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).

• PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads.

  PMID 41569288 · PMC12825295 · Briefings in bioinformatics · 2026 · 7 claims · 6 setups

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  PHScaffolding builds a weighted hypergraph from Pore-C read-to-contig alignments, with hyperedges representing multi-way contig interactions and weighted by the geometric mean of per-contig alignment lengths

  hg002 gm12878 arabidopsis contig pore-c genome hypergraph

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• Water mass specific genes dominate the Southern Ocean microbiome.

  PMID 41803086 · PMC12972064 · Nature communications · 2026 · 8 claims · 8 setups

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  The Southern Ocean microbial gene catalog is highly original and largely distinct from existing marine gene catalogs

  seawater ace tara polar-specific shotgun comparative agnostos

• The diploid genome sequence of an individual human.

  PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups

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  Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing

  donor huref whole-genome assembly-to-assembly snp

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

  PMID 34025601 · PMC8134036 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

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  ABAA reduces the number of false-positives with all metabarcoding methods tested

  fungal same mock raw its1 blastn hierarchical