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).

• Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

  PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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  S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

  enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative

• Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

  PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

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  OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

  thp-1 hek293 tandem co-immunoprecipitation oas2

• NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.

  PMID 19818133 · PMC2784325 · Genome biology · 2009 · 8 claims · 5 setups

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  Determined and manually annotated the complete genome sequence of N. meningitidis clinical isolate strain 8013

  meningitidis archived strain neisseria whole-genome transposon targeted

• Proteomics analysis of the nucleolus in adenovirus-infected cells.

  PMID 19812395 · PMC2808258 · Molecular & cellular proteomics : MCP · 2010 · 7 claims · 5 setups

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  SILAC-based quantitative MS identified 351 nucleolar proteins, with 24 showing at least a 2-fold change in abundance after adenovirus infection

  hela silac gel maldi-tof

• Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

  PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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  The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

  pooled 16s sequenced topo 16s primer taxonomic

• Identification of recombinant human papillomavirus type 16 variants.

  PMID 19758676 · PMC2769496 · Virology · 2009 · 8 claims · 5 setups

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  Concurrent infection with 8 HPV16 variants (1 prototype/European, 6 recombinant clones, plus later African-2) was detected in a single woman via PCR-based cloning and sequencing

  cervical pcr-based recombinant-specific direct

• Discrimination of double primary lung cancer from intrapulmonary metastasis by p53 gene mutation.

  PMID 10188905 · PMC2362717 · British journal of cancer · 1999 · 7 claims · 3 setups

  Full-text index only

  p53 mutation patterns can be used as a clonal marker to discriminate double primary lung cancer from intrapulmonary metastasis in synchronous double lung tumours.

  paraffin-embedded pcr lung pcr-single-strand sequencing extraction

• Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy.

  PMID 19094986 · PMC3388947 · Experimental eye research · 2009 · 8 claims · 3 setups

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  Three lead hhRz candidates (CUC↓266, CUC↓1411, AUA↓1414) significantly knock down human RHO protein expression relative to control (p<0.05)

  rho expression secondary western dicistronic

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a novel promoter motif enriched in TATA-less CpG island-associated promoters of ribosomal protein and housekeeping genes

  k562 hek293t hek293t-derived motif gro-cap luciferase

• Whole genome sequences of Yersinia pestis strains of ancient phylogenetic branch 0.ANT5 isolated in the 21st century in the Tien-Shan in Kyrgyzstan.

  PMID 39206953 · PMC11478111 · Microbiology resource announcements · 2024 · 6 claims · 5 setups

  Full-text index only

  Eleven Yersinia pestis strains of the ancient phylogenetic branch 0.ANT5, isolated in the Tien Shan focus (Kyrgyzstan) in 1952, 1971, and 2013–2023, were hybrid-sequenced (MGI short reads + ONT long reads)

  yersinia whole-genome hybrid plasmid

• Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.

  PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups

  Has reproduction · 80

  α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination

  rhizobium core same site intragenic nucleotide

• Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

  PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Oncogenes MITF, KIT, CDH1, NRAS, AKT1, EGFR, TP53, and CDK4 are elevated while tumor suppressors PTEN, cAMP, and BCL2 are reduced in melanoma

  tcga-skcm melanoma-related intradermal keratinocytes rna-seq kegg copy

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

  rhizobium strains genotype genome whole-genome orthologous snp

• Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancers.

  PMID 39183332 · PMC11345443 · Cell death & disease · 2024 · 7 claims · 8 setups

  Has reproduction · 69

  Pax5 is an important transcription factor driving neuronal gene expression and is specific to t-NEPC

  ne-like prostate lucap mcrpc atac-seq acetylated-histone rna-seq

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• A conserved glycan motif induces broadly reactive functional antibodies against the zoonotic pathogen Streptococcus suis.

  PMID 41880495 · PMC13015895 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 77

  Pathogenic S. suis lineages express two structural RPS variants that differ by presence/absence of glucose but share a conserved glycan core

  publicly suis rps δsrpp comparative plant glycosyl

• Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility.

  PMID 34021225 · PMC8140134 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 70

  Sulfate-reducing Desulfovibrio are the key players responsible for H2S production in swine manure slurry

  manure sediment desulfovibrio solid-liquid radioactive 16s shotgun

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins.

  PMID 35301123 · PMC9189052 · Metabolic engineering · 2022 · 8 claims · 7 setups

  Has reproduction · 71

  Swapping expression host from CHO to HEK293 improves secreted titers for roughly one third of difficult-to-express human proteins

  expicho choebnalt85-1e9 freestyle culture transient semi-stable targeted