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).

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• Inferring combinatorial regulation of transcription in silico.

  PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

  upstream monocytes same tfbs microarray permutation

• A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

  PMID 16420688 · PMC1382211 · BMC genomics · 2006 · 7 claims · 4 setups

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  PBEC and KC SAGE libraries show approximately 80% overlap in expressed tags, indicating high similarity in gene repertoire

  bronchial keratinocytes pbec types sage rt-pcr

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation