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).

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

  PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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  PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

  subset drosophila ensembl lc-ms icat peptide-to-genome

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

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  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

  PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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  Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

  surgical standardized glioma gbm western principal k-means

• Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.

  PMID 19665049 · PMC2774817 · Neuroscience · 2009 · 8 claims · 7 setups

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  Accumulation of mutant torsinA(ΔE) in the nuclear envelope is not sufficient to cause transcriptional dysregulation

  pc6-3 hek293 microarray 2-dige mass

• The application of genomic technology to combat parasitic disease.

  PMID 16454893 · PMC1914215 · Parasitology · 2004 · 8 claims · 8 setups

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  Genomic resources from mammalian hosts can be exploited to understand parasitic processes from the host's standpoint, illustrated by host cell penetration by Trypanosoma cruzi.

  trypanosoma toxoplasma parasite eimeria host proteomics comparative

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

  sycon ciliatum sponges differential go-term genome