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).

• X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

  PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

  ensembl breast mcf7 25-mer probe-to-transcript microarray

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

  PMID 19050890 · PMC2690858 · Annals of hematology · 2009 · 7 claims · 7 setups

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  HBG2:g.-109G>T is a novel promoter mutation causing a distinct ('Hellenic type') nd-HPFH

  peripheral genomic nuclear mel cation reverse-phase denaturing

• Endogenous Fatty Acid Synthesis Drives Brown Adipose Tissue Involution.

  PMID 33440156 · PMC8240962 · Cell reports · 2021 · 8 claims · 8 setups

  Has reproduction

  Endogenous fatty acid synthesis (DNL), regulated by ChREBP, is the central driver of BAT whitening/involution at thermoneutrality.

  bat fatty lipidomics qpcr

• Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

  PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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  emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

  streptococcus pyogenes emm values multilocus emm comparative

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups

  Has reproduction · 84

  DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks

  tcga breast metabric brca bulk mirna methylation

• Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

  PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 71

  CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.

  monocyte-macrophage cd4+ kidney metabolic bulk single-cell codon

• Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.

  PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 41

  A CPAN-index prognostic model built from 11 PANoptosis-related differentially expressed genes (CPAN_DEGs) stratifies CRC patients into high-risk and low-risk groups with distinct survival and immunophenotypes.

  crc merged hct116 bulk single-cell immune

• Influence of two vaccination campaigns on genetic diversity of invasive Neisseria meningitidis isolates in northern Spain (1997-2008).

  PMID 20041148 · PMC2794534 · PloS one · 2009 · 7 claims · 7 setups

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  Overall diversity of the invasive meningococcal population, measured by ST/clonal complex frequencies, allele numbers, polymorphic sites, and index of association, remained relatively constant throughout the 12-year study period despite the two vaccination campaigns.

  invasive non-serogroupable meningitidis mlst latex real-time pcr

• Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

  PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups

  Has reproduction · 59

  Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.

  healthy six ahba neurons resting-state microarray wgcna

• Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

  PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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  Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

  european african individuals nondiabetic snp variant direct

• Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

  PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

  Has reproduction · 84

  Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

  elegans short-read whole-animal rt-pcr

• Brown fat activation reduces hypercholesterolaemia and protects from atherosclerosis development.

  PMID 25754609 · PMC4366535 · Nature communications · 2015 · 7 claims · 8 setups

  Has reproduction

  β3-AR agonist-mediated BAT activation reduces plasma triglycerides and cholesterol and protects against atherosclerosis development in APOE*3-Leiden.CETP mice.

  e3l.cetp interscapular liver aortic indirect histology plasma

• Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

  PMID 16507150 · PMC1413975 · Breast cancer research : BCR · 2006 · 6 claims · 7 setups

  Full-text index only

  kConFab is a collaborative resource providing epidemiological, clinical, and biospecimen data from high-risk familial breast/ovarian cancer families, available to researchers worldwide for ethically approved, peer-reviewed projects.

  germline unaffected index randomly brca1 tyrer-cuzick strp

• Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

  PMID 18174378 · PMC2605348 · Blood · 2008 · 7 claims · 8 setups

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  Homozygous SLC4A1 Ser667Phe mutation causes both hereditary spherocytosis and incomplete distal renal tubular acidosis in the proband

  erythrocyte genomic erythrocytes xenopus sds-page sscp dids

• Charting and probing the activity of ADARs in human development and cell-fate specification.

  PMID 39537590 · PMC11561244 · Nature communications · 2024 · 8 claims · 7 setups

  Has reproduction · 100

  RNA editing (AEI) and ADAR enzyme expression follow tissue-specific temporal dynamics across human organs from fetal to adult stages, with ADARB1 dynamics tracking AEI increase in hindbrain development.

  organs bulk 8-week 8–10-week bulk site-specific single-cell

• Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

  PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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  The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

  clinical concatenated cereus isolates multilocus phylogenetic pcr

• Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

  PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 99

  Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).

  southeastern lake muskegon lake-type 16s within-phylum phylogenetic

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 7 setups

  Has reproduction · 45

  Eight distinct T cell populations are identifiable in CRC tumor tissue and seven in peripheral blood by unsupervised clustering of scRNA-seq data.

  tumor peripheral cd4+ eight single-cell unsupervised ligand-receptor

• Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

  PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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  HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

  genomic genotype 293t pcr-amplified pcr haplotype cell-cell