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).

• CONSULT: accurate contamination removal using locality-sensitive hashing.

  PMID 34377979 · PMC8340999 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 90

  CONSULT uses locality-sensitive hashing to test whether query k-mers fall within a user-defined Hamming distance of a reference k-mer database, allowing inexact matching against tens of thousands of microbial species.

  tree gtdb kraken-ii genome k-mer genome-skim organelle

• Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

  PMID 37243151 · PMC10224212 · Viruses · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  An exhaustive-search workflow can recover intra-host co-existing SARS-CoV-2 strains from the reference-genome read set (SRR11092062) that de Bruijn-graph assemblers discard.

  sars-cov-2 spike predicted california short-read read sequence

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

  clover-associated plasmids plasmidome replicons long-read k-mer genome

• 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

• 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 · 6 claims · 8 setups

  Has reproduction · 82

  Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

  klebsiella isolate a55848 assembled short-read phenotypic genome-based

• Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

  PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

  blood charlesbogerti reptile annotated whole-genome novo repeat

• Evolutionary toggling of the MAPT 17q21.31 inversion region.

  PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

  chimpanzee lymphoblastoid donor whole-genome reciprocal bac

• 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

• High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

  PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

  salmonella sequenced typhi whole-genome snp-based selection

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 8 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture introduced by stocking, especially with the Atlantic lineage.

  salmo brown subset five ddrad-seq read population

• 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

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• 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

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Ensembl 2008.

  PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

  embryonic amniota multi-species individuals automated chip-chip comparative

• The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

  PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups

  Has reproduction · 90

  The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application

  tuberculosis outlier whole-genome maximum-likelihood read

• Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

  PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

  Has reproduction · 92

  A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

  panax ginseng whole-genome genome rna-seq

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic