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).

• Cell Specific eQTL Analysis without Sorting Cells.

  PMID 25955312 · PMC4425538 · PLoS genetics · 2015 · 7 claims · 4 setups

  Has reproduction · 90

  A genotype x predicted-cell-count interaction (GxE) meta-analysis across whole blood datasets can detect neutrophil-specific cis-eQTLs without cell sorting

  blood neutrophils cis-eqtl cell-count rna-seq

• Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

  PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 83

  188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

  blood degs peripheral hub microarray kegg cibersort

• Early days: genomics and human responses to infection.

  PMID 16679048 · PMC7108404 · Current opinion in microbiology · 2006 · 8 claims · 8 setups

  Full-text index only

  DNA microarray-based transcript profiling of primate/human responses to infection has begun to yield new insights into host-pathogen interactions but is limited by unresolved methodological challenges.

  peripheral liver gastric brain microarray

• ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method.

  PMID 38247911 · PMC10813502 · Bioengineering (Basel, Switzerland) · 2023 · 8 claims · 4 setups

  Has reproduction · 75

  ResnetAge, a ResNet-based neural network using 22,278 shared Illumina 27K/450K CpG sites, predicts DNA methylation age from beta values.

  shared independent methylation resnet comparative

• Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.

  PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 68

  CEP120 and SPDL1 were identified as diagnostic genes for IDD using a random forest model

  blood gse150408 cep120 pbmcs bulk machine single-sample

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.

  blood merged deg microarray coconut pseudotime

• Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

  PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 8 setups

  Has reproduction · 73

  Developed OutlierMeth, an R package that computes probe-specific thresholds and flags DNA methylation outliers from array data

  normal blood tcga gse40279 illumina logistic unsupervised

• Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

  PMID 37563310 · PMC10457199 · Nature immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  Genome-wide pQTL mapping of 91 inflammation-related plasma proteins in 14,824 participants identified 180 significant pQTLs (59 cis, 121 trans) across 108 genomic regions and 70 proteins

  plasma blood tissues gut genome-wide pqtl cis-eqtl