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 · 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 · 78
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.
PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups
annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.
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Has reproduction · 100
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups
TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.
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Has reproduction · 91
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.
PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups
73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3
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Has reproduction · 51
Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.
PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups
Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.
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Has reproduction · 57
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.
PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups
ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads
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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 · 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 · 73
Genetic polyploid phasing from low-depth progeny samples.
PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups
WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling
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Has reproduction · 73
Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.
PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups
An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.