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).
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A model-based approach to selection of tag SNPs.
PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups
The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.
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A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.
PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups
Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections
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Assaying chromosomal inversions by single-molecule haplotyping.
PMID 16721377 · PMC2690135 · Nature methods · 2006 · 8 claims · 4 setups
Haplotype Fusion PCR (HF-PCR) juxtaposes sequences flanking an inversion breakpoint on single DNA molecules via emulsion PCR, generating orientation-specific fusion products diagnostic of inversion genotype
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Direct maximum parsimony phylogeny reconstruction from genotype data.
PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups
The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.
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Genomic views of distant-acting enhancers.
PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups
Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.
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The future is genome-wide.
PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups
Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level
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Whole genome association mapping by incompatibilities and local perfect phylogenies.
PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups
Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association
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Catechol-O-methyltransferase (COMT) gene variants: possible association of the Val158Met variant with opiate addiction in Hispanic women.
PMID 18270997 · PMC2909109 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 8 claims · 5 setups
The G/A and A/A genotypes of G472A (Val158Met) are point-wise significantly associated with opiate addiction in Hispanic women but not men (P=0.049)
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HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.
PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups
Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.
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Has reproduction · 100
Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.
PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).
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Complex genetic diseases: controversy over the Croesus code.
PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups
The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.
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HaploSNPer: a web-based allele and SNP detection tool.
PMID 18307806 · PMC2288614 · BMC genetics · 2008 · 6 claims · 2 setups
HaploSNPer is a web-based tool integrating BLASTN, CAP3/PHRAP, and QualitySNP into a single pipeline for allele and SNP detection from diploid and polyploid species
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Are p.I148T, p.R74W and p.D1270N cystic fibrosis causing mutations?
PMID 15287992 · PMC509248 · BMC medical genetics · 2004 · 8 claims · 7 setups
A CF-causing second mutation (c.3199del6 or the novel c.3395insA) was found in cis with p.I148T in all CF patients in this cohort who carried p.I148T
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Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.
PMID 16212661 · PMC1282566 · BMC genetics · 2005 · 8 claims · 4 setups
The previously proposed P2-specific markers -551_-550insC and -160A>G do not correlate with P1/P2 phenotype, since they occur homozygously in many P1 individuals too
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The vertebrate genome annotation (Vega) database.
PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups
Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.