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).

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing

• Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

  PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

  fecal horse dominant plasma shotgun taxonomic functional

• MODBASE: a database of annotated comparative protein structure models and associated resources.

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

  PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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  A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

  cdna full-length tentative non-redundant est codon snp

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• The Universal Protein Resource (UniProt) in 2010.

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

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  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

• ARED 3.0: the large and diverse AU-rich transcriptome.

  PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

  records est est-derived combined computational est sequence

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene