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).

• DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.

  PMID 31694669 · PMC6836538 · Genome biology · 2019 · 8 claims · 8 setups

  Has reproduction · 56

  DESE is a unified iterative framework that estimates driver tissues of complex diseases/traits from tissue-selective expression of GWAS-associated genes, and outputs prioritized susceptibility genes as a byproduct

  tissues schizophrenia bipolar coronary rna-seq gwas gene

• 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

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

  Full-text index only

  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

  PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

  cfs most candidate second microarray snp weighted

• Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

  PMID 18769486 · PMC2518524 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  Unsupervised clustering of expression profiles from 62 medulloblastomas identifies 5 molecular subtypes (A–E)

  relapsed medulloblastoma independent expression array targeted

• Developmental and genetic regulation of human surfactant protein B in vivo.

  PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

  Full-text index only

  Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

  amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene

• Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

  PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

  peripheral genomic genotype independent linkage targeted genotyping

• Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

  PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

  fregene-simulated 80k-snp 480k 192k simulated null whole-genome