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 · 78
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.
PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups
In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.
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Has reproduction · 81
Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups
Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.
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Has reproduction · 52
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
PMID 31980607 · PMC6981202 · Nature communications · 2020 · 6 claims · 4 setups
A meta-analysis (MetaMEx) of 66 published human skeletal muscle datasets reveals pathways selectively activated by inactivity, aerobic versus resistance, and acute versus chronic exercise training.
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Has reproduction · 69
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.
PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups
Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis
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Has reproduction · 37
RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).
PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups
RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.
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Has reproduction · 76
Correcting scale distortion in RNA sequencing data.
PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups
Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)
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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 · 95
OptiType: precision HLA typing from next-generation sequencing data.
PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups
OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.
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Has reproduction · 59
Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.
PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups
PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups
An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.
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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 · 90
Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.
PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 6 claims · 3 setups
Representing the genome as a binary string (1/0) of peak presence and computing Hamming distances enables hierarchical clustering of ATAC-seq samples with reduced computational cost while preserving cell-type classification.
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Has reproduction · 93
Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.
PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups
snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.
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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