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).

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

  Full-text index only

  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

  PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

  kegg 8192x8192 user-submitted species pathway zoomable sequence

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

  Full-text index only

  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.

  PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  Phylogenomic analysis of the MAG clarified the taxonomic position of D. lemmermannii within the genus Dolichospermum and the ADA (Anabaena/Dolichospermum/Aphanizomenon) group

  surface bloom environmental dolichospermum shotgun lc-ms metagenome

• Discovery and characterization of Alu repeat sequences via precise local read assembly.

  PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups

  Has reproduction · 69

  Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads

  hgdp insertion-supporting candidate assembled genome discordant novo

• Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.

  PMID 40191587 · PMC11970367 · NAR genomics and bioinformatics · 2025 · 8 claims · 5 setups

  Full-text index only

  44 individuals' fully haplotyped diploid genome assemblies (88 haplotypes) from the 1000 Genomes Project were used to comprehensively assess homozygous and heterozygous sequence variations around and within 5'ss

  healthy reconstructed same 5'ss long-read computational statistical

• DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

  PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

  Full-text index only

  A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

  chromosome dog macaque genomic comparative segmental

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood