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).

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome

• Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

  PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

  baumannii ranked lpta representative pooled string mic

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• Genetic polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg

• Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

  PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups

  Has reproduction · 80

  Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei

  brucei hydrapsiseq small primer

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

  PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.

  pearl old oxford bionano illumina

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

  Full-text index only

  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• WAF1/CIP1 structural abnormalities do not contribute to cell cycle deregulation in ovarian cancer.

  PMID 8645586 · PMC2074480 · British journal of cancer · 1996 · 7 claims · 5 setups

  Full-text index only

  No WAF1/CIP1 coding mutations were found in any of 36 ovarian carcinomas sequenced, including tumors with LOH on 6p and those lacking p53 mutations

  ovarian blood tumor pcr sequencing loss

• Role of p16/MTS1, cyclin D1 and RB in primary oral cancer and oral cancer cell lines.

  PMID 10389982 · PMC2363027 · British journal of cancer · 1999 · 7 claims · 5 setups

  Full-text index only

  p16/MTS1 mutations and loss of expression are very common in OSCC cell lines and less frequent in primary OSCC tumours

  oscc same frozen pcr western extraction

• Genetic variation in Pneumocystis carinii isolates from different geographic regions: implications for transmission.

  PMID 10827116 · PMC2640877 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

  Full-text index only

  Genotype frequency distribution patterns varied significantly by patient's place of diagnosis but not by place of birth

  pneumocystis ethanol-preserved genotype pcr nested purification

• Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

  PMID 11572763 · PMC5926839 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 4 setups

  Full-text index only

  No mutations were found in the coding sequence of the hsMAD2 gene in 32 primary gastric cancers

  gastric cancer formalin-fixed near-diploid pcr semi-quantitative immunohistochemistry

• CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

  PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

  Full-text index only

  Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

  genomic radiolabelled tig-er u2os sscp protein-protein retroviral

• TP53 mutations, amplification of P63 and expression of cell cycle proteins in squamous cell carcinoma of the oesophagus from a low incidence area in Western Europe.

  PMID 11531258 · PMC2364124 · British journal of cancer · 2001 · 8 claims · 5 setups

  Full-text index only

  TP53 mutations were detected in 36% (12/33) of SCCE from the low-incidence Lyon area, lower than the 56-80% reported in high-incidence areas

  microdissected deparaffinized oesophageal genomic ttge immunohistochemistry western

• 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

  Has reproduction · 78

  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.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer.

  PMID 14562025 · PMC2394328 · British journal of cancer · 2003 · 8 claims · 4 setups

  Full-text index only

  Women with bilateral breast cancer show greater genetic predisposition (higher family history prevalence) than women with unilateral breast cancer

  blood-derived blood random dhplc microsatellite duplicate

• Analysis of human prostate cancers and cell lines for mutations in the TP53 and KLF6 tumour suppressor genes.

  PMID 12915879 · PMC2376923 · British journal of cancer · 2003 · 4 claims · 4 setups

  Full-text index only

  KLF6 exon2 miscoding mutations are uncommon in prostate cancer, contrary to the earlier report of ~55% mutation frequency

  prostate tumors pcr oligonucleotide

• Clinico-pathogenetic findings and management of chondrodystrophic myotonia (Schwartz-Jampel syndrome): a case report.

  PMID 12839625 · PMC166146 · BMC neurology · 2003 · 8 claims · 7 setups

  Full-text index only

  The patient is a compound heterozygote with a different splicing mutation in each Perlecan allele, causing a significant reduction in production of the normal (wild-type) protein.

  8-year-old muscle lower skeletal molecular immunostaining electromyogram

• Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

  PMID 12592375 · PMC2377180 · British journal of cancer · 2003 · 7 claims · 5 setups

  Full-text index only

  Unmutated VH gene CLL cases have significantly shorter telomeres than mutated VH gene CLL cases

  cll subset pcr southern real-time

• Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

  PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

  Full-text index only

  Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

  pestis combined dental contemporary spacer phylogenetic pcr