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).

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Geographically Distinct Circulation of Genotype II and III St. Louis Encephalitis Virus, Texas, USA, 2009-2024.

  PMID 41986946 · PMC13094854 · Emerging infectious diseases · 2026 · 7 claims · 7 setups

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  Genotype II and genotype III SLEV circulated concurrently in Texas during 2009–2024 but were geographically segregated, with no county having both.

  slev-positive vero extracted slev tiled-amplicon virus real-time

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• Epidemiology and phylogenomic characterization of the Clade IIb C.1 Mpox outbreak in Phnom Penh, Cambodia (2023-2024).

  PMID 41575511 · PMC12978180 · Emerging microbes & infections · 2026 · 8 claims · 8 setups

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  All Cambodian Mpox genomes belong to lineage C.1, nested within Clade IIb

  skin mpxv-positive raw cambodian real-time viral bioinformatic

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr

• Is replication the gold standard for validating genome-wide association findings?

  PMID 19112512 · PMC2605260 · PloS one · 2008 · 8 claims · 4 setups

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  The probability of replicating a specific GWA-identified variant decreases as the number of independent GWA/replication studies increases, when individual study power is less than 100%.

  simulated diallelic hypothetical four statistical marker bayesian

• Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.

  PMID 18631403 · PMC2500032 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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  Function2Gene is a set of Perl programs that queries public databases (NCBI, GeneCards, Harvester, with Uniprot/Ensembl also supported) using expert-selected keywords to rank genes by prior probability of disease association.

  gene nuclear sle tdt keyword-based snp transmission

• New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

  PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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  The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

  skin cloned mixed-type gene nested sequencing molecular

• Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

  PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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  Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

  g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic

• Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.

  PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Bhlhb4−/− and Islet1−/− pluripotent cell lines differentiate into retinal organoids with similar timing, morphology, and gene expression to wt lines up to around DD15

  bhlhb4− nrl-gfp rd1 fluorescence rt-pcr microarray