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 Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.
PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups
An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.
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Has reproduction · 53
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.
PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 7 setups
Current effective population size for all four farmed fish populations is small (≤50 fish), potentially threatening breeding-programme sustainability
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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
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.
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Accuracy of predicting the genetic risk of disease using a genome-wide approach.
PMID 18852893 · PMC2561058 · PloS one · 2008 · 8 claims · 4 setups
Deterministic equations can predict the accuracy (r_gĝ) of genome-wide genetic risk/value prediction for continuous, dichotomous, and case-control study designs.
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Has reproduction · 98
Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters.
PMID 38632535 · PMC11022492 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 3 setups
The most precise estimates of genetic parameters and genetic trends are obtained when breeding queens are mated with drones of a single DPQ that is correctly assigned in the pedigree (SS mating).
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Analysis of concordance of different haplotype block partitioning algorithms.
PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups
Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.
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Calculating expected DNA remnants from ancient founding events in human population genetics.
PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups
Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.
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Subfunctionalization of duplicated genes as a transition state to neofunctionalization.
PMID 15831095 · PMC1112588 · BMC evolutionary biology · 2005 · 8 claims · 2 setups
Subfunctionalization plays an important role in duplicate gene retention but functions as a transition state leading to neofunctionalization rather than as a terminal fate.
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Importance sampling for the infinite sites model.
PMID 18976228 · PMC2832804 · Statistical applications in genetics and molecular biology · 2008 · 7 claims · 2 setups
A new importance sampling proposal distribution for the ISM, derived from a new result on exact sampling from a single segregating site, generally shows greater efficiency than the GT and SD proposals.
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Digital evolution.
PMID 14551915 · PMC212697 · PLoS biology · 2003 · 7 claims · 5 setups
Digital organisms (Avidians) evolved from simple self-replicators, through an unexpected transitional form, to complex performers of many logic functions, with the full genealogy traceable and no missing links.
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Population history and natural selection shape patterns of genetic variation in 132 genes.
PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups
Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection
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Inferring human colonization history using a copying model.
PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups
A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.
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Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.
PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups
Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements
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Has reproduction · 89
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
Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes
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Modeling the amplification dynamics of human Alu retrotransposons.
PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups
Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.
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Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.
PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups
A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation
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Iterative pruning PCA improves resolution of highly structured populations.
PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups
ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data
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Positive selection for the male functionality of a co-retroposed gene in the hominoids.
PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups
PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives
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Processing and population genetic analysis of multigenic datasets with ProSeq3 software.
PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups
ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets
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Has reproduction · 85
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups
EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)