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 · 69
Fluent genomics with plyranges and tximeta.
PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 3 setups
A three-step fluent genomics workflow (import, model, integrate) using plyranges and tximeta provides a coherent, reproducible framework for integrating RNA-seq and ATAC-seq data within the Bioconductor ecosystem.
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Has reproduction · 67
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.
PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups
RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 7 claims · 7 setups
LncRNA-mRNA competitive regulatory network topology and function differ substantially between control and cytokine-treated (IL-1β+IFN-γ) islet exosomes
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Has reproduction · 50
Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.
PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups
A 279-gene 'iMSC signature' is upregulated in BM MSCs from MM patients compared to healthy donors, identified by reanalysis of single-cell RNA-seq data.
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Has reproduction · 100
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.
PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups
Oncogenes MITF, KIT, CDH1, NRAS, AKT1, EGFR, TP53, and CDK4 are elevated while tumor suppressors PTEN, cAMP, and BCL2 are reduced in melanoma
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Has reproduction · 68
Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.
PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups
Arg1 is highly and specifically induced in lung CD4+ T cells during in vivo influenza infection
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 8 claims · 8 setups
CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.
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Has reproduction · 62
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.
PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups
A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform
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Has reproduction · 59
Nucleosome regulatory dynamics in response to TGFβ.
PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups
SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.
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Has reproduction · 88
Vaccine-induced ICOS(+)CD38(+) circulating Tfh are sensitive biosensors of age-related changes in inflammatory pathways.
PMID 34095875 · PMC8149371 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Vaccine-induced ICOS+CD38+ cTfh from elderly adults show increased TNF-NF-κB pathway transcriptional signaling compared to young adults at day 7 post-vaccination
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Has reproduction · 61
Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.
PMID 39736644 · PMC11687009 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups
Dedifferentiation via MITF knockdown renders 624Mel melanoma cells hypersensitive to IFNγ, producing non-additive (synergistic) upregulation of IFNγ-induced genes.
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Has reproduction · 55
Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.
PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups
eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release
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Has reproduction · 83
Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups
Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds
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Has reproduction · 75
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 6 claims · 6 setups
The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival across three independent cohorts.
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups
TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene
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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 · 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 · 67
Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.
PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups
Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing
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Has reproduction · 80
Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.
PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 8 setups
After ~2 decades of ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin, especially centromeric/peri-centromeric satellite and micro-satellite DNA
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Has reproduction · 87
Covalent binding of thioredoxin to TXNIP is required for diet-induced insulin resistance in the liver.
PMID 40345590 · PMC12180993 · The Journal of biological chemistry · 2025 · 8 claims · 9 setups
TXNIP Cysteine 247 is required for high-fat diet-induced hepatic and whole-body insulin resistance in mice