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).

• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

  PMID 35338232 · PMC8956664 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  Two computational approaches (sub-sampling and phenotype-simulation) can be implemented to perform power calculations for bacterial GWAS using existing genome collections, packaged as the PowerBacGWAS pipeline

  enterococcus klebsiella mycobacterium faecium pan-genome burden variant

• Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

  PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

  Full-text index only

  Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

  env u373 mt4-r5 u373-r5 phylogenetic infectivity flow

• Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

  PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

  Full-text index only

  Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

  sperm donor hgr1b3 single-molecule fluorescent radioactive

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

  Full-text index only

  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• Genome sequence, comparative analysis, and population genetics of the domestic horse.

  PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

  Full-text index only

  Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

  single horse eight twelve genome fish chip-on-chip

• Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

  PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

  Has reproduction · 69

  Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

  colon gut single-cell 16s western

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups

  Has reproduction · 53

  A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.

  metastatic top breast tnbc single-cell functional mutational

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

  Full-text index only

  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• Structure of the intergenic spacers in chicken ribosomal DNA.

  PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

  Has reproduction · 80

  Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

  wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative

• Inferring human colonization history using a copying model.

  PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

  simulated populations coalescent snp ascertainment

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

  Full-text index only

  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

  PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

  Full-text index only

  Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

  hiv-1 longitudinal 0-month single pseudovirus single site-directed

• Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome.

  PMID 33294007 · PMC7691466 · Evolutionary applications · 2020 · 7 claims · 8 setups

  Has reproduction · 84

  Lingcod comprise two distinct genetic clusters separated latitudinally at a break near Point Reyes off Northern California, with a high frequency of admixed individuals near the break.

  ophiodon single lingcod subset radseq genome bayesian

• 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

  Full-text index only

  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

• The gene guessing game.

  PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

  Full-text index only

  Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

  genomic ests tetraodon genome cpg est comparative

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

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

  Full-text index only

  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