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 · 92
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
cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.
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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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The sequence and de novo assembly of the giant panda genome.
PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups
A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing
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Has reproduction · 85
High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.
PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups
SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.
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Has reproduction · 91
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.
PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups
De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads
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Has reproduction · 72
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.
PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups
A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.
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Has reproduction · 94
A Deluge of Complex Repeats: The Solanum Genome.
PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups
~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements
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Has reproduction · 50
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.
PMID 34110280 · PMC8461470 · Microbial genomics · 2021 · 8 claims · 8 setups
rMAP is a pipeline capable of profiling the resistomes of ESKAPE pathogens using Illumina WGS data
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Has reproduction · 99
A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.
PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups
This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).
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Has reproduction · 87
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
Subgenus Houzingenia originated via transoceanic dispersal from Africa ~6.6 Ma, with most biodiversity arising from rapid mid-Pleistocene (0.5–2.0 Ma) diversification plus multiple long-distance dispersals.
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Has reproduction · 91
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.
PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups
A hybrid de novo assembly combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X) produced the YO draft genome Ogye_1.1 with contig and scaffold NG50 of 362.3 Kbp and 16.8 Mbp.
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Has reproduction · 95
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups
P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)
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Telomere-to-telomere assembly of a complete human X chromosome.
PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups
Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line
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Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.
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Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups
MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.
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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups
A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.
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Whole genome amplification and de novo assembly of single bacterial cells.
PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups
FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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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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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.