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).
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Has reproduction · 73
Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.
PMID 38352867 · PMC10861739 · Frontiers in immunology · 2024 · 6 claims · 3 setups
A targeted panel of 176 transcripts plus 8 housekeeping genes was identified for monitoring immunological changes during pregnancy
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 6 setups
A 120-gene transcriptomic fingerprint encoding defective decidualization is present in decidua of women who developed sPE in a prior pregnancy
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Has reproduction · 50
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.
PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups
GAL08 is a dominant bacterial clade in a neutral hot spring, comprising up to 29.2% of the community by relative read abundance and up to 4.7 × 10^5 16S rRNA gene copies per gram sediment.
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Has reproduction · 75
Single-cell multiomics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response.
PMID 39503729 · PMC11540304 · eLife · 2024 · 8 claims · 5 setups
CITE-seq multiomics reveals that each CML patient harbors a unique composition of stem and progenitor cells at diagnosis
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Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.
PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups
A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species
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Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.
PMID 28789673 · PMC5549432 · BMC research notes · 2017 · 7 claims · 7 setups
Gene and transcript abundances of bacterial type III secretion system (T3SS) genes are positively correlated with methane yield in sheep
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Has reproduction · 85
Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.
PMID 39384533 · PMC11650866 · FEMS microbiology ecology · 2024 · 8 claims · 8 setups
Chloroflexota populations are partitioned according to alternative electron acceptors (Anaerolineae) and electron donors (Dehalococcoidia) among respiratory and fermentative metabolites at and below the sediment-water interface
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Has reproduction · 75
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups
geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data
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Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.
PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups
Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.
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Evolutionary origins of human apoptosis and genome-stability gene networks.
PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups
The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.
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Has reproduction · 41
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.
PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups
Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.
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Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.
PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups
The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.
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Has reproduction · 63
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.
PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration
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Has reproduction · 93
Global and precise identification of functional miRNA targets in mESCs by integrative analysis.
PMID 35899551 · PMC9442311 · EMBO reports · 2022 · 8 claims · 8 setups
Fewer than 10% of expressed genes are directly and functionally regulated by miRNAs in mESCs
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Has reproduction · 71
Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.
PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups
The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown
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Has reproduction · 78
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.
PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups
TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.
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Biased exon/intron distribution of cryptic and de novo 3' splice sites.
PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups
Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns
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Has reproduction · 74
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.
PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups
RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).