Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

  PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

  urothelial clustered genome-wide confocal k-means

• Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo.

  PMID 18681965 · PMC2519092 · BMC genomics · 2008 · 8 claims · 6 setups

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  1-h and 6-h intraduodenal exposure of human small intestinal mucosa to L. plantarum WCFS1 induces differential expression of 669 and 424 gene reporters, respectively.

  duodenal microarray combined whole-genome proteome real-time

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

  PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

  Has reproduction

  The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

  ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• Vaccine-induced ICOS(+)CD38(+) circulating Tfh are sensitive biosensors of age-related changes in inflammatory pathways.

  PMID 34095875 · PMC8149371 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 88

  Vaccine-induced ICOS+CD38+ cTfh from elderly adults show increased TNF-NF-κB pathway transcriptional signaling compared to young adults at day 7 post-vaccination

  pbmc sorted rna-seq icos+cd38+ flow bulk gene