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).

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

  Full-text index only

  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.

  hapmap encode enr112 tag cross-validated entropy tagged

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

  Full-text index only

  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

  PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

  Full-text index only

  Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

  hla-homozygous same mhc indel clone-by-clone gene hla

• 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

• Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

  PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

  Full-text index only

  Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

  eye genomic tnnt1 cdna genomic snp

• 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

  Full-text index only

  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

  Full-text index only

  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample.

  PMID 19800201 · PMC2783814 · Schizophrenia research · 2009 · 8 claims · 7 setups

  Full-text index only

  Common alleles at DTNBP1 SNPs, particularly rs760761, are associated with schizophrenia in the ICCSS sample

  irish chimpanzee dtnbp1 snp haplotype case

• Sequence variation in the human transcription factor gene POU5F1.

  PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

  Full-text index only

  POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

  genomic multi-species inferred international resequencing comparative haplotype

• The Genographic Project public participation mitochondrial DNA database.

  PMID 17604454 · PMC1904368 · PLoS genetics · 2007 · 7 claims · 4 setups

  Full-text index only

  The Genographic Project created the largest standardized human mtDNA database to date, comprising 78,590 genotypes from the first 18 months of public participation.

  buccal reference entire direct coding-region leave-one-out

• PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

  PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

  Full-text index only

  None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

  blood finnish combined formalin-fixed direct additional statistical

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

  Full-text index only

  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

  PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

  Full-text index only

  A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

  consanguineous same affected family sanger multiplex microsatellite

• An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

  PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

  Full-text index only

  Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

  unrelated shanghai tsnps snp allele linkage

• Molecular characterization of retinitis pigmentosa in Saudi Arabia.

  PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

  Full-text index only

  The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

  blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional

• A disease model resource reveals core principles of tissue-specific cancer evolution.

  PMID 41741657 · PMC13149333 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  The Mouse Cancer Cell line Atlas (MCCA) is a broad-utility resource of 590 comprehensively characterized mouse cancer cell line models spanning 22 lineages and 46 disease types, accessible via a web portal (www.mcca.tum.de)

  mcca tumour immunocompetent paca whole-genome microscopy-based histopathology

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript