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).

• Analyses and comparison of accuracy of different genotype imputation methods.

  PMID 18958166 · PMC2569208 · PloS one · 2008 · 8 claims · 3 setups

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  Stronger LD produces higher imputation accuracy rates for all five methods

  simulated real linux genotype computational

• Updated three-stage model for the peopling of the Americas.

  PMID 18797500 · PMC2527656 · PloS one · 2008 · 8 claims · 3 setups

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  Removing nine non-Native American mtDNA sequences eliminates the previously reported early (~40 kya) expansion signal for the proto-Amerind population

  native mitochondrial new bayesian mtdna molecular

• Alignoth: portable and interactive visualization of read alignments.

  PMID 41392197 · PMC12777968 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  Alignoth is a command-line tool that generates self-contained, portable HTML reports of DNA sequencing read alignment pileups, with export to PNG, SVG, PDF, and JSON.

  synthetic test genomic report browser output

• nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.

  PMID 41563008 · PMC12950615 · GigaScience · 2026 · 8 claims · 3 setups

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  nf-core/proteinfamilies is a scalable, parametrizable, open-source Nextflow pipeline that generates new protein families or assigns sequences to existing families using profile HMMs and MSAs

  uniprot-swissprot input family diamond computational

• randPedPCA: rapid approximation of principal components from large pedigrees.

  PMID 40877802 · PMC12392600 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 2 setups

  Has reproduction · 84

  Matrix-vector multiplication with the dense additive relationship matrix A can be performed implicitly and efficiently via forward/backward substitution using the sparse inverse relationship (Cholesky) factor L^-1, avoiding explicit construction of A.

  simulated kennel computational pedigree

• Mutation rate at commonly used forensic STR loci: paternity testing experience.

  PMID 15665391 · PMC3839336 · Disease markers · 2004 · 8 claims · 2 setups

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  Microsatellite (STR) loci mutate at a higher rate than bulk genomic DNA, causing interpretation problems in paternity testing.

  parent edta str extraction

• Genetic analysis of MEFV gene pyrin domain in patients with Behçet's disease.

  PMID 16951489 · PMC1592598 · Mediators of inflammation · 2006 · 6 claims · 2 setups

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  No deletion, insertion, or point mutations were found in the pyrin domain of the MEFV gene in any of the 54 Turkish BD patients analyzed.

  genomic pcr pcr direct

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

  PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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  The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

  schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis

• Cryptosporidium: genomic and biochemical features.

  PMID 19187778 · PMC2819285 · Experimental parasitology · 2010 · 8 claims · 8 setups

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  C. parvum lacks a plastid and mitochondrial genome, unlike other apicomplexans, limiting plastid-targeted drug strategies

  parvum yeast recombinant gp40 pulsed-field happy genome

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• Whole genome sequences of Yersinia pestis strains of ancient phylogenetic branch 0.ANT5 isolated in the 21st century in the Tien-Shan in Kyrgyzstan.

  PMID 39206953 · PMC11478111 · Microbiology resource announcements · 2024 · 6 claims · 5 setups

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  Eleven Yersinia pestis strains of the ancient phylogenetic branch 0.ANT5, isolated in the Tien Shan focus (Kyrgyzstan) in 1952, 1971, and 2013–2023, were hybrid-sequenced (MGI short reads + ONT long reads)

  yersinia whole-genome hybrid plasmid

• The genome sequence of True's beaked whale, Mesoplodon mirus True, 1913 (Artiodactyla: Ziphiidae).

  PMID 41625987 · PMC12853023 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A genome assembly is presented for an individual female Mesoplodon mirus (True's beaked whale)

  mesoplodon pacbio hi-c sequencing

• The genome sequence of the Purple Cloud, Actinotia polyodon (Clerck, 1759) (Lepidoptera: Noctuidae).

  PMID 41696496 · PMC12902673 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosomal-level genome assembly was generated for Actinotia polyodon (Purple Cloud moth) from a single female specimen

  actinotia pacbio hi-c k-mer

• The genome sequence of the soldier beetle, Malthodes minimus (Linnaeus, 1758) (Coleoptera: Cantharidae).

  PMID 41769330 · PMC12949377 · Wellcome open research · 2026 · 8 claims · 8 setups

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  The Malthodes minimus genome assembly has a total length of 583.60 Mb, with 97.75% scaffolded into 7 chromosomal pseudomolecules including X and Y sex chromosomes

  malthodes pacbio assembled alternate pacbio hi-c barcoding

• The genome sequence of the Carline Skipper, Pyrgus carlinae (Rambur, 1839) (Lepidoptera: Hesperiidae).

  PMID 41841042 · PMC12989058 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly was generated for a female Pyrgus carlinae specimen (ilPyrCarl1) as part of Project Psyche

  pyrgus pacbio hi-c k-mer

• The genome sequence of the Madeiran Speckled Wood, Pararge xiphia Hübner, 1819 (Lepidoptera: Nymphalidae).

  PMID 41908930 · PMC13022564 · Wellcome open research · 2026 · 6 claims · 8 setups

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  A chromosome-level genome assembly was generated for a male Pararge xiphia specimen, containing two haplotypes of 528.41 Mb and 523.51 Mb

  organism pacbio assembled pacbio hi-c k-mer

• The genome sequence of the Oriental Meadow Brown, Cercyonis lupina (Lepidoptera: Nymphalidae).

  PMID 41924386 · PMC13036442 · Wellcome open research · 2026 · 8 claims · 8 setups

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  Genome of Cercyonis lupina assembled into two haplotypes with total lengths of 508.65 Mb (haplotype 1) and 467.75 Mb (haplotype 2)

  organism pacbio assembled scaffolded pacbio hi-c k-mer

• The genome sequence of a window fly, Scenopinus jerei Pohjoismäki & Haarto, 2021 (Diptera: Scenopinidae).

  PMID 41953045 · PMC13054250 · Wellcome open research · 2026 · 8 claims · 8 setups

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  This assembly provides the first genomic resource for the family Scenopinidae (window flies)

  organism idscejere3 assembled pacbio hi-c rna-seq

• The genome sequence of the sweet violet, Viola odorata L. (Malpighiales: Violaceae).

  PMID 41960579 · PMC13058574 · Wellcome open research · 2026 · 8 claims · 8 setups

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  The Viola odorata genome assembly has a total length of 698.62 megabases, with 99.9% scaffolded into 10 chromosomal pseudomolecules.

  viola flow barcoding pacbio