The DEE2 Hall of FAME

Other articles

• Yang et al. Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection. Cell Stem Cell. 2024 Nov 7;31(11):1612-1629.e8.

  The DEE2 RNA-seq pipeline was used to process bulk RNA-seq data to understand gene regulation in islet organoids upon viral infection

• Kleverov et al. Phantasus, a web application for visual and interactive gene expression analysis. Elife. 2024 Jun 3;13:e85722.

  Phantasus is a new web-based tool for RNA-seq analysis enabling differential expression and pathway enrichment from the browser. The tool natively uses data from DEE2 and ARCHS4. Phantasus is available here: https://alserglab.wustl.edu/phantasus/

• Zrimec et al. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun. 2020 Dec 1;11(1):6141.

  Bulk Saccharomyces cerevisiae data from DEE2 was the main dataset used in this study. Deep learning analysis was used to associate genomic sequence features with mRNA expression levels.

• Ramalingam et al. Suppression of thrombospondin-1-mediated inflammaging prolongs hematopoietic health span. Sci Immunol. 2025 Jan 3;10(103):eads1556.

  The DEE2 pipeline was used for the processing of RNA-seq data derived from HSC of young control and Thbs1KO mice to understand the gene regulatory role of thrombospondin-1.

• Wijesooriya et al. Urgent need for consistent standards in functional enrichment analysis. PLoS Comput Biol. 2022 Mar 9;18(3):e1009935.

  DEE2.io was used to fetch RNA-seq data to demonstrate the impact of common errors in pathway enrichment analysis. [Note: this publication is from Ziemann's team.]

• Mansouri et al. Mesenchymal stromal cell exosomes prevent and revert experimental pulmonary fibrosis through modulation of monocyte phenotypes. JCI Insight. 2019 Nov 1;4(21):e128060.

  DEE2 data was used to understand expression of BM-derived Ly6Cpos and Ly6Cneg monocytes.

• Ramalingam et al. Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response. Nat Commun. 2023 Apr 10;14(1):2018.

  DEE2 data was used to understand patterns of Netrin-1 in bone marrow.

• Yang et al, SARS-CoV-2 infection causes dopaminergic neuron senescence. Cell Stem Cell. 2024 Feb 1;31(2):196-211.e6.

  DEE2 pipeline was used to study the transcriptome of human neurons infected with SARS-CoV-2.

• Hisata et al. Reversal of emphysema by restoration of pulmonary endothelial cells. J Exp Med. 2021 Aug 2;218(8):e20200938.

  DEE2 data was used to make the key discovery that emphasema is associated with loss of endothelial gene expression.

• Ge X. iDEP Web Application for RNA-Seq Data Analysis. Methods Mol Biol. 2021;2284:417-443.

  In a new version of iDEP, there is a new feature which is able to fetch gene expression data from DEE2.

• Ziemann et al. Two subtle problems with overrepresentation analysis. Bioinform Adv. 2024 Oct 21;4(1):vbae159.

  DEE2 data is used to demonstrate the subtle differences between ORA enrichment analysis implementations. [Note: this publication is from Ziemann's team.]

• Gomez-Salinero et al. Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis. Nat Cardiovasc Res. 2022 Oct;1:882-899.

  The DEE2 pipeline was used to explore the early events by which loss of ERG and Fli1 leads to global vascular collapse in heart, liver and lung.

• Trivedi et al. Lung lymphatic endothelial cells undergo inflammatory and prothrombotic changes in a model of chronic obstructive pulmonary disease. Front Cell Dev Biol. 2024 Feb 19;12:1344070.

  DEE2 was used to investigate gene expression changes caused by cigarette smoke in an animal model.