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).

• Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

  PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 48

  A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

  metabric scan-b gene rna-seq feature

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

  PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 7 setups

  Has reproduction · 73

  Probe-specific upper and lower thresholds for flagging aberrant DNA methylation can be derived from a reference database of >2,000 normal and tumour-adjacent normal samples spanning 25 tissue types.

  blood tcga gse40279 most illumina supervised unsupervised

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

  Full-text index only

  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

  Full-text index only

  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free