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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Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.
PMID 18974170 · PMC2638935 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 3 setups
Slider aligns reads using all bases above a probability threshold (baseMinPrb) from prb files, generating all possible read sequences above a read probability threshold (read_0_MinPrb), rather than only the most probable sequence
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Has reproduction · 71
A crowdsourced set of curated structural variants for the human genome.
PMID 32559231 · PMC7329145 · PLoS computational biology · 2020 · 7 claims · 6 setups
A crowdsourcing web application (SVCurator) enables curators to manually review and label large indels and SVs by displaying short, long, and linked read sequencing evidence from GIAB HG002.
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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 · 58
Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.
PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups
Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)
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SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.
PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups
SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.
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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 · 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 · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.