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 chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.

  PMID 42232316 · PMC13224822 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for the sponge Rhopaloeides odorabile using the Tree of Life pipeline

  rhopaloeides odorabile-associated odorabile recovered pacbio hi-c sequencing

• 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

  Has reproduction · 82

  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.

  exemplar paired-end cleaned assembled transcriptome read novo

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome

• Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.

  PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction · 78

  Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay

  river edna extracted raw edna concentration quantitative

• 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

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

  PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A combined mechanical and enzymatic dissociation protocol using the gentleMACS Dissociator yields a single-cell suspension from mouse pancreatic tumor tissue suitable for scRNA-seq while preserving cell characteristics

  pancreatic dissociated single-cell scrna-seq tumor dead red

• CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

  PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

  Has reproduction · 97

  CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

  simulated wgs reference same novo blast-based k-mer

• MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.

  PMID 41850290 · PMC13030959 · Cell reports methods · 2026 · 8 claims · 5 setups

  Full-text index only

  MASTR-seq couples Cas9-mediated target enrichment, fragment size selection, and PCR-free multiplexed barcoding to increase on-target read proportion and enable pooling of 8-12 samples per Nanopore MinION flow cell

  patient-derived fmr1 hipsc cas9 cas9-mediated pcr hmw