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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Mass spectrometry group has mass appeal.
PMID 15598607 · PMC1247668 · Environmental health perspectives · 2004 · 7 claims · 4 setups
Mass spectrometry can identify proteins and their post-translational modifications with high specificity and sensitivity, making it central to toxicoproteomics.
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Systems biology of gene regulation fulfills its promise.
PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups
Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.
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Has reproduction · 99
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups
Across 253 manually curated studies (164,000+ samples), over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available overall.
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TRED: a transcriptional regulatory element database, new entries and other development.
PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups
TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes
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An "omics" approach to uropathogenic Escherichia coli vaccinology.
PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups
An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates
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Repeating patterns of mimicry.
PMID 17048984 · PMC1617347 · PLoS biology · 2006 · 7 claims · 4 setups
The Yb locus controls presence of a yellow wing band in H. melpomene
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Charting the map of life.
PMID 11171541 · PMC1242061 · Environmental health perspectives · 2001 · 8 claims · 8 setups
Only 3-5% of the human genome, corresponding to 30,000-100,000 genes, is thought to be biologically functional
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From single cells to whole organisms.
PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups
The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods
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Microbial metagenomics.
PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups
Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides
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The UCSC Genome Browser Database: 2008 update.
PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.
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Has reproduction
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.
PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups
Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas
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Has reproduction · 84
Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.
PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups
Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 71
A crowdsourced set of curated structural variants for the human genome.
PMID 32559231 · PMC7329145 · PLoS computational biology · 2020 · 8 claims · 8 setups
1235 manually curated SVs were produced that can be used to evaluate SV callers or train machine learning models
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Has reproduction · 60
A comparative analysis of blastoid models through single-cell transcriptomics.
PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups
EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.
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Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics
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Has reproduction · 71
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.
PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups
109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules
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Has reproduction · 50
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.
PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups
829 genes are overexpressed in regions of increased calcite spicule formation in S. ciliatum, including known sclerocyte-specific biomineralization genes.
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Has reproduction · 52
Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.
PMID 41345487 · PMC12739157 · Scientific reports · 2025 · 7 claims · 8 setups
Sulfate reduction rates (SRR) at in-situ ambient temperature in acidic Bom-Gorkhon tailings sediments are unexpectedly high, up to 9.86 µmol SO4 cm-3 day-1.
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Has reproduction · 84
Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.
PMID 40416609 · PMC12103846 · PeerJ · 2025 · 8 claims · 6 setups
GBS colonization was detected in 51 of 1,924 (2.7%) pregnant women screened