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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The UCSC Genome Browser database: update 2010.
PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups
The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes
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Has reproduction · 90
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.
PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups
The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.
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Genetic variation in an individual human exome.
PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups
The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.
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MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.
PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups
MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations
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Has reproduction
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.
PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups
Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.
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Has reproduction · 80
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.
PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 8 claims · 5 setups
GenomeChronicler is, to the authors' knowledge, the first pipeline that can be run offline or in the cloud to generate non-disease-limited personal genomics reports from whole genome or whole exome sequencing data.
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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 · 100
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.
PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups
poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data
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Has reproduction
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.
PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups
An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.
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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 · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Has reproduction · 55
Natural clines and human management impact the genetic structure of Algerian honey bee populations.
PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups
No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.
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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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Has reproduction · 75
Sequencing of human genomes with nanopore technology.
PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups
A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.
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Has reproduction · 97
Determination of complete chromosomal haplotypes by bulk DNA sequencing.
PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups
A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts
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Has reproduction · 54
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.
PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups
EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology
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Enrichment of sequencing targets from the human genome by solution hybridization.
PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups
Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing
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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
The 196 R. leguminosarum sv. trifolii strains constitute a five-species complex (genospecies gsA-gsE) that occur in sympatry but show little recent between-species gene transfer in core or accessory genomes, except for a few highly mobile regions.
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.