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).

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• GenBank.

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

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  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

• mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

  PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

  mitochondrial aligned compilation sequence multi-locus

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

  PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.

  pig cattle blast comparative database

• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

  PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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  A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

  pooled genome est novel tandem whole-genome est

• Population genomics: diversity and virulence in the Neisseria.

  PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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  Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

  neisseria meningitidis meningococcal multi-locus microarray genome

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

  edna khumbu genome metabarcoding satellite

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

  PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

  bombyx whole-genome snp novo

• Ensembl's 10th year.

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

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  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

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• 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

• Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

  PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

  blood charlesbogerti reptile annotated whole-genome novo repeat

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative