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).

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

  PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

  Has reproduction · 67

  GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

  oryza arabidopsis generic rna-seq workflow

• Comparing time series transcriptome data between plants using a network module finding algorithm.

  PMID 31164912 · PMC6544932 · Plant methods · 2019 · 8 claims · 6 setups

  Has reproduction · 59

  Converting time-series expression data into co-expression networks and applying network module finding (OrthoClust) enables cross-species comparison without requiring one-to-one developmental stage mapping.

  soybean arabidopsis combined module reciprocal time-series cross-species

• Charting and probing the activity of ADARs in human development and cell-fate specification.

  PMID 39537590 · PMC11561244 · Nature communications · 2024 · 8 claims · 7 setups

  Has reproduction · 100

  RNA editing (AEI) and ADAR enzyme expression follow tissue-specific temporal dynamics across human organs from fetal to adult stages, with ADARB1 dynamics tracking AEI increase in hindbrain development.

  organs bulk 8-week 8–10-week bulk site-specific single-cell

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only