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).

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• Molecular Epidemiology of Invasive Group B Streptococcus in South Africa, 2019-2020.

  PMID 39737783 · PMC11998550 · The Journal of infectious diseases · 2025 · 8 claims · 8 setups

  Has reproduction

  β-lactam antibiotics remain appropriate for treatment of invasive GBS in South Africa, as only 1 isolate showed reduced penicillin susceptibility.

  invasive viable high-quality isolates phenotypic antimicrobial whole-genome

• Genome-wide survey of allele-specific splicing in humans.

  PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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  A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

  genome cdna hapmap computational est exon

• HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

  PMID 18215327 · PMC2265691 · Virology journal · 2008 · 8 claims · 6 setups

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  N-linked glycosylation of HIV-1 gp120 differs between plasma and leukocyte compartments

  plasma hiv-1 nlg presence env phylogenetic signature

• 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 · 6 claims · 8 setups

  Has reproduction · 82

  Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

  klebsiella isolate a55848 assembled short-read phenotypic genome-based

• The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

  PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups

  Has reproduction · 90

  The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application

  tuberculosis outlier whole-genome maximum-likelihood read

• High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia.

  PMID 19924307 · PMC2775629 · PloS one · 2009 · 7 claims · 5 setups

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  mtDNA control-region instability is not the primary causal factor in B-CLL

  lymphocytes paired clinical-pathological pcr autosomal likelihood

• 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

• Phenotype, genotype, and worldwide genetic penetrance of LRRK2-associated Parkinson's disease: a case-control study.

  PMID 18539534 · PMC2832754 · The Lancet. Neurology · 2008 · 8 claims · 7 setups

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  LRRK2-associated PD can be distinguished from idiopathic PD by a more benign motor and non-motor phenotype

  unrelated patients people homozygous genetic standardized olfaction

• Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

  PMID 19915672 · PMC2772813 · PloS one · 2009 · 8 claims · 8 setups

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  MLSA of 89 genes across 108 global MTBC strains yields a single, highly robust phylogeny with virtually no homoplasy, congruent across parsimony, NJ, ML, and Bayesian methods.

  global mtbc miru-vntr multilocus spoligotyping 15-loci-miru-vntr

• 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