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 · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.
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Has reproduction · 30
Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.
PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups
BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors
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Has reproduction · 78
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.
PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups
A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response
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Has reproduction · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups
Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.
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Has reproduction · 93
Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.
PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups
SIRT6 regulates tryptophan catabolism by balancing usage between the kynurenine pathway and the serotonin/melatonin pathway, conserved from Drosophila to mouse and human cells.
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Has reproduction · 68
Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.
PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups
200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations
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Has reproduction · 88
Age Deceleration and Reversal Gene Patterns in Dauer Diapause.
PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups
Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption
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Has reproduction · 77
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups
spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.
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Has reproduction · 74
L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.
PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups
L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C
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Has reproduction · 10
Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.
PMID 41253754 · PMC12627582 · Nature communications · 2025 · 8 claims · 8 setups
Gli1+ fetal cells are the precursors of postnatal long-lived chondroprogenitors (LLCPs) in the growth plate
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Has reproduction · 67
NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.
PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups
NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.
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Has reproduction · 69
JunB Is Critical for Survival of T Helper Cells.
PMID 35837408 · PMC9273772 · Frontiers in immunology · 2022 · 7 claims · 7 setups
JunB is required for clonal expansion of Th1, Th2, and Th17 cells
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Has reproduction · 75
Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.
PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups
Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple
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Has reproduction · 93
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.
PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups
An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.
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Has reproduction · 78
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.
PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups
Inactivation of the orphan 4mC methyltransferase (LomA) causes complete abrogation of CTAG motif methylation genome-wide
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Has reproduction · 98
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.
PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups
Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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Has reproduction · 50
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.
PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups
BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes
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Has reproduction · 53
Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.
PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 8 claims · 6 setups
1,613 genes were differentially expressed in leprosy progressors before diagnosis (t=1) compared to household contacts.
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Has reproduction · 69
TC-hunter: identification of the insertion site of a transgenic gene within the host genome.
PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups
TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.