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 13

System / cell line: age ✕ Assay: simulation ✕ Clear

A universal mechanism ties genotype to phenotype in trinucleotide diseases.

PMID 18039028 · PMC2082501 · PLoS computational biology · 2007 · 8 claims · 5 setups

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A universal mechanism of somatic, length-dependent trinucleotide repeat expansion toward a disease-specific pathological threshold explains genotype-phenotype correlations common to trinucleotide diseases

dominant recessive patients homozygous computer mathematical
Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

transmembrane simulated age duplicate maximum kernel monte
RADAR: differential analysis of MeRIP-seq data with a random effect model.

PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 10

RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.

simulated fallopian pancreatic liver merip-seq m6a-merip-seq pca
Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

PMID 36882868 · PMC9991879 · BMC medicine · 2023 · 8 claims · 6 setups

Has reproduction · 89

Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes

population-level age-structured same ethiopia dynamic epidemiological daly
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

PMID 39549198 · PMC11979089 · GeroScience · 2025 · 9 claims · 2 setups

Has reproduction · 54

The Multi-State Epigenetic Pacemaker (MSEPM) can accurately model multiple methylation-associated factors (e.g., age, sex, cell-type) simultaneously.

blood simulated methylation simulation
The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

peripheral brca1 same simulated fluorescent cox weighted
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

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The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

rumen blood beef metagenome snp longitudinal
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Multilocus analysis of SNP and metabolic data within a given pathway.

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

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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
Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

egfr tp53 laci lung literature comparative statistical
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

Has reproduction · 43

TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

mdr-tb paired-end raw bam whole-genome kraken raw
Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

PMID 18567820 · PMC2518507 · Diabetes · 2008 · 8 claims · 5 setups

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CDC123/CAMK1D rs12779790 risk allele (homozygous) is associated with decreased insulinogenic index, corrected insulin response (CIR), and AUC-insulin/AUC-glucose ratio, indicating impaired insulin release

inter99 same taqman oral general

Experiments

A universal mechanism ties genotype to phenotype in trinucleotide diseases.

Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

RADAR: differential analysis of MeRIP-seq data with a random effect model.

Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

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

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.