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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Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.
PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups
LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)
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Has reproduction · 76
Tracing human genetic histories and natural selection with precise local ancestry inference.
PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups
Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.
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The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.
PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups
1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions
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Has reproduction · 97
Determination of complete chromosomal haplotypes by bulk DNA sequencing.
PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups
A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts
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Has reproduction · 78
Detecting tipping points of complex diseases by network information entropy.
PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups
NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data
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Has reproduction · 64
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.
PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups
Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.
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In vivo application of RNA interference: from functional genomics to therapeutics.
PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups
RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA
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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
Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.
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Identifying repeat domains in large genomes.
PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups
A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.