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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Patterns of evolutionary constraints on genes in humans.
PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups
BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint
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Widely variable endogenous retroviral methylation levels in human placenta.
PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups
Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters
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Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.
PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups
Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity
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Has reproduction · 65
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.
PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups
UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.
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Technical challenges in using human induced pluripotent stem cells to model disease.
PMID 19951687 · PMC2921621 · Cell stem cell · 2009 · 8 claims · 8 setups
hiPSCs generated from patient somatic cells (skin, blood) can be differentiated into disease-relevant cell types to model disease pathogenesis in vitro
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Ontological visualization of protein-protein interactions.
PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups
Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks
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Has reproduction · 94
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 6 setups
EiaD is a reproducible, versioned pan-eye and body RNA-seq transcriptome dataset built from 916 eye and 1375 GTEx samples via a Snakemake pipeline output as a single SQLite database.
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons
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Has reproduction · 10
Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.
PMID 41253754 · PMC12627582 · Nature communications · 2025 · 7 claims · 8 setups
Fetal Gli1+ cells (including cells outside the cartilage) are the precursors of postnatal long-lived chondroprogenitors and give rise to most growth-plate chondrocytes juvenile/adult.
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Has reproduction · 68
Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.
PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups
viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.
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Independent component analysis reveals new and biologically significant structures in micro array data.
PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups
ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone
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From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.
PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups
There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins
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Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.
PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups
CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad
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Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.
PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups
An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.