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 · 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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Full-text index only
Using ESTs to improve the accuracy of de novo gene prediction.
PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups
TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome
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Has reproduction · 97
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups
CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly
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Has reproduction · 75
A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.
PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups
Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.
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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 · 89
A near complete genome for goat genetic and genomic research.
PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.
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Has reproduction · 93
Experimental identification and in silico prediction of bacterivory in green algae.
PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups
Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry
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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 · 82
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
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.
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Has reproduction · 87
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
A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.
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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 · 87
CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.
PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups
CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.
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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 · 89
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.
PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups
STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).