ArticleBMC bioinformatics2010
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 385 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
385 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Flimma: a federated and privacy-aware tool for differential gene expression analysis.Genome biology · 2021Pooled it
- RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis.F1000Research · 2021Pooled it
- Early amyloid pathology in mice synergistically worsens post-sepsis behavioral impairment and microglial synaptic phagocytosis.Brain, behavior, & immunity - health · 2026Article
- Deciphering the genetic underlying causes of sex differences in multiple myeloma incidence and mortality.HGG advances · 2026Article
- Losartan shows limited benefit in preclinical models of Geleophysic dysplasia.Scientific reports · 2026Article
- Complementary ROC-Derived Indices for Screening Improper Expression Profiles in RNA-Seq Differential Expression Analysis.Balkan medical journal · 2026Article
- Resources Modulate Developmental Shifts but Not Infection Tolerance Upon Co-Infection in an Insect System.Molecular ecology · 2025Article
- Distilling Direct Effects via Conditional Differential Gene Expression Analysis.bioRxiv : the preprint server for biology · 2025Article
- scDETECT: a novel statistical model accounting for cell type correlation in single-cell RNA-seq differential expression analysis.Briefings in bioinformatics · 2025Article
- Artificial Intelligence in Ocular Transcriptomics: Applications of Unsupervised and Supervised Learning.Cells · 2025Review
- Poisson Beta Regression for Count Data With an Application to Hospital Length of Stay Data.Statistics in medicine · 2025Article
- Dysregulation of cell migration by matrix metalloproteinases in geleophysic dysplasia.Scientific reports · 2025Article
- Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization.Genome biology · 2025Article
- Resiquimod induces a mixed Th1 and Th2 response via STAT1 and STAT3 signalling in chickens.Biochemistry and biophysics reports · 2025Article
- Article
- Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review.Computational and structural biotechnology journal · 2024Review
- Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance inbioRxiv : the preprint server for biology · 2024Article
- The frequency and function of nucleoprotein-specific CD8Journal of virology · 2024Article
- Resources modulate developmental shifts but not infection tolerance upon coinfection in an insect system.bioRxiv : the preprint server for biology · 2024Article
- Buccal Swab Samples from Japanese Brown Cattle Fed with Limonite Reveal Altered Rumen Microbiome.Animals : an open access journal from MDPI · 2024Article
325 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundHigh throughput sequencing has become an important technology for studying expression levels in many types of genomic, and particularly transcriptomic, data. One key way of analysing such data is to look for elements of the data which display particular patterns of differential expression in order to take these forward for further analysis and validation.
resultsWe propose a framework for defining patterns of differential expression and develop a novel algorithm, baySeq, which uses an empirical Bayes approach to detect these patterns of differential expression within a set of sequencing samples. The method assumes a negative binomial distribution for the data and derives an empirically determined prior distribution from the entire dataset. We examine the performance of the method on real and simulated data.
conclusionsOur method performs at least as well, and often better, than existing methods for analyses of pairwise differential expression in both real and simulated data. When we compare methods for the analysis of data from experimental designs involving multiple sample groups, our method again shows substantial gains in performance. We believe that this approach thus represents an important step forward for the analysis of count data from sequencing experiments.
Indexed as
Identifiers
What OpenQuestion holds
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.