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).

• Rfam 15: RNA families database in 2025.

  PMID 39526405 · PMC11701678 · Nucleic acids research · 2025 · 8 claims · 6 setups

  Has reproduction · 68

  Rfamseq was expanded to 26 106 genomes, a 76% increase, by incorporating the latest UniProt reference proteomes and additional viral genomes

  rfamseq rfam hepatitis mirbase covariance structure covariation

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• DDBJ in collaboration with mass-sequencing teams on annotation.

  PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data

  chimpanzee silkworm mus homo whole-chromosome whole-genome cage

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

  PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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  The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

  coli se11 rapd whole-genome gene

• Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

  PMID 17319955 · PMC1808054 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  TGFβ1 is a crucial mediator in the pathogenesis of diabetic nephropathy, promoting renal hypertrophy and extracellular matrix accumulation.

  genomic healthy irish case mutation direct taqman

• High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

  PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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  Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

  salmonella sequenced typhi whole-genome snp-based selection

• NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

  PMID 15608248 · PMC539979 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  RefSeq provides a curated, non-redundant, explicitly linked collection of genomic, transcript and protein sequences spanning prokaryotes, eukaryotes and viruses.

  refseq honey sequence computational conserved

• Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

  PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

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  The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

  plasmodium pvama-1 vivax pcr molecular merozoite

• Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

  PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

  ulcerans collection snp whole-genome comparative read

• Identification and characterization of insect-specific proteins by genome data analysis.

  PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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  Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

  drosophila insect-core locusta insect-specific comparative est functional