The MSA array design and analysis is described in:

Goldberg D, Cloud C, Lee S, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majounie E, Manian M, Zhu Q, Tran C, Hansen M, Stojakovic J, Parker J, Kohli R, Porecha R, Renke N, Zhou W (2025). “Scalable screening of ternary-code DNA methylation dynamics associated with human traits.” Cell Genomics, 5(9). doi:10.1016/j.xgen.2025.100929.

The mLiftOver feature is described in:

Chen B, Zhou W (2024). “mLiftOver: harmonizing data across Infinium DNA methylation platforms.” Bioinformatics, 40(7). ISSN 1367-4811. doi:10.1093/bioinformatics/btae423.

The ELBAR detection calling is described in:

Lee S, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W (2024). “Low-input and single-cell methods for Infinium DNA methylation BeadChips.” Nucleic acids research. ISSN 1362-4962. doi:10.1093/nar/gkae127.

Data analysis on non-standard genome is described in:

Ding W, Kaur D, Horvath S, Zhou W (2023). “Comparative epigenome analysis using Infinium DNA methylation BeadChips.” Briefings in bioinformatics, 24(1). ISSN 1477-4054. doi:10.1093/bib/bbac617. 36617464.

Mouse (MM285) array informatics is described in:

Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee K, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Schaaf NAV, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW (2022). “DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse.” Cell genomics, 2(7). ISSN 2666-979X. doi:10.1016/j.xgen.2022.100144. 35873672.

pOOBAH detection calling is described in:

Zhou W, Triche TJ, Laird PW, Shen H (2018). “SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.” Nucleic Acids Research, gky691. doi:10.1093/nar/gky691.

noob background correction is described in:

Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD (2013). “Low-level processing of Illumina Infinium DNA Methylation BeadArrays.” Nucleic Acids Research, 41(7), e90. doi:10.1093/nar/gkt090.

Corresponding BibTeX entries:

  @Article{goldberg2025msa,
    title = {Scalable screening of ternary-code DNA methylation
      dynamics associated with human traits},
    author = {David C Goldberg and Cameron Cloud and Sol Moe Lee and
      Bret Barnes and Steven Gruber and Elliot Kim and Anita Pottekat
      and Maximillian S Westphal and Luana McAuliffe and Elisa Majounie
      and Manesh Kalayil Manian and Qingdi Zhu and Christine Tran and
      Mark Hansen and Jelena Stojakovic and Jared B Parker and Rahul M
      Kohli and Rishi Porecha and Nicole Renke and Wanding Zhou},
    year = {2025},
    month = {Sep},
    journal = {Cell Genomics},
    volume = {5},
    number = {9},
    doi = {10.1016/j.xgen.2025.100929},
    language = {eng},
  }

  @Article{chen2024mliftover,
    title = {mLiftOver: harmonizing data across Infinium DNA
      methylation platforms},
    author = {Brian H Chen and Wanding Zhou},
    year = {2024},
    month = {Jul},
    journal = {Bioinformatics},
    volume = {40},
    number = {7},
    doi = {10.1093/bioinformatics/btae423},
    language = {eng},
    issn = {1367-4811},
  }

  @Article{lee2024input,
    title = {Low-input and single-cell methods for Infinium DNA
      methylation BeadChips},
    author = {Sol Moe Lee and Christian Loo and Rexxi Prasasya and
      Marisa Bartolomei and Rahul Kohli and Wanding Zhou},
    year = {2024},
    month = {Feb},
    journal = {Nucleic acids research},
    doi = {10.1093/nar/gkae127},
    language = {eng},
    issn = {1362-4962},
  }

  @Article{BIB,
    title = {Comparative epigenome analysis using Infinium DNA
      methylation BeadChips},
    author = {Wubin Ding and Diljeet Kaur and Steve Horvath and Wanding
      Zhou},
    year = {2023},
    month = {Jan},
    journal = {Briefings in bioinformatics},
    volume = {24},
    number = {1},
    eprint = {36617464},
    doi = {10.1093/bib/bbac617},
    language = {eng},
    issn = {1477-4054},
  }

  @Article{MM285,
    title = {DNA methylation dynamics and dysregulation delineated by
      high-throughput profiling in the mouse},
    author = {Wanding Zhou and Toshinori Hinoue and Bret Barnes and
      Owen Mitchell and Waleed Iqbal and Sol Moe Lee and Kelly K Foy
      and Kwang-Ho Lee and Ethan J Moyer and Alexandra VanderArk and
      Julie M Koeman and Wubin Ding and Manpreet Kalkat and Nathan J
      Spix and Bryn Eagleson and John Andrew Pospisilik and Piroska E
      Szabó and Marisa S Bartolomei and Nicole A Vander Schaaf and
      Liang Kang and Ashley K Wiseman and Peter A Jones and Connie M
      Krawczyk and Marie Adams and Rishi Porecha and Brian H Chen and
      Hui Shen and Peter W Laird},
    year = {2022},
    month = {Jul},
    journal = {Cell genomics},
    volume = {2},
    number = {7},
    eprint = {35873672},
    doi = {10.1016/j.xgen.2022.100144},
    language = {eng},
    issn = {2666-979X},
    eprinttype = {pubmed},
  }

  @Article{sesame,
    title = {{SeSAMe: reducing artifactual detection of DNA methylation
      by Infinium BeadChips in genomic deletions}},
    author = {Wanding Zhou and Timothy J. Triche and Peter W. Laird and
      Hui Shen},
    year = {2018},
    journal = {Nucleic Acids Research},
    volume = {gky691},
    doi = {10.1093/nar/gky691},
    pubmed = {30085201},
  }

  @Article{noob,
    author = {Timothy J. Triche and Daniel J. Weisenberger and David
      {Van Den Berg} and Peter W. Laird and Kimberly D. Siegmund},
    title = {Low-level processing of {Illumina} {Infinium} {DNA}
      {Methylation} {BeadArrays}},
    journal = {Nucleic Acids Research},
    year = {2013},
    volume = {41},
    number = {7},
    pages = {e90},
    doi = {10.1093/nar/gkt090},
    pubmed = {23476028},
  }