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).

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

  Full-text index only

  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• Human chromosome 7: DNA sequence and biology.

  PMID 12690205 · PMC2882961 · Science (New York, N.Y.) · 2003 · 6 claims · 2 setups

  Full-text index only

  Presents the DNA sequence and annotation of the entire human chromosome 7

  chromosome genomic comparative

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• IMGT, the international ImMunoGeneTics information system.

  PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

  igh mhc pairs automated junction structure

• 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

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript

• Ensembl 2008.

  PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

  embryonic amniota multi-species individuals automated chip-chip comparative

• The UCSC Genome Browser database: update 2010.

  PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes

  genome vertebrate individuals personal snp sequence genome-wide

• Ensembl's 10th year.

  PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

  anole western genome cd4+ whole-genome gene cross-database

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• Atlas - a data warehouse for integrative bioinformatics.

  PMID 15723693 · PMC554782 · BMC bioinformatics · 2005 · 8 claims · 3 setups

  Full-text index only

  Atlas is a biological data warehouse that locally stores and integrates sequences, molecular interactions, homology information, functional annotations, and ontologies

  in-house gene omim genome molecular gene-disease

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

  avian bird chicken covariance trna microrna

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction · 94

  ~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements

  tuberosum orthologous novo synteny orthologous

• Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

  PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

  Has reproduction

  A streamlined RNA-guided workflow combining OUTRIDER, FRASER, Borzoi, and MOLGENIS VIP was developed to identify gene-disease associations by linking outlier gene expression/splicing to prioritized patient-level variants

  udn blood clinvar wgs wgs bulk rna-seq

• Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

  PMID 41490125 · PMC12768360 · PloS one · 2026 · 6 claims · 5 setups

  Has reproduction · 69

  The original BRAKER3-based NWR annotation was of poor quality: only 51% of transcripts were correctly called, many were assigned uninformative protein names, and some were misassigned to incorrect or bacterial sequences.

  granulosa nwr aligned unassigned bulk reference transcript

• Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).

  PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups

  Has reproduction

  Coniophanes DVG transcriptomes contain 18 toxin families, with toxins comprising 38.8% to 66% of total transcriptome expression depending on species

  duvernoy's fissidens venom imperialis rna-seq dicect quantitative

• Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

  PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

  cupriavidus stm taiwanensis genome 16s average

• The gene guessing game.

  PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

  Full-text index only

  Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

  genomic ests tetraodon genome cpg est comparative

• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

  PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

  Full-text index only

  The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

  genomic predicted cdna tissues genomic sequence pcr