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).

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

  PMID 28789673 · PMC5549432 · BMC research notes · 2017 · 7 claims · 7 setups

  Full-text index only

  Gene and transcript abundances of bacterial type III secretion system (T3SS) genes are positively correlated with methane yield in sheep

  rumen reassembled succinivibrio dextrinosolvens metagenomic metatranscriptomic 16s

• MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

  PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism

  arabidopsis grapevine pangenome invertebrate genome novo gene

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

  PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 75

  Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

  pure enriched stec-negative extracted ont real-time artificial

• The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.

  PMID 41625985 · PMC12859430 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Phakellia ventilabrum genome assembly spans 211.92 Mb with 99.97-99.98% scaffolded into 25 chromosomal pseudomolecules

  phakellia pacbio genome microbial pacbio hi-c sequencing

• Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

  PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups

  Full-text index only

  ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets

  software authors sequence polymorphism phylogenetic

• VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

  PMID 37129547 · PMC10191607 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 1 setups

  Has reproduction · 83

  VirPipe is a new bioinformatics pipeline for detecting viral genomes from Nanopore or Illumina sequencing input with streamlined installation and customization.

  lung nanopore

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

  Has reproduction · 91

  175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

  one sinensis small-molecular-weight leaves small genome mirna

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

  holacanthella duospinosa genome transcriptome phylogenomics

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

  Has reproduction · 82

  An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

  michiganensis a55848 african assembled whole-genome novo genome-based

• Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

  PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

  Has reproduction · 73

  De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

  suaeda rna-seq novo blastx

• Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

  PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

  sonnei same shigella assembled illumina oxford novo

• Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon.

  PMID 35814690 · PMC9257098 · Frontiers in microbiology · 2022 · 6 claims · 6 setups

  Has reproduction · 86

  CholerAegon, a Nextflow-based pipeline, predicts AMR profiles of V. cholerae from assembled genomes using CARD ontology

  vibrio assembled genome hybrid amr

• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

  edna khumbu genome metabarcoding satellite

• Pharokka: a fast scalable bacteriophage annotation tool.

  PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command

  enterobacteria staphylococcus crass-like predicted genome large-scale homology

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome