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 · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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Has reproduction · 85
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
18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.
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Has reproduction · 87
Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.
PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups
A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi
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Has reproduction · 90
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.
PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups
Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified
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Has reproduction · 76
Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.
PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 7 setups
Multiple partially or fully intron-spliced intermediates co-exist within an organelle, and both cis- and trans-splicing introns are spliced randomly (no fixed order), generating diverse intermediates.
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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Genetic diversity among five T4-like bacteriophages.
PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups
A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.
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Comparative genomic analysis of three Leishmania species that cause diverse human disease.
PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups
L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species
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Has reproduction · 78
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.
PMID 28045932 · PMC5207757 · PloS one · 2017 · 7 claims · 5 setups
Metavisitor is an open-source suite of modular Galaxy tools and preset workflows enabling non-experts to detect and assemble viral genomes from deep sequence data.
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Has reproduction · 98
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.
PMID 35136576 · PMC8804904 · F1000Research · 2021 · 8 claims · 6 setups
metashot/prok-quality is a container-enabled Nextflow pipeline for quality assessment and dereplication of draft prokaryotic genomes
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Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
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Has reproduction · 94
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
The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.
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Has reproduction · 58
HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.
PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups
HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers
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Has reproduction
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.
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Ensembl 2006.
PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups
Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.
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The UCSC Genome Browser database: update 2010.
PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups
The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes
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Has reproduction · 84
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.
PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups
The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.
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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 · 76
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups
The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.
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The global landscape of sequence diversity.
PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups
Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.