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 reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

  Has reproduction

  Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

  duroc 1000-individual real low-coverage genome-wide genomic

• Re-evaluating early breast neoplasia.

  PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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  The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

  dcis breast patient-matched premalignant comparative combined cdna

• SNP-specific extraction of haplotype-resolved targeted genomic regions.

  PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

  genomic diploid quantitative sanger low

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

  Has reproduction · 59

  382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

  semibalanus individual rocky barnacles pool-seq sanger temperature

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.

  PMID 17375191 · PMC1810429 · PloS one · 2007 · 7 claims · 6 setups

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  The Genomic Assay can detect 100 copies of Bacillus globigii genomic dsDNA, including in the presence of human genomic dsDNA background, without PCR amplification

  bacillus drosophila genomic triplex

• 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

• High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

  PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

  Has reproduction · 85

  SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

  atlantic low-coverage genotyping genome

• SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

  PMID 16262895 · PMC1280925 · BMC genomics · 2005 · 8 claims · 5 setups

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  Poorly performing SNPs (NoCall rate ≥25%) fail primarily due to inadequate training/localization of the MPAM statistical model call zone, not detection filter failure

  genomic genotype genotyped chromosomal snp clustering mendelian

• Large genomic rearrangements in the CFTR gene contribute to CBAVD.

  PMID 17448246 · PMC1876208 · BMC medical genetics · 2007 · 7 claims · 6 setups

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  Large genomic rearrangements in CFTR contribute to CBAVD and should be systematically investigated alongside point mutation screening

  genomic pcr cftr semi-quantitative junction direct

• Evidence for a novel gene associated with human influenza A viruses.

  PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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  A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

  influenza pre-1950 avian neg8 comparative neighbour-joining fixed

• Genetical genomic determinants of alcohol consumption in rats and humans.

  PMID 19874574 · PMC2777866 · BMC biology · 2009 · 8 claims · 6 setups

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  A genetical genomics approach combining brain gene expression, bQTL, and eQTL analysis in HXB/BXH RI rats identifies candidate genes for alcohol consumption

  hxb naive caucasian two-bottle behavioral brain

• Toxicogenomics: an emerging discipline.

  PMID 12460812 · PMC1241126 · Environmental health perspectives · 2002 · 8 claims · 6 setups

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  Toxicogenomics applies genomic tools (microarrays, proteomics, metabolomics) to characterize how cells and organisms respond to chemical/drug exposures.

  drug stated acetaminophen tissues microarray gene genomic

• Alstrom syndrome (OMIM 203800): a case report and literature review.

  PMID 18154657 · PMC2266715 · Orphanet journal of rare diseases · 2007 · 8 claims · 8 setups

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  The proband is a compound heterozygote for two novel ALMS1 mutations, V424I (exon 6) and H3882Y (exon 17), causative for Alstrom syndrome

  genomic healthy proband pcr pcr-rflp plasma

• Mutations of the Igbeta gene cause agammaglobulinemia in man.

  PMID 17709424 · PMC2118692 · The Journal of experimental medicine · 2007 · 6 claims · 5 setups

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  A homozygous nonsense mutation (Gln80X) in the Igβ (B29) gene causes agammaglobulinemia in a human patient

  genomic drosophila pbmcs sorted pcr transfection flow

• Familial Wolfram syndrome due to compound heterozygosity for two novel WFS1 mutations.

  PMID 18660851 · PMC2483297 · Molecular vision · 2008 · 8 claims · 6 setups

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  The four affected siblings are compound heterozygotes for two novel WFS1 mutations, one from each parent, causing Wolfram syndrome.

  genomic affected microsatellite pcr allele-specific

• Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

  PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

  cd4+ computational hep direct simulation epigraph

• Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

  PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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  Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

  genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent

• The D2 dopamine receptor gene and nicotine dependence among bladder cancer patients and controls.

  PMID 19842028 · PMC3719969 · Behavior genetics · 2010 · 8 claims · 5 setups

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  Among ever-smoking controls, A1 and B1 genotypes were associated with greater smoking intensity and younger age at smoking initiation than A2A2/B2B2

  peripheral bladder current genotype pcr-rflp structured fagerström