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).

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• 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

• Adaptations to climate in candidate genes for common metabolic disorders.

  PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

  individuals population genic compiled snp spearman bayesian

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

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups

  Has reproduction · 83

  A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data

  arabidopsis tripartite affymetrix metabolite-centric network

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA-derived hub genes with a VAE-derived 10-dimensional representation as features for an SVM classifier achieves high accuracy (0.9692) and AUC (0.9981) for colorectal cancer prediction.

  colorectal combined differentially crc microarray differential weighted

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

  clover-associated plasmids plasmidome replicons long-read k-mer genome

• Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

  PMID 15984912 · PMC1166350 · PLoS biology · 2005 · 8 claims · 6 setups

  Full-text index only

  Most mtDNA lineages in Taiwanese aboriginal populations are distinct from those in China and the Taiwan Han population, consistent with descent from the island's initial late Pleistocene settlers

  indigenous b4a-lineage southeast populations mtdna complete rflp

• 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

• Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

  PMID 18680585 · PMC2529308 · BMC evolutionary biology · 2008 · 8 claims · 7 setups

  Full-text index only

  R7a1, a recently derived sub-branch of haplogroup R7, is particularly frequent among Munda-speaking tribal groups

  mtdnas haplogroup genetic geographic complete hvs-i reduced-median

• 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

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

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

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

  pubmed invasive geo cancer semantic computational gene

• Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

  PMID 19772609 · PMC2759955 · BMC genetics · 2009 · 8 claims · 5 setups

  Full-text index only

  Saudi Arabia differs from other Arabian Peninsula countries by a significantly higher presence of J2-M172 lineages.

  saudi same j1-m267 y-chromosome y-str amova

• HUPO Highlights.

  PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing

  liver subcellular models fetal mass antibody-based quantitative

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups

  Has reproduction · 87

  A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).

  euglena gracilis five transcriptomes bulk novo transcriptome