ArticleBioinformatics (Oxford, England)2023
Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- A pediatric randomized, controlled trial of German cockroach subcutaneous immunotherapy.The Journal of allergy and clinical immunology · 2024Trial
- Co-regulation of innate and adaptive immune responses induced by ID93+GLA-SE vaccination in humans.Frontiers in immunology · 2024Trial
- Clinical and transcriptomic risk factors for post-tuberculosis lung disease in a cohort of Kenyan adults.American journal of respiratory and critical care medicine · 2026Observational
- Human iPSC-derived alveolar macrophages reveal macrophage subtype functions of itaconate in M. tuberculosis defense.JCI insight · 2026Article
- Bronchial epithelial transcriptome reveals dysregulated interferon and inflammatory responses to rhinovirus in exacerbation-prone pediatric asthma.JCI insight · 2025Article
- Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.Nature communications · 2025Article
- Shared and distinct responses of human and murine alveolar macrophages and monocyte-derived macrophages to Mycobacterium tuberculosis.ImmunoHorizons · 2025Article
- Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma.bioRxiv : the preprint server for biology · 2025Article
- Cathepsin Z is a conserved susceptibility factor underlying tuberculosis severity.PLoS biology · 2025Article
- Myeloid cell genome-wide screen identifies variants associated with Mycobacterium tuberculosis-induced cytokine transcriptional responses.The Journal of clinical investigation · 2025Article
- Reduced Function of the Adaptor SH2B3 Promotes T1D via Altered Cytokine-Regulated, T-Cell-Intrinsic Immune Tolerance.Diabetes · 2025Article
- Article
- Weight loss and metabolic effects of an ALDH1A1-specific inhibitor, FSI-TN42, in a diet induced mouse model of obesity.International journal of obesity (2005) · 2025Article
- Epigenetic programming of host lipid metabolism associated with resistance to TST/IGRA conversion after exposure tomSystems · 2024Article
- Human Alveolar and Monocyte-Derived Human Macrophage Responses to Mycobacterium tuberculosis.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop.The Journal of allergy and clinical immunology · 2024Article
- Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure tobioRxiv : the preprint server for biology · 2024Article
- Tuberculosis Infectiousness is Associated with Distinct Clinical and Inflammatory Profiles.Research square · 2024Article
- Limitations of the human iPSC-derived neuron model for early-onset Alzheimer's disease.Molecular brain · 2023Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
motivationThe identification of differentially expressed genes (DEGs) from transcriptomic datasets is a major avenue of research across diverse disciplines. However, current bioinformatic tools do not support covariance matrices in DEG modeling. Here, we introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling including covariates, weights, random effects, covariance matrices, and fit metrics.
resultsIn simulated datasets, kimma detects DEGs with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like Akaike information criterion (AIC). Utilizing genetic kinship covariance, kimma revealed that kinship impacts model fit and DEG detection in a related cohort. Thus, kimma equals or outcompetes current DEG pipelines in sensitivity, computational time, and model complexity. AVAILABILITY AND IMPLEMENTATION: Kimma is freely available on GitHub https://github.com/BIGslu/kimma with an instructional vignette at https://bigslu.github.io/kimma_vignette/kimma_vignette.html.
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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.