ArticleeLife2021
Standardizing workflows in imaging transcriptomics with the abagen toolbox.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 326 papers, 5 of them syntheses that pooled it.
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Who cites it
326 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Shared genetic underpinnings of gray matter volume alterations and metabolic traits in major depressive disorder.BMC psychiatry · 2026Pooled it
- Altered resting-state brain function in diabetic retinopathy: a meta-analysis of combined transcriptome-neuroimaging study.Frontiers in endocrinology · 2026Pooled it
- Brain maps of general cognitive functioning: neuroimaging and neurobiological signatures.Translational psychiatry · 2025Pooled it
- The multimodal neuroimaging signatures and gene expression profiles for adverse childhood experiences.BMC medicine · 2025Pooled it
- Shared neuroimaging and molecular profiles in type 2 diabetes mellitus and major depressive disorder: an integrative analysis of genetic, transcriptomic, and neuroimaging data.Translational psychiatry · 2025Pooled it
- GABRB3 Gene Polymorphisms Influences the Analgesic Response to Acupuncture Treatment in Patients With Chronic Knee Pain: A Randomized Controlled Neuroimaging Transcriptomics Study.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Trial
- Functional gradient reorganization and transcriptomic signatures underlying 1 Hz rTMS treatment in first-episode schizophrenia following right orbitofrontal cortex stimulation.NeuroImage. Clinical · 2026Trial
- Subtyping OCD based on individual symptom networks: subtype-specific neural dynamics and morphometric similarity linked to molecular profiles.Molecular psychiatry · 2026Article
- A Hypothalamic Oxytocinergic-Sympathetic Axis Couples Anxiety Dysregulation With Impaired Tendon-Bone Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Stable depression subtypes identified using functional connectome normative deviation models and their response to rTMS.Molecular psychiatry · 2026Article
- Altered seed-to-whole-brain functional connectivity of goal-directed/habitual systems in obsessive-compulsive disorder: associated genes and preliminary classification potential.European archives of psychiatry and clinical neuroscience · 2026Article
- Comprehensive profiling of brain dynamics during anesthesia across phylogeny.Nature neuroscience · 2026Article
- Spatial organization of AQP4 water channel expression in the human brain.Science advances · 2026Article
- Spatial pattern-driven interpretable model and biological correlates in brain glioblastoma-lymphoma differentiation.iScience · 2026Article
- Transcranial direct current stimulation and lesions hierarchically reorganize brain network dynamics with biological annotations.Fundamental research · 2026Article
- Anatomical white matter tracts span the cortical hierarchy to support cognitive diversity.Nature human behaviour · 2026Article
- BriGHT: transcriptome-regularized multimodal neuroimaging for brain disorder prediction.Bioinformatics (Oxford, England) · 2026Article
- Molecular, cellular and network mapping of brain structural deviations in patients with Post-COVID19 syndrome.Brain, behavior, & immunity - health · 2026Article
- Article
- Dynamic limbic-executive decoupling underpins the reciprocal link between drug-resistant state and depression in temporal lobe epilepsy.Epilepsia · 2026Article
266 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Gene expression fundamentally shapes the structural and functional architecture of the human brain. Open-access transcriptomic datasets like the Allen Human Brain Atlas provide an unprecedented ability to examine these mechanisms in vivo; however, a lack of standardization across research groups has given rise to myriad processing pipelines for using these data. Here, we develop the abagen toolbox, an open-access software package for working with transcriptomic data, and use it to examine how methodological variability influences the outcomes of research using the Allen Human Brain Atlas. Applying three prototypical analyses to the outputs of 750,000 unique processing pipelines, we find that choice of pipeline has a large impact on research findings, with parameters commonly varied in the literature influencing correlations between derived gene expression and other imaging phenotypes by as much as ρ ≥ 1.0. Our results further reveal an ordering of parameter importance, with processing steps that influence gene normalization yielding the greatest impact on downstream statistical inferences and conclusions. The presented work and the development of the abagen toolbox lay the foundation for more standardized and systematic research in imaging transcriptomics, and will help to advance future understanding of the influence of gene expression in the human brain.
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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.