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A comprehensive platform for analyzing longitudinal multi-omics data

Author

Listed:
  • Suhas V. Vasaikar

    (Allen Institute for Immunology)

  • Adam K. Savage

    (Allen Institute for Immunology)

  • Qiuyu Gong

    (Allen Institute for Immunology)

  • Elliott Swanson

    (Allen Institute for Immunology
    University of Washington School of Medicine)

  • Aarthi Talla

    (Allen Institute for Immunology)

  • Cara Lord

    (Allen Institute for Immunology
    GlaxoSmithKline)

  • Alexander T. Heubeck

    (Allen Institute for Immunology)

  • Julian Reading

    (Allen Institute for Immunology)

  • Lucas T. Graybuck

    (Allen Institute for Immunology)

  • Paul Meijer

    (Allen Institute for Immunology)

  • Troy R. Torgerson

    (Allen Institute for Immunology)

  • Peter J. Skene

    (Allen Institute for Immunology)

  • Thomas F. Bumol

    (Allen Institute for Immunology)

  • Xiao-jun Li

    (Allen Institute for Immunology)

Abstract

Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a platform that contains five analytical modules to examine longitudinal bulk and single-cell multi-omics data from multiple perspectives, including decomposition of sources of variations within the data, collection of stable or variable features across timepoints and participants, identification of up- or down-regulated markers across timepoints of individual participants, and investigation on samples of same participants for possible outlier events. We have tested PALMO performance on a complex longitudinal multi-omics dataset of five data modalities on the same samples and six external datasets of diverse background. Both PALMO and our longitudinal multi-omics dataset can be valuable resources to the scientific community.

Suggested Citation

  • Suhas V. Vasaikar & Adam K. Savage & Qiuyu Gong & Elliott Swanson & Aarthi Talla & Cara Lord & Alexander T. Heubeck & Julian Reading & Lucas T. Graybuck & Paul Meijer & Troy R. Torgerson & Peter J. Sk, 2023. "A comprehensive platform for analyzing longitudinal multi-omics data," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37432-w
    DOI: 10.1038/s41467-023-37432-w
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    1. Ankur Sharma & Elaine Yiqun Cao & Vibhor Kumar & Xiaoqian Zhang & Hui Sun Leong & Angeline Mei Lin Wong & Neeraja Ramakrishnan & Muhammad Hakimullah & Hui Min Vivian Teo & Fui Teen Chong & Shumei Chia, 2018. "Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy," Nature Communications, Nature, vol. 9(1), pages 1-17, December.
    2. Kip D. Zimmerman & Mark A. Espeland & Carl D. Langefeld, 2021. "A practical solution to pseudoreplication bias in single-cell studies," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    3. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    4. Jason D. Buenrostro & Beijing Wu & Ulrike M. Litzenburger & Dave Ruff & Michael L. Gonzales & Michael P. Snyder & Howard Y. Chang & William J. Greenleaf, 2015. "Single-cell chromatin accessibility reveals principles of regulatory variation," Nature, Nature, vol. 523(7561), pages 486-490, July.
    5. Wenyu Zhou & M. Reza Sailani & Kévin Contrepois & Yanjiao Zhou & Sara Ahadi & Shana R. Leopold & Martin J. Zhang & Varsha Rao & Monika Avina & Tejaswini Mishra & Jethro Johnson & Brittany Lee-McMullen, 2019. "Longitudinal multi-omics of host–microbe dynamics in prediabetes," Nature, Nature, vol. 569(7758), pages 663-671, May.
    6. Jordan W. Squair & Matthieu Gautier & Claudia Kathe & Mark A. Anderson & Nicholas D. James & Thomas H. Hutson & Rémi Hudelle & Taha Qaiser & Kaya J. E. Matson & Quentin Barraud & Ariel J. Levine & Gio, 2021. "Confronting false discoveries in single-cell differential expression," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
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