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).

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

  Full-text index only

  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature

• Proteomics data repositories.

  PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

  Full-text index only

  The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

  multi-organism yeast proteomes cerevisiae tandem yeast fluorescence

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 6 claims · 4 setups

  Has reproduction

  ArrayExpress (AE) discontinued importing data from GEO in 2017, causing new GEO entries to become unavailable from AE

  geo arrayexpress aoe cross-database metadata keyword

• pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

  PMID 16381926 · PMC1347407 · Nucleic acids research · 2006 · 8 claims · 3 setups

  Full-text index only

  pSTIING is a publicly accessible web-based knowledgebase integrating protein-protein, protein-lipid, protein-small molecule interactions, transcriptional regulatory associations, ligand-receptor-cell type information, and signal transduction modules, with a focus on inflammation, cell migration and cancer.

  model gene molecular sequence clustering literature

• The genome sequence of the Chalk Yellow-face Bee, Hylaeus dilatatus (Kirby, 1802) (Hymenoptera: Colletidae).

  PMID 41657665 · PMC12881847 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A two-haplotype genome assembly of Hylaeus dilatatus was produced, with total lengths of 307.38 Mb (haplotype 1) and 314.32 Mb (haplotype 2)

  hylaeus pacbio assembled barcoding pacbio hi-c

• The genome sequence of the cabbage seedpod weevil, Ceutorhynchus obstrictus (Marsham, 1802) (Coleoptera: Curculionidae).

  PMID 42109707 · PMC13153772 · Wellcome open research · 2026 · 8 claims · 4 setups

  Full-text index only

  A chromosome-level genome assembly for Ceutorhynchus obstrictus was generated with total length 728.81 Mb

  organism dissected pacbio hi-c rna-seq

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est

• The genome sequence of the leafhopper, Arthaldeus pascuellus (Fallén, 1826) (Hemiptera: Cicadellidae).

  PMID 41625988 · PMC12859417 · Wellcome open research · 2026 · 6 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was generated for Arthaldeus pascuellus, the first high-quality genome for the genus Arthaldeus

  organism pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the European Pepper moth, Duponchelia fovealis (Zeller, 1847) (Lepidoptera: Crambidae).

  PMID 41929846 · PMC13040225 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level, haplotype-resolved genome assembly was generated for Duponchelia fovealis

  organism pacbio assembled pacbio hi-c k-mer

• The genome sequence of a greenbottle fly, Lucilia caesar (Linnaeus, 1758) (Diptera: Calliphoridae).

  PMID 42064354 · PMC13125994 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosomally complete genome assembly was generated for a male Lucilia caesar specimen, with total length 615.55 Mb

  organism head abdomen dissected pacbio hi-c sequencing

• The genome sequence of the Club-Horned Wood Borer Wasp, Trypoxylon clavicerum Lepeletier de Saint Fargeau & Audinet-Serville, 1828 (Hymenoptera: Crabronidae).

  PMID 42255363 · PMC13237539 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A genome assembly was generated for an individual female Trypoxylon clavicerum (Club-Horned Wood Borer Wasp) as part of the Darwin Tree of Life project

  trypoxylon pacbio assembled barcoding high pacbio

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene

• Information-based methods for predicting gene function from systematic gene knock-downs.

  PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.

  caenorhabditis elegans saccharomyces interference computational genome-wide

• The genome sequence of the barkfly, Loensia variegata (Latreille, 1799) (Psocodea: Psocidae).

  PMID 42222608 · PMC13219991 · Wellcome open research · 2026 · 8 claims · 6 setups

  Full-text index only

  A chromosome-level genome assembly was generated for Loensia variegata (barkfly) as part of the Darwin Tree of Life project

  loensia assembled pacbio hi-c barcoding

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 71

  13,401 lncRNAs were identified in the A. crassicauda transcriptome using the ECF pipeline

  crassicauda rna-seq coding sequence

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• The genome sequence of the soldier beetle, Malthodes minimus (Linnaeus, 1758) (Coleoptera: Cantharidae).

  PMID 41769330 · PMC12949377 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Malthodes minimus genome assembly has a total length of 583.60 Mb, with 97.75% scaffolded into 7 chromosomal pseudomolecules including X and Y sex chromosomes

  malthodes pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the Bicolour Sedge, Triaenodes bicolor (Curtis, 1834) (Trichoptera: Leptoceridae).

  PMID 41852352 · PMC12993304 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A genome assembly was generated for a male Triaenodes bicolor specimen, comprising two haplotypes of 615.75 Mb and 613.86 Mb.

  triaenodes pacbio hi-c barcoding