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 · 23
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.
PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups
COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.
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Has reproduction · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 57
Data-driven projections of candidate enhancer-activating SNPs in immune regulation.
PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups
A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.
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Has reproduction · 98
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups
maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors
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Has reproduction · 100
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.
PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups
Hsp90-dependent gene expression varies among different yeast strains
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Has reproduction · 66
Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.
PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups
A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.
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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 · 5 setups
A 120-gene endometrial transcriptomic fingerprint encodes defective decidualization associated with severe preeclampsia.
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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
A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.
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Has reproduction · 50
Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.
PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups
VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.
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Has reproduction · 76
Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.
PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups
mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed
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Have microarrays failed to deliver for developmental biology?
PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups
Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC
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Has reproduction · 95
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.
PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups
Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature
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Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes
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Has reproduction · 100
Sox8 remodels the cranial ectoderm to generate the ear.
PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups
Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity
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Has reproduction · 59
The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.
PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups
p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se
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Has reproduction · 83
Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.
PMID 35953471 · PMC9372134 · Nature communications · 2022 · 8 claims · 8 setups
ATX1, ATX2, and ATXR7 redundantly mediate H3K4 monomethylation genome-wide
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Cohesin regulates alternative splicing.
PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups
Cohesin regulates alternative splicing independently of its effects on transcription.
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Has reproduction · 68
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.
PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups
Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.
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Has reproduction · 88
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.
PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups
SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC