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).

• Human QTL linkage mapping.

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

  Full-text index only

  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

• 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

  Full-text index only

  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

• Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

  PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

  Has reproduction · 80

  The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

  mpm mesomics whole-genome bulk methylation

• Melanesian mtDNA complexity.

  PMID 17327912 · PMC1803017 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  Among-group mtDNA variation in Northern Island Melanesia is structured by island, island size, and language affiliation.

  populations near mtdna mtdna analysis coalescence

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• A macaque's-eye view of human insertions and deletions: differences in mechanisms.

  PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

  Full-text index only

  Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

  chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis

• Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

  PMID 19043545 · PMC2581785 · PLoS genetics · 2008 · 7 claims · 4 setups

  Full-text index only

  A GWA study using serum metabolomics identifies SNPs associated with metabolite concentrations, explaining up to 12% of variance for single metabolites

  kora fasting genome-wide targeted metabolite

• Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

  PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

  Full-text index only

  The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

  population-based cohorts gwa plasma genome-wide replication candidate

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

  Full-text index only

  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

  Full-text index only

  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

  Full-text index only

  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• A genome wide linkage scan of metacarpal size and geometry in the Framingham Study.

  PMID 18449921 · PMC2574919 · American journal of human biology : the official journal of the Human Biology Council · 2008 · 8 claims · 4 setups

  Full-text index only

  Metacarpal geometric indices (length, midshaft width, MCT, MCI, MZ) show significant heritability, ranging from 0.51 (MCT) to 0.82 (length)

  hand individuals same radiogrammetry genome-wide variance

• 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

  Has reproduction · 100

  Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  individuals dutch phased drenthe whole-genome principal phylogenetic

• Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

  PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

  Has reproduction · 51

  K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

  uniflora whole-genome phylogenomic population

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

  PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

  Full-text index only

  X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

  ensembl breast mcf7 25-mer probe-to-transcript microarray

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

  PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

  angora domesticated candidate low-coverage multivariate principal

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

  Full-text index only

  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence