ArticleBioinformatics (Oxford, England)2021
Dream: powerful differential expression analysis for repeated measures designs.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers, 3 of them syntheses that pooled it.
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Who cites it
215 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Cross-Study Meta-Analysis of Blood Transcriptomes in Type 2 Diabetes.International journal of molecular sciences · 2025Pooled it
- Updated annotation and meta-analysis of Brugia malayi transcriptomics data reveals consistent transcriptional profiles across time and space with some study-specific differences in adult female worm transcriptional profiles.PLoS neglected tropical diseases · 2024Pooled it
- Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies.Nature genetics · 2022Pooled it
- Brigimadlin versus Doxorubicin in Advanced Dedifferentiated Liposarcoma: Efficacy, Safety, and Translational Data from Brightline-1, a Randomized Phase II/III Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Trial
- Gemcitabine plus Nivolumab with Carboplatin or Oxaliplatin in Cisplatin-Ineligible Patients with Metastatic Urothelial Carcinoma: A Randomized Phase II Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Trial
- Time-Restricted Eating Promotes Weight Loss and Favorable Changes in Adipose in Obesity: The TREAD Randomized Control Trial.Obesity (Silver Spring, Md.) · 2026Trial
- Efficacy and Safety of Ravagalimab in Patients with Moderate-to-Severe Ulcerative Colitis: Data from a Phase 2a Trial.Advances in therapy · 2026Trial
- Human Skeletal Muscle Mitochondria Responses to Weight Loss Induced by Bariatric Surgery or Lifestyle Intervention.Acta physiologica (Oxford, England) · 2026Trial
- Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapy.Cell reports. Medicine · 2025Trial
- A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.Science translational medicine · 2024Trial
- Type I interferon blockade with anifrolumab in patients with systemic lupus erythematosus modulates key immunopathological pathways in a gene expression and proteomic analysis of two phase 3 trials.Annals of the rheumatic diseases · 2024Trial
- Tumor-Immune Signatures of Treatment Resistance to Brentuximab Vedotin with Ipilimumab and/or Nivolumab in Hodgkin Lymphoma.Cancer research communications · 2024Trial
- A microbiota-directed complementary food intervention in 12-18-month-old Bangladeshi children improves linear growth.EBioMedicine · 2024Trial
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- Impact of interspecies colostrum and milk replacement on circulating sncRNA dynamics of neonatal goat kids.RNA biology · 2026Article
- Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis.bioRxiv : the preprint server for biology · 2026Article
- Fast, flexible analysis of differences in cellular composition with crumblr.Nature communications · 2026Article
- Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet.Nature communications · 2026Article
155 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
summaryLarge-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings. AVAILABILITY AND IMPLEMENTATION: Dream is available within the variancePartition Bioconductor package at http://bioconductor.org/packages/variancePartition. CONTACT: gabriel.hoffman@mssm.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.