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).

• Genetic diversity among Enterococcus faecalis.

  PMID 17611618 · PMC1899230 · PloS one · 2007 · 7 claims · 7 setups

  Full-text index only

  Virulence and antibiotic resistance traits are distributed across many diverse E. faecalis lineages rather than confined to one clade

  faecalis multi-locus dot pcr

• Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon.

  PMID 35814690 · PMC9257098 · Frontiers in microbiology · 2022 · 6 claims · 6 setups

  Has reproduction · 86

  CholerAegon, a Nextflow-based pipeline, predicts AMR profiles of V. cholerae from assembled genomes using CARD ontology

  vibrio assembled genome hybrid amr

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

  Has reproduction · 82

  An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

  michiganensis a55848 african assembled whole-genome novo genome-based

• Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.

  PMID 40416609 · PMC12103846 · PeerJ · 2025 · 8 claims · 6 setups

  Has reproduction · 84

  GBS colonization was detected in 51 of 1,924 (2.7%) pregnant women screened

  vaginal-rectal agalactiae microbiological latex whole-genome

• getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

  PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

  genome complete same coronavirus nuclescore resistance mlst

• Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

  PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups

  Has reproduction · 69

  Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII

  gbs whole-genome multilocus capsular

• Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.

  PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups

  Has reproduction · 92

  Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.

  sciuri bacterial assembled 2254a long-read maldi-tof genome

• Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

  PMID 19788831 · PMC2819849 · Emerging infectious diseases · 2009 · 8 claims · 5 setups

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  NA gene sequences of oseltamivir-resistant viruses (ORVs) form a distinct phylogenetic cluster separate from oseltamivir-sensitive viruses (OSVs)

  influenza clinical partial sanger pyrosequencing molecular

• Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

  PMID 15737014 · PMC549606 · PLoS medicine · 2005 · 7 claims · 6 setups

  Full-text index only

  A secondary EGFR exon 20 mutation (T790M) is found in tumors from patients with acquired resistance to gefitinib or erlotinib

  tumor 293t nsclc direct fluorescent rt-pcr

• Comparative genomics of multidrug resistance in Acinetobacter baumannii.

  PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

  Full-text index only

  A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

  baumannii resistance clinical whole-genome comparative sequence

• Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.

  PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups

  Full-text index only

  Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.

  tuberculosis additional whole-genome spoligotyping comparative

• The HIV positive selection mutation database.

  PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

  hiv-1 stanford codon-specific selection conditional

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon

• Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

  PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

  sonnei same shigella assembled illumina oxford novo

• Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

  PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 73

  An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.

  putative enterica selected assembled endpoint genome long-read

• High genetic variability of HIV-1 in female sex workers from Argentina.

  PMID 17697319 · PMC1971708 · Retrovirology · 2007 · 7 claims · 6 setups

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  HIV-1 genetic diversity among Argentine FSWs is extensive, with BF recombinants predominating over subtypes B and C

  pbmc-derived aligned near pro heteroduplex pcr near

• Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

  PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups

  Has reproduction · 91

  73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3

  monocytogenes isolate whole-genome core minimum

• Stability analysis of mixtures of mutagenetic trees.

  PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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  Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

  simulated hiv-1 hiv timed simulation genotypic mutagenetic

• Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

  PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 70

  AR chromatin binding is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites (ARBS) shared by half of the 88 tumors analyzed

  prostate normal pca lncap chip-seq starr-seq luciferase

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo