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).

• Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

  PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

  brain exon targeted principal

• Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

  PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

  scrna-seq tcga-gbm gse131928 tumor gene pairwise principal

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

  Full-text index only

  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• 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 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 8 claims · 8 setups

  Has reproduction · 83

  Metabolite-centric reporter pathway analysis (RPAm) computes reporter metabolites and reporter pathways from transcriptome P-values by aggregating Z-scores of neighboring genes in a genome-scale metabolic network

  arabidopsis gene-metabolite-pathway tripartite microarray metabolite-centric reporter

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

  PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

  daf-2 wild-type same dauer developmental lifespan brood

• COVID-19 vaccination atlas using an integrative systems vaccinology approach.

  PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups

  Has reproduction · 69

  mRNA vaccines induce transient but strong immune responses after booster doses

  pbmcs immune pbmc bulk gene principal

• A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

  PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

  Has reproduction · 90

  A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

  kidney gene combined microarray machine sequential

• GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

  PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

  Full-text index only

  GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

  ligand gpcr glida principal sequence gene

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups

  Has reproduction · 59

  TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene

  cd8+ tce manual gene principal

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late

  mus mefs bulk independent allele-specific fluorescence-activated live

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

  PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 52

  A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

  vespid single-copy brain caste-biased bulk orthology principal

• 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