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).

• Modeling the amplification dynamics of human Alu retrotransposons.

  PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

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  Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

  simulated genome population computer comparative population

• 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

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• The application of genomics to emerging zoonotic viral diseases.

  PMID 19855817 · PMC2734983 · PLoS pathogens · 2009 · 8 claims · 8 setups

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  High-throughput sequencing, mRNA expression profiling, and SNP microarray analysis enable rapid identification and genomic characterization of emerging zoonotic pathogens and host responses to them.

  siv-infected plasmacytoid migratory influenza transcriptional tlr fecal

• Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

  PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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  The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

  healthy mrp1 population novo population functional

• Evolutionary origins of human apoptosis and genome-stability gene networks.

  PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

  apoptosis fully same orthologous protein-protein comparative orthology

• Complex genetic diseases: controversy over the Croesus code.

  PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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  The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

  chromosome northern disease large-scale genome-wide database

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

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  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

• Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

  PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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  O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

  serum hbv full-length o-hbv nested phylogenetic quasispecies

• Discovering the phylodynamics of RNA viruses.

  PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

  h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.

  PMID 36810800 · PMC9944229 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 50

  Yevis is a system that builds a workflow registry which automatically validates and tests workflows prior to publication, ensuring they are 'reusable with confidence'.

  github submitter's zenodo yevis-based workflow file trs

• Gene losses during human origins.

  PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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  A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

  pseudogene chimpanzee human-specific population comparative phylogenetic fisher's

• Chemical genomics: what will it take and who gets to play?

  PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups

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  Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.

  iccb fluorescently yeast engineered cell-based small-molecule expression