ArticleNAR genomics and bioinformatics2020
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,037 papers, 4 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
1,037 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Dynamic Remodeling of Oocyte-Granulosa Cell Communication During Bovine Folliculogenesis Revealed by Transcriptomic Meta-Analyses.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Pooled it
- Systematic Review and Transcriptomic Meta-analysis of Environmental Enrichment Reveal Core Molecular Programs of Brain Plasticity.Molecular neurobiology · 2026Pooled it
- The respiratory microbiome in pulmonary tuberculosis: a meta-analysis reveals niche-specific microbial and functional signatures.mSystems · 2026Pooled it
- Genetic landscape and functional exploration of kidney cancer predisposition in cross-ancestral populations.Nature communications · 2026Pooled it
- Alterations to the Bronchial Gene-Expression Effects of Tobacco Smoking in People Living With HIV.Journal of acquired immune deficiency syndromes (1999) · 2026Trial
- Systematic Analysis of Tumor Microenvironment Using IOBR.Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Cross-species transcriptomics uncovers shared responses to water deficiency in plants.The plant genome · 2026Article
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- Impact of matched samples on domain harmonization in cross-cohort NMR metabolomics.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- A Living Multi-Omics PDX Biobank of High-Risk Sarcomas Reveals ecDNA-Driven Oncogene Amplification in Osteosarcoma and Enables Preclinical Precision Oncology.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unique circulating miRNAome signatures captured with distinct molecular states in Lynch syndrome and sporadic colorectal cancer.Molecular oncology · 2026Article
- Obesity Promotes Lung Carcinogenesis Through Airway Immune Dysfunction.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2026Article
- Lack of evidence for transcription-to-RNA maturation lags across G1-to-G2-phase boundary in fibroblasts.Life science alliance · 2026Article
- Chronic Cigarette Smoke Extract Exposure Promotes Genomic and Phenotypic Reprogramming in Lung Cancer Cells.Thoracic cancer · 2026Article
- ATF4 Modulates Group 1 mGluR-Dependent molecular signaling, hippocampal plasticity and behavior.Molecular psychiatry · 2026Article
- MStargetR: a reproducible, containerised workflow for end-to-end targeted (MRM/SRM) mass spectrometry data processing in R.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Pseudomonas aeruginosa induces the generation of pathogenic IFNγNature microbiology · 2026Article
- Molecular underpinnings of metastatic small renal masses.JCI insight · 2026Article
- Intramuscular plasmid DNA electroporation sequesters neoantigen-specific CD8Molecular therapy. Oncology · 2026Article
977 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
3 authors.
Funding
Abstract
The benefit of integrating batches of genomic data to increase statistical power is often hindered by batch effects, or unwanted variation in data caused by differences in technical factors across batches. It is therefore critical to effectively address batch effects in genomic data to overcome these challenges. Many existing methods for batch effects adjustment assume the data follow a continuous, bell-shaped Gaussian distribution. However in RNA-seq studies the data are typically skewed, over-dispersed counts, so this assumption is not appropriate and may lead to erroneous results. Negative binomial regression models have been used previously to better capture the properties of counts. We developed a batch correction method, ComBat-seq, using a negative binomial regression model that retains the integer nature of count data in RNA-seq studies, making the batch adjusted data compatible with common differential expression software packages that require integer counts. We show in realistic simulations that the ComBat-seq adjusted data results in better statistical power and control of false positives in differential expression compared to data adjusted by the other available methods. We further demonstrated in a real data example that ComBat-seq successfully removes batch effects and recovers the biological signal in the data.
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.