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EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

https://doi.org/10.1093/bioinformatics/btt087

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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inferred← citeshttps://doi.org/10.1016/j.aquaculture.2025.742878openalex-snapshot

The IolR regulon contributes to Aeromonas hydrophila virulence in channel catfish (Ictalurus punctatus)

inferred← citeshttps://doi.org/10.1016/j.aquaculture.2025.743584openalex-snapshot

Transcriptomic and physiological responses of Epinephelus akaara to chronic cold stress

inferred← citeshttps://doi.org/10.1016/j.aquaculture.2026.744489openalex-snapshot

Transcriptomic insights into the algicidal mechanism of citric acid-activated ClO2 against the green tide alga Ulva prolifera

inferred← citeshttps://doi.org/10.1016/j.aquatox.2016.05.012openalex-snapshot

Combined exposure to pyrene and fluoranthene and their molecular effects on the Sydney rock oyster, Saccostrea glomerata

inferred← citeshttps://doi.org/10.1016/j.bbagen.2018.07.032openalex-snapshot

Transcriptome analyses reveal molecular mechanisms that regulate endochondral ossification in amphibian Bufo gargarizans during metamorphosis

inferred← citeshttps://doi.org/10.1016/j.bbamcr.2019.01.002openalex-snapshot

IKKε regulates the breast cancer stem cell phenotype

inferred← citeshttps://doi.org/10.1016/j.bbamcr.2019.118523openalex-snapshot

Microenvironment-regulated lncRNA-HAL is able to promote stemness in breast cancer cells

inferred← citeshttps://doi.org/10.1016/j.bbamcr.2025.120103openalex-snapshot

Mutant-specific dysfunction of RHOBTB2 impairs mitochondrial function and Na+/K+-ATPase levels in a cell model

inferred← citeshttps://doi.org/10.1016/j.bbrc.2015.09.129openalex-snapshot

Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep

inferred← citeshttps://doi.org/10.1016/j.bcp.2020.114226openalex-snapshot

Cardiac glycosides inhibit cancer through Na/K-ATPase-dependent cell death induction

inferred← citeshttps://doi.org/10.1016/j.bcp.2022.115187openalex-snapshot

Human 5-lipoxygenase regulates transcription by association to euchromatin

inferred← citeshttps://doi.org/10.1016/j.biomaterials.2020.120575openalex-snapshot

Chitosan 3D cell culture system promotes naïve-like features of human induced pluripotent stem cells: A novel tool to sustain pluripotency and facilitate differentiation

inferred← citeshttps://doi.org/10.1016/j.biortech.2026.135992openalex-snapshot

Alanine aminotransferase–acetyl-CoA carboxylase switching produces starch-rich bioethanol feedstock in Desmodesmus

inferred← citeshttps://doi.org/10.1016/j.brainres.2025.150006openalex-snapshot

Interaction of matrix components and cells regulating cellular and molecular processes of glioma cells

inferred← citeshttps://doi.org/10.1016/j.cbd.2019.05.001openalex-snapshot

Transcriptome analysis of body wall reveals growth difference between the largest and smallest individuals in the pure and hybrid populations of Apostichopus japonicus

inferred← citeshttps://doi.org/10.1016/j.cbd.2025.101740openalex-snapshot

Hypoxia and reoxygenation induce changes in oxidative stress, histological structure, and transcriptome in the liver of mandarin fish (Siniperca chuatsi)

inferred← citeshttps://doi.org/10.1016/j.cbpb.2025.111189openalex-snapshot

Aerial exposure and seawater immersion induce distinct transcriptomic responses of the marine pulmonate gastropod, Siphonaria japonica (Donovan, 1824), as determined by Iso-seq and RNA-seq analysis

inferred← citeshttps://doi.org/10.1016/j.ccell.2017.08.018openalex-snapshot

Coordinated Splicing of Regulatory Detained Introns within Oncogenic Transcripts Creates an Exploitable Vulnerability in Malignant Glioma

inferred← citeshttps://doi.org/10.1016/j.ccell.2018.02.011openalex-snapshot

GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth

inferred← citeshttps://doi.org/10.1016/j.ccell.2018.09.001openalex-snapshot

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis

inferred← citeshttps://doi.org/10.1016/j.ccell.2020.02.003openalex-snapshot

Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer

inferred← citeshttps://doi.org/10.1016/j.cell.2017.09.003openalex-snapshot

Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation

inferred← citeshttps://doi.org/10.1016/j.cell.2018.12.040openalex-snapshot

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells

inferred← citeshttps://doi.org/10.1016/j.cell.2019.01.036openalex-snapshot

FXR Regulates Intestinal Cancer Stem Cell Proliferation

inferred← citeshttps://doi.org/10.1016/j.cell.2022.11.004openalex-snapshot

Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer

inferred← citeshttps://doi.org/10.1016/j.cell.2024.10.030openalex-snapshot

A Zea genus-specific micropeptide controls kernel dehydration in maize

inferred← citeshttps://doi.org/10.1016/j.cell.2025.11.003openalex-snapshot

A stepwise decoding mechanism for heat sensing in plants connects lipid remodeling to a nuclear signaling cascade

