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).
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Has reproduction · 86
Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.
PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups
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.
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Has reproduction · 92
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.
PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups
Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes
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Has reproduction · 86
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
CholerAegon, a Nextflow-based pipeline, predicts AMR profiles of V. cholerae from assembled genomes using CARD ontology
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Has reproduction · 91
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
73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Rise of the machines.
PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups
New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.
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Has reproduction · 92
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
bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B
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Has reproduction · 92
Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.
PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups
Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.
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Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
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.
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Has reproduction · 100
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.
PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups
NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.
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High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.
PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups
Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.
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Has reproduction · 85
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.
PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups
An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.
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Has reproduction · 73
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
An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.
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Has reproduction · 90
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.
PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups
The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application
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Has reproduction · 74
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups
Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.
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Has reproduction · 100
Genomic analysis of bacteria in the Acute Oak Decline pathobiome.
PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups
All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens
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Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.
PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups
Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99
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Has reproduction · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.
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Has reproduction · 99
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.
PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups
getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.