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).

• Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.

  PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 84

  TEPs in NSCLC show 111 upregulated and 108 downregulated genes versus non-cancer control platelets, enriched in ECM interaction, cytoskeleton, immune signaling, and platelet activation pathways.

  platelets degs platelet tep bulk pathway k-means

• E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

  PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

  Has reproduction · 62

  E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

  preimplantation genome erna bulk computational motif

• sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 3 setups

  Has reproduction

  sRNAtoolbox 2019 adds all major small RNA library preparation protocols (including UMI-based) to sRNAbench with automatic protocol-specific preprocessing.

  biological srp046046 ensembl small consensus genome

• WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.

  PMID 25254103 · PMC4168754 · F1000Research · 2014 · 8 claims · 7 setups

  Has reproduction · 76

  The open-source WikiPathways app for Cytoscape imports biological pathways from WikiPathways for data visualization and network analysis.

  cardiac cytoscape rna-seq pathway network

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

  PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts

  barley pacbio illumina read