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).

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr

• A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

  PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

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  FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

  chimpanzee hepg2 promoters liver quantitative western sirna

• Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.

  PMID 41650962 · PMC12985389 · Stem cell reports · 2026 · 8 claims · 8 setups

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  Analysis of 532 RNA-seq datasets constructed a high-resolution promoter activity landscape across hematopoietic lineages

  hematopoietic major monocytes candidate rna-seq h3k4me3 motif

• Modeling nascent transcription from chromatin landscape and structure with CLASTER.

  PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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  CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

  embryonic mescs chromatin k562 eu-seq chip-seq micro-c

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• Spatial transcriptomics identifies differentiation, lipid metabolism, and retinoid pathway alterations in acne vulgaris.

  PMID 41657309 · PMC12892907 · JCI insight · 2026 · 8 claims · 6 setups

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  A custom KRT5-directed segmentation pipeline improves transcript assignment accuracy in the spatially complex sebaceous gland compared with standard multimodal or nuclei-expansion segmentation

  skin inflammatory tert gtrd spatial immunohistochemistry reanalysis