inferred← citeshttps://doi.org/10.1016/j.celrep.2016.12.063openalex-snapshot

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

inferred← citeshttps://doi.org/10.1016/j.celrep.2017.09.036openalex-snapshot

Precocious Interleukin 21 Expression in Naive Mice Identifies a Natural Helper Cell Population in Autoimmune Disease

inferred← citeshttps://doi.org/10.1016/j.celrep.2017.11.084openalex-snapshot

Hepatic Leukemia Factor Maintains Quiescence of Hematopoietic Stem Cells and Protects the Stem Cell Pool during Regeneration

inferred← citeshttps://doi.org/10.1016/j.celrep.2018.07.009openalex-snapshot

Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer

inferred← citeshttps://doi.org/10.1016/j.celrep.2018.10.094openalex-snapshot

Widespread Accumulation of Ribosome-Associated Isolated 3′ UTRs in Neuronal Cell Populations of the Aging Brain

inferred← citeshttps://doi.org/10.1016/j.celrep.2018.12.064openalex-snapshot

A Persistence Detector for Metabolic Network Rewiring in an Animal

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.05.013openalex-snapshot

Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.06.037openalex-snapshot

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.07.090openalex-snapshot

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.08.060openalex-snapshot

Identification of FUBP1 as a Long Tail Cancer Driver and Widespread Regulator of Tumor Suppressor and Oncogene Alternative Splicing

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.11.065openalex-snapshot

Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells

inferred← citeshttps://doi.org/10.1016/j.celrep.2021.109279openalex-snapshot

Pumilio2 and Staufen2 selectively balance the synaptic proteome

inferred← citeshttps://doi.org/10.1016/j.celrep.2023.112879openalex-snapshot

Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma

inferred← citeshttps://doi.org/10.1016/j.celrep.2024.114496openalex-snapshot

Citrate metabolism controls the senescent microenvironment via the remodeling of pro-inflammatory enhancers

inferred← citeshttps://doi.org/10.1016/j.celrep.2025.115726openalex-snapshot

Machine-guided cell-fate engineering

inferred← citeshttps://doi.org/10.1016/j.celrep.2025.116141openalex-snapshot

Circadian clocks and periodic anticipated fasting prevent fasting-associated hepatic steatosis in calorie restriction

inferred← citeshttps://doi.org/10.1016/j.celrep.2026.118022openalex-snapshot

Anticipatory metabolic regulation drives the distinct and improved metabolic state of caloric restriction compared to Fasting-Refeeding cycles

inferred← citeshttps://doi.org/10.1016/j.cels.2020.10.003openalex-snapshot

Large-Scale Multi-omic Analysis of COVID-19 Severity

inferred← citeshttps://doi.org/10.1016/j.cels.2024.12.005openalex-snapshot

Inferring metabolic objectives and trade-offs in single cells during embryogenesis

inferred← citeshttps://doi.org/10.1016/j.chemosphere.2015.08.079openalex-snapshot

Non-monotonic dose–response effect of bisphenol A on rare minnow Gobiocypris rarus ovarian development

inferred← citeshttps://doi.org/10.1016/j.chemosphere.2018.09.133openalex-snapshot

Genome-wide identification of the interactions between key genes and pathways provide new insights into the toxicity of bisphenol F and S during early development in zebrafish

inferred← citeshttps://doi.org/10.1016/j.chom.2017.07.021openalex-snapshot

Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption

inferred← citeshttps://doi.org/10.1016/j.chom.2024.10.015openalex-snapshot

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

inferred← citeshttps://doi.org/10.1016/j.cj.2019.01.001openalex-snapshot

Involvement of sulfur assimilation in the low β subunit content of soybean seed storage protein revealed by comparative transcriptome analysis

inferred← citeshttps://doi.org/10.1016/j.cj.2022.07.012openalex-snapshot

Identification of a candidate QTG for seed number per silique by integrating QTL mapping and RNA-seq in Brassica napus L.

inferred← citeshttps://doi.org/10.1016/j.cmet.2018.01.014openalex-snapshot

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2017.07.004openalex-snapshot

SRSF shape analysis for sequencing data reveal new differentiating patterns

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2022.107795openalex-snapshot

A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP)

inferred← citeshttps://doi.org/10.1016/j.copbio.2014.01.007openalex-snapshot

Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing

inferred← citeshttps://doi.org/10.1016/j.csbj.2015.08.004openalex-snapshot

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.05.040openalex-snapshot

Robustness of differential gene expression analysis of RNA-seq

inferred← citeshttps://doi.org/10.1016/j.csbj.2022.06.001openalex-snapshot

Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes

inferred← citeshttps://doi.org/10.1016/j.csbj.2022.11.051openalex-snapshot

Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods

inferred← citeshttps://doi.org/10.1016/j.csbj.2024.02.018openalex-snapshot

Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

inferred← citeshttps://doi.org/10.1016/j.cub.2019.05.059openalex-snapshot

A Maternal Effect on Queen Production in Honeybees

inferred← citeshttps://doi.org/10.1016/j.devcel.2017.02.017openalex-snapshot

Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program

inferred← citeshttps://doi.org/10.1016/j.devcel.2021.01.015openalex-snapshot

N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles

inferred← citeshttps://doi.org/10.1016/j.dib.2018.09.086openalex-snapshot

RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis

inferred← citeshttps://doi.org/10.1016/j.dib.2020.106442openalex-snapshot

Transcriptomic dataset of zebrafish tissues following chronic alcohol exposure and withdrawal

inferred← citeshttps://doi.org/10.1016/j.dnarep.2015.03.007openalex-snapshot

Cell cycle regulation of human DNA repair and chromatin remodeling genes

inferred← citeshttps://doi.org/10.1016/j.ebiom.2019.04.048openalex-snapshot

Disrupted Folate Metabolism with Anesthesia Leads to Myelination Deficits Mediated by Epigenetic Regulation of ERMN

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2019.01.126openalex-snapshot

Metabolism disruption analysis of zebrafish larvae in response to BPA and BPA analogs based on RNA-Seq technique

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2019.109957openalex-snapshot

Transcriptome and physiology analysis identify key metabolic changes in the liver of the large yellow croaker (Larimichthys crocea) in response to acute hypoxia

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2020.110650openalex-snapshot

Effects of octylphenol exposure on the lipid metabolism and microbiome of the intestinal tract of Rana chensinensis tadpole by RNAseq and 16s amplicon sequencing

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2022.114217openalex-snapshot

Dual RNA and 16S ribosomal DNA sequencing reveal arbuscular mycorrhizal fungi-mediated mitigation of selenate stress in Zea mays L. and reshaping of soil microbiota

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2023.115263openalex-snapshot

Detoxification mechanism of herbicide in Polypogon fugax and its influence on rhizosphere enzyme activities

inferred← citeshttps://doi.org/10.1016/j.envpol.2019.06.032openalex-snapshot

Combination analysis of the physiology and transcriptome provides insights into the mechanism of silver nanoparticles phytotoxicity

inferred← citeshttps://doi.org/10.1016/j.envpol.2025.126210openalex-snapshot

Mechanisms of BpTT2 overexpression in enhancing cadmium tolerence of Broussonetia papyrifera

inferred← citeshttps://doi.org/10.1016/j.exer.2015.05.009openalex-snapshot

Tools and resources for analyzing gene expression changes in glaucomatous neurodegeneration

inferred← citeshttps://doi.org/10.1016/j.exphem.2013.05.066openalex-snapshot

Induced pluripotent stem cell model of chronic myeloid leukemia revealed olfactomedin 4 as a novel therapeutic target in leukemia stem cells

inferred← citeshttps://doi.org/10.1016/j.exphem.2018.10.009openalex-snapshot

RUNX1 and the endothelial origin of blood

inferred← citeshttps://doi.org/10.1016/j.foodres.2023.112587openalex-snapshot

Widely targeted metabolomic, transcriptomic, and metagenomic profiling reveal microbe–plant–metabolic reprogramming patterns mediated by Streptomyces pactum Act12 enhance the fruit quality of Capsicum annuum L

inferred← citeshttps://doi.org/10.1016/j.fsi.2015.12.005openalex-snapshot

Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress

inferred← citeshttps://doi.org/10.1016/j.fsi.2018.08.052openalex-snapshot

Comparative transcriptomics analysis of the river pufferfish (Takifugu obscurus) by tributyltin exposure: Clues for revealing its toxic injury mechanism

inferred← citeshttps://doi.org/10.1016/j.fsi.2018.12.039openalex-snapshot

Transcriptome of white shrimp Litopenaeus vannamei induced with rapamycin reveals the role of autophagy in shrimp immunity

inferred← citeshttps://doi.org/10.1016/j.fsi.2020.10.020openalex-snapshot

Transcriptome analysis reveals temperature-dependent early immune response in flounder (Paralichthys olivaceus) after Hirame novirhabdovirus (HIRRV) infection

inferred← citeshttps://doi.org/10.1016/j.gecco.2021.e01532openalex-snapshot

Comparative transcriptome analysis of Salix cupularis under drought stress

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