMC bioinformatics},
    volume = {13},
    number = {1},
    pages = {86},
    year = {2012},
  }

  @Article{,
    author = {Aaron M. Newman and Chih L. Liu and Michael R. Green and
      Andrew J. Gentles and Weiguo Feng and Yue Xu and Chuong D. Hoang
      and Maximilian Diehn and Ash A. Alizadeh},
    title = {Robust enumeration of cell subsets from tissue expression
      profiles},
    journal = {Nature Methods},
    volume = {12},
    number = {5},
    pages = {453},
    year = {2015},
  }

  @Article{,
    author = {Andrew E. Teschendorff and Shijie C. Zheng},
    title = {Cell-type deconvolution in epigenome-wide association
      studies: a review and recommendations},
    journal = {Epigenomics},
    volume = {9},
    number = {5},
    pages = {757},
    year = {2017},
  }