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 · 100
Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.
PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).
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Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.
PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups
QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies
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Has reproduction · 96
In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma.
PMID 36650150 · PMC9845242 · Nature communications · 2023 · 8 claims · 9 setups
Alveolar macrophages support lung cancer cell proliferation and contribute to unfavourable outcomes.
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.
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Has reproduction · 93
A comparative study on recombination activity in cattle.
PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups
Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)
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Analysis of chimpanzee history based on genome sequence alignments.
PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups
Bonobos and common chimpanzees separated approximately 1.29 million years ago
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups
A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.
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Has reproduction · 35
Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.
PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes
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Has reproduction · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.