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 · 56
DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.
PMID 31694669 · PMC6836538 · Genome biology · 2019 · 8 claims · 8 setups
DESE is a unified iterative framework that estimates driver tissues of complex diseases/traits from tissue-selective expression of GWAS-associated genes, and outputs prioritized susceptibility genes as a byproduct
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Has reproduction · 85
The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.
PMID 33772001 · PMC7998036 · Nature communications · 2021 · 8 claims · 8 setups
AAMDC is an amplified/overexpressed oncogene in a subgroup of ER-positive breast cancers (IntClust2) associated with poor prognosis
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Has reproduction · 63
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date
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Has reproduction · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors
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Has reproduction · 59
Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.
PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups
Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes
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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Has reproduction · 81
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.
PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups
scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication
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Has reproduction · 92
Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.
PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups
cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.
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Has reproduction · 85
What defines a photosynthetic microbial mat in western Antarctica?
PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups
Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions
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Has reproduction · 59
The motor neuron m6A repertoire governs neuronal homeostasis and FTO inhibition mitigates ALS symptom manifestation.
PMID 40307231 · PMC12043976 · Nature communications · 2025 · 8 claims · 8 setups
m6A hypomethylation (not hypermethylation) is consistently associated with ALS across patient iPSC-MNs, postmortem tissue, and independent transcriptomic datasets
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Has reproduction · 64
Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.
PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups
Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important
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Has reproduction · 82
Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.
PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups
Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.
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Has reproduction · 73
RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.
PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups
RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML
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Has reproduction · 64
Early life-stage thermal resilience is determined by climate-linked regulatory variation.
PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups
Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X
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Has reproduction · 50
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.
PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups
BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length
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Has reproduction · 50
Cis-Regulation of the CFTR Gene in Pancreatic Cells.
PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups
Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model
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Has reproduction · 92
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.
PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups
A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)
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Has reproduction · 90
Sediment Resuspension as a System-Wide Driver of Legacy and Bioavailable Phosphorus Release in Lake Erie.
PMID 41960750 · PMC13130958 · Environmental science & technology · 2026 · 7 claims · 8 setups
Sediment resuspension is a major episodic internal phosphorus source releasing bioavailable P far exceeding previously reported aerobic diffusive fluxes.
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Has reproduction · 95
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.
PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups
Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns