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).

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• The truth about mouse, human, worms and yeast.

  PMID 15601543 · PMC3525071 · Human genomics · 2004 · 8 claims · 8 setups

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  Comparing genomes in pairs or larger sets (mouse-human, C. elegans-C. briggsae, multiple Saccharomyces, human-pufferfish, etc.) reveals unsuspected genes and helps eliminate false-positive gene predictions

  mouse-human homo tetraodon region comparative est cross-species

• The excess of 5' introns in eukaryotic genomes.

  PMID 16314314 · PMC1292992 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  All 21 eukaryotic genomes studied show a statistically significant 5′-biased distribution of introns in protein-coding genes

  eukaryotic same housekeeping comparative chi-square bidirectional

• The impact of low-cost, genome-wide resequencing on association studies.

  PMID 16004723 · PMC3525269 · Human genomics · 2005 · 8 claims · 4 setups

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  The HapMap project provides more than 500,000 SNPs across three major human populations, enabling genome-wide association studies via linkage disequilibrium tagging.

  bacterial phi-x case genome massively genome snp

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• Comparative genomics of emerging human ehrlichiosis agents.

  PMID 16482227 · PMC1366493 · PLoS genetics · 2006 · 8 claims · 5 setups

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  Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins (OMP-1/P44/Msp2 family) facilitating antigenic variation

  phagocytophilum representative concatenated rickettsiales whole-genome comparative phylogenetic

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• U7 snRNAs: a computational survey.

  PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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  A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

  mammalian drosophilid aligned basal blast sequence consensus

• Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

  PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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  Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

  genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• GPCR genes are preferentially retained after whole genome duplication.

  PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups

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  WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)

  vertebrate ngpcr nigroviridis syntenic phylogenetic chromosomal

• Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

  PMID 18304319 · PMC2268676 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  Comparative synteny conservation around a horizontally transferred gene (HTgene) can distinguish single versus multiple independent HGT events even without a robust phylogenetic tree.

  poxvirus core psi-blast comparative molecular

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

  PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

  genomes 1000gp internal whole-genome whole-transcriptome wgs

• Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.

  PMID 41787358 · PMC13064042 · BMC biology · 2026 · 8 claims · 8 setups

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  The Norwegian lemming population is geographically structured into distinct subpopulations showing an isolation-by-distance pattern, contrary to earlier microsatellite-based findings of weak structure

  lemmus single norwegian lemmings whole-genome novo principal

• Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

  PMID 42007585 · PMC13245728 · The ISME journal · 2026 · 8 claims · 8 setups

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  Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (Nematoda, Mollusca, and Cnidaria)

  pseudoalteromonas mollusca individual live pangenomic core-genome average

• 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

• Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.

  PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups

  Has reproduction · 38

  Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.

  diverse annotated same comparative enzyme trait

• The signal in the genomes.

  PMID 16683016 · PMC1447653 · PLoS computational biology · 2006 · 7 claims · 3 setups

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  A high breakpoint reuse rate in the output of rearrangement algorithms indicates loss of historical signal, not good evidence for genomic fragile regions

  simulated genome

• Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.

  PMID 41777052 · PMC13010820 · Genome biology and evolution · 2026 · 8 claims · 3 setups

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  tRNA genes and their flanking regions show signatures of high historical transcription-associated mutagenesis (TAM) combined with strong purifying selection on the gene body

  reference strains computational population full-length