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 transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 8 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific transcriptome signatures in cord blood, with a significant sex-by-exposure interaction for many genes.

  cord maternal pm2.5-associated blood whole-genome spatial-temporal overrepresentation

• A common haplotype within the PON1 promoter region is associated with sporadic ALS.

  PMID 18618303 · PMC2739087 · Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases · 2008 · 7 claims · 6 setups

  Full-text index only

  Two SNPs (rs987539 in PON2 intron 6 and rs2074351 upstream of PON1 exon 2) within the paraoxonase gene cluster are significantly associated with susceptibility to sporadic ALS

  genomic case-control sporadic serum snp allelic sliding-window

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

  Full-text index only

  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

  PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

  genomes 1000gp internal whole-genome whole-transcriptome wgs

• Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.

  PMID 41680899 · PMC12903587 · Genome medicine · 2026 · 7 claims · 6 setups

  Full-text index only

  A novel batch-effect correction method (log-normal gene usage modeling, Z-score normalization, and roulette-wheel resampling) allows combining AIRR-seq data from different batches and protocols.

  blood peripheral batch-corrected airr-seq airr-seq hla tcrβ

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

  Full-text index only

  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• Blood-based epigenetic instability linked to human aging and disease.

  PMID 41690920 · PMC13018287 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  31,744 unmethylated (and 6143 methylated) CpG loci in blood show highly consistent, stable methylation in young healthy individuals and are defined as Epigenetically Stable Loci (ESLs)

  blood normal paired aml illumina whole-genome methylation

• Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.

  PMID 34435438 · PMC9290141 · Molecular ecology resources · 2022 · 6 claims · 6 setups

  Full-text index only

  Bisulphite conversion of unmethylated cytosines to thymines violates strand-complementarity assumptions of SNP callers and confounds true C->T SNPs with unmethylated cytosines, complicating SNP calling from bisulphite sequencing data.

  blood bismark-aligned bwa-mem-based gem3-based whole-genome snp

• A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.

  PMID 41792601 · PMC13077969 · BMC genomics · 2026 · 6 claims · 8 setups

  Full-text index only

  A new haplotype-resolved, chromosome-level reference genome assembly (SLU_Cpb5.0) was generated for C. picta bellii using combined PacBio HiFi, 10x Genomics Chromium, Hi-C, and Bionano optical mapping data from a single individual.

  genomic ultra-high tissues heart 10x pacbio hi-c

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

  Full-text index only

  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

  PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

  Full-text index only

  RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

  tcga cell-line same gtex bulk whole-exome whole-genome

• Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

  PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 5 setups

  Has reproduction · 90

  Gene expression, exon expression, and intron excision ratio (splicing) molecular phenotypes are significantly heritable in sheep liver and muscle

  liver sheep sequencing snp heritability

• DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

  PMID 42021404 · PMC13251264 · Clinical epigenetics · 2026 · 7 claims · 5 setups

  Full-text index only

  DNA methylation profiles at hospital admission differ among disease trajectory groups (TGs) and are associated with subsequent disease progression.

  pbmcs blood immune end-stage targeted rna-seq mass