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).

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  The 196 R. leguminosarum sv. trifolii strains constitute a five-species complex (genospecies gsA-gsE) that occur in sympatry but show little recent between-species gene transfer in core or accessory genomes, except for a few highly mobile regions.

  rhizobium leguminosarum strains orthologous whole-genome long-read 16s

• Experimental identification and in silico prediction of bacterivory in green algae.

  PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

  Has reproduction · 93

  Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

  prasinophyte same green pelagibaca flow epifluorescence gene-based

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

  PMID 15916705 · PMC1180443 · BMC microbiology · 2005 · 8 claims · 8 setups

  Full-text index only

  H. pylori strains from England are genetically distinct from strains obtained from other countries based on virulence gene analysis (cagT, cagE, cagA, vacA, iceA, oipA, babB)

  pylori english pcr sequencing fluorescent

• Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

  PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

  Full-text index only

  A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

  hcv 5'ncr serum maximum sequence recombination

• Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

  PMID 18431496 · PMC2292242 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  South African HS:41 strains are clearly distinct from the other South African strains by comparative genomic analysis

  clinical genomic jejuni multilocus microarray phylogenetic

• Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

  PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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  Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

  geographically cjd novel jejuni multilocus comparative phenotypic

• Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

  PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

  anthropi same candidate multi-locus pulsed-field antibiotyping

• Cryptococcus neoformans strains and infection in apparently immunocompetent patients, China.

  PMID 18439357 · PMC2600263 · Emerging infectious diseases · 2008 · 8 claims · 8 setups

  Full-text index only

  71% (91/129) of Chinese cryptococcosis clinical isolates (1985-2006) came from patients with no apparent risk factor, versus only 8.5% from AIDS patients, contrasting sharply with other countries

  clinical neoformans randomly balb pcr ura5 igs1-5.8s

• Global genetic diversity of human metapneumovirus fusion gene.

  PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

  Full-text index only

  Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

  hmpv llc-mk2 clinical rt-pcr sequence phylogenetic

• Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

  PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

  pylori peruvian spanish fluorescent multilocus oipa

• Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

  PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

  Full-text index only

  The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

  cloned clinical hominis pcr culture sanger

• Gene function in the mammalian genome, courtesy of the mouse.

  PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

  inbred genome mice model genome-wide large-scale phenotypic

• Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

  PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

  Has reproduction · 94

  The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

  casei orthogroups unclassified selected whole-genome comparative pairwise

• Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

  PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

  Full-text index only

  Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

  hiv-1 same brazilian phylogenetic bootstrap pruning

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

  Full-text index only

  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

  Full-text index only

  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous