ArticleNature communications2023
A comprehensive platform for analyzing longitudinal multi-omics data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.Veterinary research communications · 2026Review
- Review
- Clustering longitudinal multivariate trajectories using an ensemble of principal component trees.BMC medical research methodology · 2026Article
- Decoding drug-responsive cell subpopulations in triple-negative breast cancer using single-cell multiomics.iScience · 2026Article
- scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies.bioRxiv : the preprint server for biology · 2026Article
- Longitudinal Sparse Single-Omics Factor Analysis for High-Dimensional Blood Biomarkers in Alzheimer's Disease.Statistics in medicine · 2026Article
- A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nature communications · 2026Article
- Multi-omics integration in deciphering non-small cell lung cancer drug resistance: current status, challenges, and future prospects.Hereditas · 2026Review
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.PLoS computational biology · 2025Article
- Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation.Science translational medicine · 2025Article
- Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.bioRxiv : the preprint server for biology · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim.Bioinformatics (Oxford, England) · 2025Article
- Blood plasma proteome-wide association study implicates novel proteins in the pathogenesis of multiple cardiovascular diseases.Cardiovascular diabetology · 2025Article
- LEOPARD: missing view completion for multi-timepoint omics data via representation disentanglement and temporal knowledge transfer.Nature communications · 2025Article
- Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data.BMC bioinformatics · 2025Article
- CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays.Journal of translational medicine · 2025Article
- Decoding sex differences in human immunity through systems immunology.Oxford open immunology · 2025Review
- Machine learning for precision diagnostics of autoimmunity.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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.