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).

• 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

• 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

• Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

  PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups

  Has reproduction · 84

  The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

  anoplophora glabripennis insect whole-genome genome orthology

• A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

  PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing

  oryzae whole-genome genome orthology

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• Insights into vertebrate evolution from the chicken genome sequence.

  PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

  Full-text index only

  Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

  red chicken whole-genome comparative synteny

• The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

  PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

  dentium core whole-genome 3d-structure comparative

• Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

  PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

  baumannii ranked lpta representative pooled string mic

• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

  microbial quality-filtered overflowing shotgun taxonomic alpha

• A chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern

• 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

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• Gene losses during human origins.

  PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

  Full-text index only

  A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

  pseudogene chimpanzee human-specific population comparative phylogenetic fisher's

• The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.

  PMID 36196618 · PMC9720673 · Development (Cambridge, England) · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Can-elt-3 (and orthologues in C. portoensis and C. monodelphis) is expressed in the early E lineage prior to elt-2 orthologue expression

  angaria elegans portoensis gata rnai single-molecule smifish