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).

• Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

  PMID 31980607 · PMC6981202 · Nature communications · 2020 · 6 claims · 4 setups

  Has reproduction · 52

  A meta-analysis (MetaMEx) of 66 published human skeletal muscle datasets reveals pathways selectively activated by inactivity, aerobic versus resistance, and acute versus chronic exercise training.

  skeletal healthy transcriptomic qpcr metabolic

• GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.

  PMID 33758032 · PMC8547006 · mSystems · 2021 · 7 claims · 6 setups

  Has reproduction · 70

  GAUGE automatically annotates GEO microbial microarray and RNA-seq data sets, increasing the percentage amenable to analysis from 4% to 33%.

  aeruginosa cerevisiae gauge-annotated microarray rna-seq anova

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 7 claims · 5 setups

  Has reproduction · 75

  Short- and long-term HL responses in Arabidopsis leaves are driven by distinct transcriptional programs, with duration of HL treatment as the primary factor separating transcriptomic clusters.

  arabidopsis bulk hierarchical correlation

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups

  Has reproduction · 59

  An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.

  cd8+ tce activated manual gene principal

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

  PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

  lncap androgen prostate itraq mudpit immunoblot

• Network-assisted protein identification and data interpretation in shotgun proteomics.

  PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

  Full-text index only

  Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

  yeast organs mammary organ shotgun clique-enrichment microarray