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).

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical

• iRefIndex: a consolidated protein interaction database with provenance.

  PMID 18823568 · PMC2573892 · BMC bioinformatics · 2008 · 6 claims · 3 setups

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  A reproducible key (ROG) for each protein interactor and a corresponding key (RIG) for each interaction record can be generated by anyone using only primary sequence, taxonomy identifier, and the SHA-1 algorithm (SEGUID).

  sequence nine interactor seguid parsing mapping

• Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

  PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.

  actias genomes translated luna genome hmm manual

• An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.

  PMID 15606920 · PMC544558 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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  SVD-based analysis of tetrapeptide frequency vectors can compare whole eukaryotic proteomes without pre-defining orthologs or aligning homologous sites

  predicted nine svd-derived ras svd species bootstrap

• Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

  PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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  Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

  genomic rmrp family non-finnish sequencing comparative microsatellite

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c

• Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster.

  PMID 14630516 · PMC1241748 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The mouse Cyp2a-t cluster on chromosome 7 contains 22 loci from the same six CYP2 subfamilies (Cyp2a, Cyp2b, Cyp2f, Cyp2g, Cyp2s, Cyp2t) found in the human cluster

  genomic bac nine restriction bac pcr southern

• Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP).

  PMID 15018634 · PMC356914 · BMC medical genetics · 2004 · 6 claims · 7 setups

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  MRF-SSCP method (using combined restriction digestion plus SSCP with silver staining) was developed to screen PKD1 mutations in full-length cDNA fractionated into nine overlapping nested-PCR segments

  blood pkd1 pcr-purified genomic long nested-pcr mrf-sscp

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

  PMID 18939861 · PMC2669493 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  IEF provides superior reproducibility and resolution of peptide fractionation compared to SCX, for both large (100 µg) and small (10 µg) protein inputs

  rko rectal bovine shotgun comparative ief

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read