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).

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

  PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

  Full-text index only

  SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

  african-american thai same study sanger snp genotyping

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

  Full-text index only

  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

  Full-text index only

  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

  PMID 34025601 · PMC8134036 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Full-text index only

  ABAA reduces the number of false-positives with all metabarcoding methods tested

  fungal same mock raw its1 blastn hierarchical

• Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires.

  PMID 41140028 · PMC12774592 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  Generated long-read genome assemblies for two P. theobromicola isolates (MB01960, P0449) and short-read assemblies for five additional isolates

  theobromicola additional cacao genomes long-read short-read rna-seq

• Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.

  PMID 41758556 · PMC12948150 · Microbial genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Autocycler (consensus long-read-only assembler) circularised the most chromosomes, 95% (87/92), significantly more than Unicycler, Unicycler bold, Flye and Hybracter (hybrid)

  clinical enterobacterales assembled assembler-polisher nanopore illumina comparative

• Water mass specific genes dominate the Southern Ocean microbiome.

  PMID 41803086 · PMC12972064 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  The Southern Ocean microbial gene catalog is highly original and largely distinct from existing marine gene catalogs

  seawater ace tara polar-specific shotgun comparative agnostos

• Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.

  PMID 41813906 · PMC13022341 · Communications biology · 2026 · 8 claims · 7 setups

  Full-text index only

  No evidence for recent HGT-mediated dissemination of ARGs across depth layers was detected, despite genetic compatibility among co-occurring bacteria.

  stratified freshwater predicted arg-carrying depth-resolved horizontal arg

• Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts.

  PMID 41848149 · PMC12999062 · Microbial genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Seven single-cell genomes assembled from uncultured environmental Bodo cells represent three potentially novel Bodo species

  uncultured environmental single-cell bodo single-cell fluorescence-activated whole-genome

• BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.

  PMID 41896736 · PMC13147680 · BMC microbiology · 2026 · 7 claims · 8 setups

  Full-text index only

  BaGPipe is an automated, reproducible Nextflow pipeline that integrates pre-processing, Pyseer-based association analysis, and downstream visualisation into a unified bacterial GWAS workflow

  streptococcus staphylococcus aureus pneumoniae bacterial read amr

• MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

  PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

  Full-text index only

  MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

  validated gut representative predicted acp shotgun genome

• nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.

  PMID 42057295 · PMC13141149 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.

  real simulated seven pipeline metagenomic simulated clinical

• 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

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free

• Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

  PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

  six same polished each nanopore illumina novo

• The genome sequence of the fin whale, Balaenoptera physalus (Linnaeus, 1758) (Artiodactyla: Balaenopteridae).

  PMID 41657664 · PMC12877476 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for Balaenoptera physalus (fin whale) from a male specimen collected in Orkney, Scotland, as part of the Darwin Tree of Life project

  balaenoptera pacbio hi-c k-mer