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 · 90
Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.
PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups
Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.
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Has reproduction · 88
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups
Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.
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Has reproduction · 100
Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.
PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 7 claims · 7 setups
The S. Adjame outbreak produced a heterogeneous phylogeny with multiple temporally/geographically linked sub-clusters, atypical of a point-source Salmonella outbreak and consistent with contamination from an endemic mixed-strain source (imported South Asian herbs/spices).
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Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups
MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.
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Has reproduction · 50
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.
PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups
A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.
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Has reproduction · 85
An extensive evaluation of read trimming effects on Illumina NGS data analysis.
PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups
Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.
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Has reproduction · 94
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.
PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups
BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
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Has reproduction · 85
Ensembl 2013.
PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups
Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.
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Has reproduction · 80
SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.
PMID 35046988 · PMC8761809 · Frontiers in plant science · 2021 · 8 claims · 5 setups
SLDMS is a novel method for computing overlapping regions of sequencing reads using suffix array (SA), longest common prefix (LCP) array, document array (DA), and a monotonic stack.