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).

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 8 claims · 5 setups

  Has reproduction

  AOE integrates publicly available gene expression data from GEO, ArrayExpress, and GEA into a single searchable index.

  ebi ncbi sequence arrayexpress metadata cross-database visualization

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.

  PMID 33558569 · PMC7870661 · Scientific data · 2021 · 7 claims · 7 setups

  Has reproduction · 94

  A unified collection of 101 manually curated and homogenized transcriptomics datasets covering human, mouse, and rat ENM exposures in vitro and in vivo was compiled.

  engineered geo gene rna-seq enm

• MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery.

  PMID 41729821 · PMC12927880 · Briefings in bioinformatics · 2026 · 6 claims · 3 setups

  Has reproduction · 80

  Adapting MCP to bioinformatics web server backends provides a standardized, machine-actionable semantic layer linking API endpoints to scientific concepts and metadata.

  gene string ucsc mcp

• Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.

  PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups

  Has reproduction · 38

  Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.

  diverse annotated same comparative enzyme trait

• getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

  PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

  genome complete same coronavirus nuclescore resistance mlst

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• 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 role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

  PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids

  coli st58 novo draft whole-genome pan-genome-wide plasmid

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

  PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups

  Has reproduction · 91

  73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3

  monocytogenes isolate whole-genome core minimum

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative