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).

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig

• Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.

  PMID 34287005 · PMC8386447 · mSphere · 2021 · 8 claims · 7 setups

  Has reproduction · 76

  Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states

  dental metagenomic taxonomic arg

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional

• Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.

  PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 5 claims · 8 setups

  Has reproduction · 83

  A near-complete metagenome-assembled genome (MAG) of Dolichospermum lemmermannii (FEM_B0920) was recovered from a Lake Garda bloom and clarified the species' taxonomic position within the genus Dolichospermum and the ADA group.

  dolichospermum filter fem_b0920 lake shotgun cyanotoxin phylogenomic

• Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

  PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 88

  Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

  zymo bacterial reference shotgun comparative reference

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups

  Has reproduction · 75

  geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data

  stool deduplicated reference whole-genome taxonomic functional

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

  PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

  Has reproduction · 89

  MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

  eukdetect simulated zymobiomics read holdout mutation-rate

• Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.

  PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani', 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', and Wolbachia).

  individual long endosymbiont artemisiae pcr-free pcr nucleic

• 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

• 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

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.

  PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups

  Has reproduction · 86

  Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.

  simulated kidney biological extracted shotgun taxonomic pathogen

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.

  PMID 36875992 · PMC9978240 · F1000Research · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  SnakeMAGs is a simple, efficient, flexible and scalable Snakemake workflow that processes Illumina reads from raw data to MAG classification and relative abundance estimation

  publicly bins quality-filtered assembled workflow genome megahit