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).

• Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

  PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

  influenzae novel reference codon phylogenetic comparative

• rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.

  PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups

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  rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution

  enterobacterales illumina aeruginosa pneumoniae whole-genome wgs amr

• MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

  PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.

  coli sequences nanopore basecalling demultiplexing

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates

  sdsd sdse isolates genomes genome core-genome multilocus

• Genetic variation of St. Louis encephalitis virus.

  PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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  Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

  slev rt-pcr phylogenetic recombination

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome

• Global genetic diversity of human metapneumovirus fusion gene.

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

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  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

• Endemic Venezuelan equine encephalitis in northern Peru.

  PMID 15200823 · PMC3323213 · Emerging infectious diseases · 2004 · 8 claims · 8 setups

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  Four VEE complex lineages cocirculate in the Peruvian Amazon region: subtype ID (Panama genotype and Colombia/Venezuela genotype), subtype IIIC, and a newly proposed subtype IIID

  veev pe2 subtype cotton sscp pcr phylogenetic

• Eighth major clade for hepatitis delta virus.

  PMID 17073101 · PMC3294742 · Emerging infectious diseases · 2006 · 7 claims · 7 setups

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  Three HDV isolates (dFr644, dFr2072, dFr2736) form a monophyletic group distinct from HDV-1 through HDV-7, constituting a new eighth major clade (HDV-8) of the Deltavirus genus.

  serum-derived complete same shd rt-pcr sequence phylogenetic

• Genomic signatures of human versus avian influenza A viruses.

  PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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  52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

  throat clinical 401-genome avian rt-pcr immunofluorescent sequence

• Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

  PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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  The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

  chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus

• BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

  PMID 17965094 · PMC2238987 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  BioHealthBase BRC is a public integrated bioinformatics database and analysis resource for influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin.

  avian pb2 dkxi35 ns1 sequence genome t-cell

• Environmental Burkholderia cepacia complex isolates in human infections.

  PMID 17552100 · PMC2725883 · Emerging infectious diseases · 2007 · 6 claims · 4 setups

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  More than 20% of clinical Bcc isolates examined are indistinguishable by MLST from environmental isolates, linking the natural environment to emergence of clinical infections

  clinical environmental subset stabilis multilocus cloning pulsed-field

• Isolated populations and complex disease gene identification.

  PMID 18771588 · PMC2575505 · Genome biology · 2008 · 8 claims · 5 setups

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  Isolated/founder populations are useful for identifying genes underlying common complex diseases, not just rare monogenic diseases.

  genetically icelandic finnish hutterites linkage genome-wide

• Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

  PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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  emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

  streptococcus pyogenes emm values multilocus emm comparative

• Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

  PMID 18366709 · PMC2323391 · BMC genomics · 2008 · 8 claims · 5 setups

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  Genome diversity among M. avium subspecies is mediated by large sequence polymorphisms (LSPs) commonly associated with mobile genetic elements.

  avium microarray map selected microarray blastn sequencing

• Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

  PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

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  The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

  lineage mice patients complete phylogenetic nucleotide

• 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

• 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

• Global distribution of rubella virus genotypes.

  PMID 14720390 · PMC3034328 · Emerging infectious diseases · 2003 · 8 claims · 6 setups

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  Phylogenetic analysis of 103 E1 gene sequences from 17 countries confirms at least two rubella virus genotypes, RGI and RGII

  rubella same phylogenetic genetic virus