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).

Publications 1.3k Datasets 392.5k Experiments 100

System / cell line: populations ✕ Assay: gene ✕ Clear

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

Has reproduction · 66

Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
The origins of lactase persistence in Europe.

PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

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The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

simulated simulation 910*t farming demic approximate comparison
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

diffuse-type liver renal anaplastic differential proteomic proteomics
Isolated populations and complex disease gene identification.

PMID 18771588 · PMC2575505 · Genome biology · 2008 · 8 claims · 5 setups

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Isolated/founder populations are useful for identifying genes underlying common complex diseases, not just rare monogenic diseases.

genetically icelandic finnish hutterites linkage genome-wide
Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

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A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

breast carcinogenesis-related nssnp-containing african gene snp functional
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Metabolic syndrome: from epidemiology to systems biology.

PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

populations rats adipose four genome-wide linkage gene
Easy and efficient ensemble gene set testing with EGSEA.

PMID 29333246 · PMC5747338 · F1000Research · 2017 · 8 claims · 2 setups

Has reproduction · 97

EGSEA combines results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant gene sets.

basal bulk microarray
Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

Has reproduction · 68

200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

african lion crater simulated genome principal admixture
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

Has reproduction · 66

Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

blood transcriptomic postmortem saliva gsea machine differential
Pharmacogenomic biomarkers.

PMID 12364812 · PMC3850811 · Disease markers · 2002 · 8 claims · 8 setups

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Development of a pharmacogenomic biomarker requires sequential steps: laboratory identification, retrospective confirmation in clinical samples, prospective clinical trial validation, and regulatory approval before patient stratification.

populations population tumor breast genetic array immunohistochemistry
Designing candidate gene and genome-wide case-control association studies.

PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

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Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

population monozygotic international genome-wide candidate twin
Population genomics of human gene expression.

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

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

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

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

genomic pnmt promoter pcr population haplotype
Public health genomics: translating obesity genomics research into population health benefits.

PMID 19037221 · PMC2736102 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 6 setups

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Obesity genomics research is mostly in the discovery phase (T1); a four-phase translational framework (T1-T4) is needed to move discoveries to population health impact

populations white mice humans genetic pharmacogenetic gene-by-environment
Nutritional genomics, polyphenols, diets, and their impact on dietetics.

PMID 18954579 · PMC2692306 · Journal of the American Dietetic Association · 2008 · 8 claims · 8 setups

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Nutrient-gene interactions, exemplified by the MTHFR C677T polymorphism, modulate individual metabolic responses (e.g., homocysteine metabolism) and can be offset by adjusting nutrient intake such as folate

mammary embryonic subjects rats gene histone carcinogen-induced
The dystrobrevin-binding protein 1 gene: features and networks.

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

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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
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population

Experiments

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

The origins of lactase persistence in Europe.

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

Isolated populations and complex disease gene identification.

Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Metabolic syndrome: from epidemiology to systems biology.

Easy and efficient ensemble gene set testing with EGSEA.

Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

Pharmacogenomic biomarkers.

Designing candidate gene and genome-wide case-control association studies.

Population genomics of human gene expression.

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

Public health genomics: translating obesity genomics research into population health benefits.

Nutritional genomics, polyphenols, diets, and their impact on dietetics.

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

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.