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 · 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.
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Has reproduction · 100
Genomic analysis of bacteria in the Acute Oak Decline pathobiome.
PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups
All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens
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Has reproduction · 91
Cell fixation and preservation for droplet-based single-cell transcriptomics.
PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups
Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality
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Has reproduction · 100
A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.
PMID 41924242 · PMC13037781 · Bio-protocol · 2026 · 7 claims · 5 setups
ECCFP significantly improves eccDNA detection sensitivity, accuracy, and runtime efficiency compared to other pipelines
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Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups
The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.
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Has reproduction · 80
Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.
PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups
Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing
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Has reproduction · 75
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.
PMID 38860884 · PMC11261899 · Microbial genomics · 2024 · 7 claims · 3 setups
PHA4GE developed a set of standardized contextual data tags (five fields plus controlled-vocabulary terms) for annotating pathogen sequence datasets with known quality issues.
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Has reproduction · 89
Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.
PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups
The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.
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Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.
PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups
Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs
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Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.
PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups
Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs
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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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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 · 91
Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.
PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups
A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.
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Has reproduction · 86
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.
PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups
CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome
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Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.
PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups
High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome
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COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.
PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups
COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface
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Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.
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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 · 100
Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.
PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 8 setups
The study presents comprehensive serum exosome miRNA transcriptome data from four independent Japanese cohorts of PD patients and controls.
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Has reproduction · 33
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.
PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups
C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory