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).

• Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

  PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

  Full-text index only

  Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

  riken medline sequence manual semi-automated

• 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

  Full-text index only

  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

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• Genome sequences and great expectations.

  PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

  Full-text index only

  Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

  complete annotated haemophilus automated benchmarking temporal

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio

• Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

  PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

  Full-text index only

  An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

  pcr candidate embl clinical snp manual homology

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

  PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

  scientific pubmed cyp-drug cyp text mutation manual

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Firefly genomes illuminate parallel origins of bioluminescence in beetles.

  PMID 30324905 · PMC6191289 · eLife · 2018 · 7 claims · 8 setups

  Has reproduction · 93

  Bioluminescence arose independently (parallel/convergent origins) in fireflies and click beetles rather than from a single common ancestral origin.

  photinus aquatica ignelater pyralis whole-genome linked-read gene

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative