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).

• In-frame deletion in the seventh immunoglobulin-like repeat of filamin C in a family with myofibrillar myopathy.

  PMID 19050726 · PMC2672961 · European journal of human genetics : EJHG · 2009 · 8 claims · 8 setups

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  A 12-nucleotide deletion (c.2997_3008del) in FLNC exon 18, predicting an in-frame four-residue deletion (p.Val930_Thr933del) in the seventh Ig-like repeat of filamin C, was identified in a German family with MFM (mother and daughter).

  genomic muscle skeletal direct topo genescan

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• Extensive variation between chromosomes of North American and European hop.

  PMID 42204144 · PMC13216280 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 87

  Chromosome-scale, haplotype-resolved genome assemblies of the hybrid hop cultivar Apollo were generated using hifiasm, ALLHiC, and TRITEX pipelines with PacBio HiFi and Hi-C data

  hop feral biparental accessions pacbio busco fluorescence

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.

  apis algerian ld-pruned reference whole-genome read identity-by-descent

• Ultrastructural analyses of deciduous teeth affected by hypocalcified amelogenesis imperfecta from a family with a novel Y458X FAM83H nonsense mutation.

  PMID 20160442 · PMC4432877 · Cells, tissues, organs · 2010 · 8 claims · 5 setups

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  A novel FAM83H nonsense mutation c.1374C>A (p.Y458X) in exon 5 is identified as the cause of AD hypocalcified amelogenesis imperfecta in this family

  genomic sectioned tooth family sequencing scanning energy

• Detecting natural selection by empirical comparison to random regions of the genome.

  PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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  Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

  ceu genomic simulated long-read snp population

• Personalized copy number and segmental duplication maps using next-generation sequencing.

  PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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  mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

  genomes genomic interphase na18507 whole-genome array fluorescence

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

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  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

  PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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  Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

  european african individuals nondiabetic snp variant direct

• No evidence of a Neanderthal contribution to modern human diversity.

  PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

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  There is no evidence of any Neanderthal contribution to modern human genetic diversity

  neanderthal culture modern genomic mitochondrial nuclear gene-specific

• Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II.

  PMID 19881469 · PMC4511341 · Journal of human genetics · 2009 · 8 claims · 6 setups

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  Screening all 72 exons of USH2A (long isoform) identifies significantly more mutations than screening only the short-isoform exons 1-21

  genomic ush2 ush2a sscp audiological ophthalmological

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Preselection of cases through expert clinical and radiological review significantly increases mutation detection rate in multiple epiphyseal dysplasia.

  PMID 17133256 · PMC2670452 · European journal of human genetics : EJHG · 2007 · 7 claims · 3 setups

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  Expert clinical-radiological preselection significantly increases mutation detection rate in MED

  patients genomic single clinical pcr

• Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

  PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 7 setups

  Has reproduction · 53

  Current effective population size for all four farmed fish populations is small (≤50 fish), potentially threatening breeding-programme sustainability

  turbot gilthead european common rad linkage computer

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• Analysis of human prostate cancers and cell lines for mutations in the TP53 and KLF6 tumour suppressor genes.

  PMID 12915879 · PMC2376923 · British journal of cancer · 2003 · 4 claims · 4 setups

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  KLF6 exon2 miscoding mutations are uncommon in prostate cancer, contrary to the earlier report of ~55% mutation frequency

  prostate tumors pcr oligonucleotide

• Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

  PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

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  No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

  t1d european warren resequencing database tag

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

  PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups

  Has reproduction · 90

  Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.

  global ndama target illumina whole-genome array genotype