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).

• The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.

  PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups

  Has reproduction · 99

  Over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available in publications or public repositories.

  randomly repository genomics manual automated large-scale

• 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

  Has reproduction · 100

  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

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

  PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

  genome complete same coronavirus nuclescore resistance mlst

• The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

  PMID 19914934 · PMC2808860 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  GOLD is a comprehensive, centralized resource for tracking genome and metagenome sequencing projects and their associated metadata worldwide.

  bacteria archaea eukarya environmental genome metagenome metadata

• Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

  PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 88

  Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.

  hm450k seven annotated illumina beadarray model-based

• KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.

  PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups

  Has reproduction · 57

  KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers

  fastq gse126379 research sequence download parallel literature

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• 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

  Has reproduction · 43

  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.

  mdr-tb paired-end raw bam whole-genome kraken raw

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative