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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: assemblies ✕ Assay: maximum-likelihood ✕ Clear

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

Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

novel casei genomes selected whole-genome maximum-likelihood pairwise
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

PMID 37036103 · PMC10084500 · GigaScience · 2022 · 8 claims · 8 setups

Full-text index only

GEN-ERA is a unified, publicly available toolbox of 13 Nextflow workflows supported by 14 Singularity containers for reproducible microbial genomic/phylogenomic analyses in both bacteria and small eukaryotes.

gloeobacterales gloeobacteraceae publicly ncbi-deposited phylogenomics ssu genome
First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

PMID 41436027 · PMC12958814 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

Full-text index only

This study produced the first genome assemblies of Neotropical Bombus (Thoracobombus) species, B. pauloensis and B. pullatus

pauloensis masked long-read k-mer novo
Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts.

PMID 41848149 · PMC12999062 · Microbial genomics · 2026 · 8 claims · 8 setups

Full-text index only

Seven single-cell genomes assembled from uncultured environmental Bodo cells represent three potentially novel Bodo species

uncultured environmental single-cell bodo single-cell fluorescence-activated whole-genome
From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland.

PMID 41940667 · PMC13188883 · Applied and environmental microbiology · 2026 · 8 claims · 8 setups

Full-text index only

Wastewater surveillance captures community circulation of ESBL-E. coli that overlaps with clinically relevant circulating strains

esbl-producing esbl-e coli genome core-genome ezclermont
Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

Has reproduction · 87

Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

leaf trimmed species concatenated genome novo reference-assisted
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
Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups

Has reproduction · 89

Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.

coli st372 core draft whole-genome core population
Comparative genomics of vertebrate Fox cluster loci.

PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups

Full-text index only

Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci

chimp sequences genomic blast molecular comparative
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
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
Geographically Distinct Circulation of Genotype II and III St. Louis Encephalitis Virus, Texas, USA, 2009-2024.

PMID 41986946 · PMC13094854 · Emerging infectious diseases · 2026 · 7 claims · 7 setups

Full-text index only

Genotype II and genotype III SLEV circulated concurrently in Texas during 2009–2024 but were geographically segregated, with no county having both.

slev-positive vero extracted slev tiled-amplicon virus real-time
The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

Full-text index only

R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

solani ag8-1 rhizoctonia annotated pacbio hi-c stranded
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
Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

PMID 42224013 · PMC13225438 · Microbial genomics · 2026 · 8 claims · 6 setups

Full-text index only

The H37Rv_ref reference genome, sequenced in 1998 with early technology, is incomplete relative to modern hybrid-sequenced assemblies

tuberculosis h37rv_cn a2018772 publicly hybrid comparative functional

Experiments

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

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts.

From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland.

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

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

Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

Comparative genomics of vertebrate Fox cluster loci.

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

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.

Geographically Distinct Circulation of Genotype II and III St. Louis Encephalitis Virus, Texas, USA, 2009-2024.

The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

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

Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.