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).

• Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

  PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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  Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

  family p2ry5 affected snp microsatellite sanger

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

  PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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  Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

  poodle dogs y-chromosome blast pcr nested

• Human QTL linkage mapping.

  PMID 18668207 · PMC2761031 · Genetica · 2009 · 8 claims · 6 setups

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  Human QTL linkage mapping remains a productive approach for complex traits despite the perception that it does not work, and will continue to be productive especially combined with RNA expression QTLs and dense SNP panels

  mexican pomc gene promoter genome-wide gene expression

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

  PMID 18621558 · PMC2697027 · European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery · 2008 · 8 claims · 3 setups

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  AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals

  aaa cases candidate genome-wide

• SNPs in cancer research and treatment.

  PMID 14970847 · PMC2410167 · British journal of cancer · 2004 · 8 claims · 8 setups

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  SNPs and haplotype-tagging SNPs (ht-SNPs) provide a resource for investigating genetic contributions to cancer susceptibility and outcome while reducing genotyping burden versus testing every SNP

  lung bladder colon prostate candidate snp-based haplotype

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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  Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• Mutations in alpha-tubulin cause abnormal neuronal migration in mice and lissencephaly in humans.

  PMID 17218254 · PMC1885944 · Cell · 2007 · 8 claims · 8 setups

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  A semidominant ENU-induced S140G mutation in α-1 tubulin (Tuba1) causes hyperactivity and impaired neuronal migration in Jna/+ mice

  enu-mutagenized jna cell-free hippocampus locomotor qtl gtp-binding

• Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

  PMID 19844255 · PMC2824775 · European journal of human genetics : EJHG · 2010 · 7 claims · 7 setups

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  A locus on chromosome 16q23-24 affects HDL-C levels in two independent French-Canadian family studies (QUE and SLSJ)

  que slsj candidate skin genome-wide sanger tagging

• Genetics and proteomics: deciphering gene association studies in critical illness.

  PMID 16934133 · PMC1750993 · Critical care (London, England) · 2006 · 8 claims · 8 setups

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  Most critical illnesses are complex traits (multifactorial), unlike single-gene Mendelian diseases.

  severe families caucasian tnf genetic linkage microarray

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier

• 1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas.

  PMID 17934521 · PMC2650419 · Oncogene · 2008 · 8 claims · 8 setups

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  Total 1p deletion is rare (2%) in astrocytic tumours, whereas partial deletions involving 1p36 are common and increase with malignancy grade (22% in anaplastic astrocytomas, 34% in glioblastomas)

  astrocytic glioblastomas array-cgh microsatellite quantitative

• Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

  PMID 19716302 · PMC2748900 · Current biology : CB · 2009 · 7 claims · 4 setups

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  Direct sequencing of a 13-generation pedigree yields a Y-chromosome mutation rate of 3.0 × 10^-8 mutations/nucleotide/generation

  flow-sorted cell-line family lymphoblastoid y-chromosome capillary y-str

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• ChimerDB--a knowledgebase for fusion sequences.

  PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

  genome candidate pubmed omim blat splice-site ecgene

• Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

  PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

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  Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

  pedigrees pedigree genomic ubiad1 microsatellite fine direct

• Genotype-phenotype associations: modulation by diet and obesity.

  PMID 19037211 · PMC2771769 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 7 setups

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  Obesity modulates the association between APOE genotype and fasting insulin/glucose levels in men, with obese APOE4 carriers showing higher insulin and glucose than other obese genotype groups.

  framingham spanish caucasian population apoe edn1 lpl