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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Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.
PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups
MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways
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Has reproduction · 67
Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.
PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups
Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.
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Unravelling Synaptic and Metabolic Mechanisms of Cognitive Resilience in Asymptomatic Alzheimer's Disease Across Two Alzheimer's Disease Cohorts.
PMID 41723778 · PMC12996523 · Cellular and molecular neurobiology · 2026 · 6 claims · 6 setups
Integrating DEG, DET, and DUT analyses (rather than DEGs alone) provides a more comprehensive view of the molecular mechanisms of AsymAD, since some genes/transcripts are only detected by transcript-level methods.
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A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.
PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups
The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB
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Has reproduction · 100
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.
PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups
A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.
PMID 39682743 · PMC11640164 · Cells · 2024 · 8 claims · 5 setups
Estimated T-cell infiltration differs significantly across melanoma, bladder, ovarian, and pancreatic cancers, tracking known immunogenic potential.
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Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups
A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups
A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)
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Has reproduction · 85
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.
PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups
Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.
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Transcriptional responses to proteotoxic stressors are profoundly diverse and tissue-specific.
PMID 41619802 · PMC12908066 · Cell stress & chaperones · 2026 · 8 claims · 7 setups
Heat shock, HSP90 inhibition, and polyQ aggregation launch fundamentally distinct RNA expression programs rather than a shared stress response.
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Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis.
PMID 41741465 · PMC13057173 · Nature communications · 2026 · 8 claims · 7 setups
The MTOR eQTL variant rs4845987 has context-specific, opposite effects on MTOR expression: decreasing it in activated T cells and increasing it in neutrophils.
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Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.
PMID 41776501 · PMC13162433 · Molecular cancer · 2026 · 8 claims · 6 setups
MeRLin, a single-vector high-complexity lineage tracing platform integrating cellular barcoding, scRNA-seq, RNA-FISH, and computational analysis, was developed to track clonal and transcriptional dynamics in a melanoma PDX model
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Has reproduction · 59
De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.
PMID 24586345 · PMC3929608 · 8 claims · 8 setups
A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.
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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 · 90
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.
PMID 37948380 · PMC10637681 · PloS one · 2023 · 8 claims · 8 setups
Stemness-related genes ORC1L, KIF20A, and DLGAP5 are upregulated in LUAD and correlate with altered immune cell infiltration (Th2, MDSC, HSC) and reduced patient survival.
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Temporal constraints on enhancer usage shape the regulation of limb gene transcription.
PMID 41526337 · PMC12795824 · Nature communications · 2026 · 8 claims · 6 setups
Putative enhancer repertoires at limb developmental gene loci shift over time, with distinct early-acting, common-acting, and late-acting enhancers.
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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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Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.
PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups
PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit
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FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster.
PMID 41551930 · PMC12805895 · NAR genomics and bioinformatics · 2026 · 7 claims · 8 setups
FLYNC, an explainable boosting machine (EBM) model, accurately predicts the probability that a newly identified RNA transcript in D. melanogaster is a lncRNA