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
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.
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Has reproduction · 64
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups
metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes
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Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups
About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain
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Functional role of the KLF6 tumour suppressor gene in gastric cancer.
PMID 19101139 · PMC2970616 · European journal of cancer (Oxford, England : 1990) · 2009 · 7 claims · 8 setups
The KLF6 locus undergoes loss of heterozygosity (LOH) in a majority of gastric cancer samples and is associated with advanced tumour stage
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Has reproduction · 69
Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.
PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups
Porcine kidney xenografts transplanted into NHPs show only modest growth over time.
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Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization.
PMID 16839184 · PMC1500809 · PLoS genetics · 2006 · 8 claims · 8 setups
Cre/loxP recombination in ES cells can generate megabase-scale deletions, duplications, and inversions depending on loxP orientation, cis/trans configuration, and cell cycle stage
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Has reproduction · 67
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.
PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups
RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical
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Has reproduction · 95
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.
PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups
ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids
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Has reproduction · 65
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.
PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups
comBO is a single iPSC differentiation generating lymphoid, myeloid, vascular, mesenchymal stromal, and functional osteo/adipogenic lineages within one organoid
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Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups
Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants
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Has reproduction · 50
Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.
PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups
A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.
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Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.
PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups
hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)
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Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).
PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups
MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes
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Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.
PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups
Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.
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Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.
PMID 18384686 · PMC2359743 · BMC cell biology · 2008 · 8 claims · 8 setups
β1Int-HaloTag fusion protein localizes to the cell membrane in a pattern similar to endogenous β1 integrin, indicating the fusion does not disrupt normal integrin surface expression
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Contributions of proteomics to understanding phagosome maturation.
PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups
Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).
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PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.
PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups
PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing
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Has reproduction · 84
Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.
PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 7 setups
Bhlhb4−/− and Islet1−/− grafts have markedly reduced bipolar cell populations after transplantation while retaining intact photoreceptor cell layers
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Has reproduction · 76
Lamin C is required to establish genome organization after mitosis.
PMID 34775987 · PMC8591896 · Genome biology · 2021 · 7 claims · 6 setups
Lamin C, and not lamin A or lamin B1, is required for LAD:LAD cohesion, retention of LADs near the nuclear envelope, and overall chromosome territory organization.
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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.