480 research outputs found
Diffusional Relaxation in Random Sequential Deposition
The effect of diffusional relaxation on the random sequential deposition
process is studied in the limit of fast deposition. Expression for the coverage
as a function of time are analytically derived for both the short-time and
long-time regimes. These results are tested and compared with numerical
simulations.Comment: 9 pages + 2 figure
GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments
MOTIVATION: Sequencing pools of individuals (Pool-Seq) is a cost-effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome-wide from Pool-Seq experiments. RESULTS: We showed that GWAlpha powerfully replicates the results of Genome-Wide Association Studies (GWAS) from model organisms. We perform simulation studies that illustrate the effect on power of sample size and number of pools and test the method on different experimental data. AVAILABILITY AND IMPLEMENTATION: GWAlpha is implemented in python, designed to run on Linux operating system and tested on Mac OS. It is freely available at https://github.com/aflevel/GWAlpha CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online
On the universality of a class of annihilation-coagulation models
A class of -dimensional reaction-diffusion models interpolating
continuously between the diffusion-coagulation and the diffusion-annihilation
models is introduced. Exact relations among the observables of different models
are established. For the one-dimensional case, it is shown how correlations in
the initial state can lead to non-universal amplitudes for time-dependent
particles density.Comment: 18 pages with no figures. Latex file using REVTE
Model of Cluster Growth and Phase Separation: Exact Results in One Dimension
We present exact results for a lattice model of cluster growth in 1D. The
growth mechanism involves interface hopping and pairwise annihilation
supplemented by spontaneous creation of the stable-phase, +1, regions by
overturning the unstable-phase, -1, spins with probability p. For cluster
coarsening at phase coexistence, p=0, the conventional structure-factor scaling
applies. In this limit our model falls in the class of diffusion-limited
reactions A+A->inert. The +1 cluster size grows diffusively, ~t**(1/2), and the
two-point correlation function obeys scaling. However, for p>0, i.e., for the
dynamics of formation of stable phase from unstable phase, we find that
structure-factor scaling breaks down; the length scale associated with the size
of the growing +1 clusters reflects only the short-distance properties of the
two-point correlations.Comment: 12 page
Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.
The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observed among multiple ethnic groups sampled throughout Ethiopia. Anthropologists have proposed two competing theories to explain the origins of the Ari Blacksmiths as (i) remnants of a population that inhabited Ethiopia prior to the arrival of agriculturists (e.g. Cultivators), or (ii) relatively recently related to the Cultivators but presently marginalized in the community due to their trade. Two recent studies by different groups analysed genome-wide DNA from samples of Ari Blacksmiths and Cultivators and suggested that genetic patterns between the two groups were more consistent with model (i) and subsequent assimilation of the indigenous peoples into the expanding agriculturalist community. We analysed the same samples using approaches designed to attenuate signals of genetic differentiation that are attributable to allelic drift within a population. By doing so, we provide evidence that the genetic differences between Ari Blacksmiths and Cultivators can be entirely explained by bottleneck effects consistent with hypothesis (ii). This finding serves as both a cautionary tale about interpreting results from unsupervised clustering algorithms, and suggests that social constructions are contributing directly to genetic differentiation over a relatively short time period among previously genetically similar groups
Group testing with Random Pools: Phase Transitions and Optimal Strategy
The problem of Group Testing is to identify defective items out of a set of
objects by means of pool queries of the form "Does the pool contain at least a
defective?". The aim is of course to perform detection with the fewest possible
queries, a problem which has relevant practical applications in different
fields including molecular biology and computer science. Here we study GT in
the probabilistic setting focusing on the regime of small defective probability
and large number of objects, and . We construct and
analyze one-stage algorithms for which we establish the occurrence of a
non-detection/detection phase transition resulting in a sharp threshold, , for the number of tests. By optimizing the pool design we construct
algorithms whose detection threshold follows the optimal scaling . Then we consider two-stages algorithms and analyze their
performance for different choices of the first stage pools. In particular, via
a proper random choice of the pools, we construct algorithms which attain the
optimal value (previously determined in Ref. [16]) for the mean number of tests
required for complete detection. We finally discuss the optimal pool design in
the case of finite
Accurate Liability Estimation Improves Power in Ascertained Case Control Studies
Linear mixed models (LMMs) have emerged as the method of choice for
confounded genome-wide association studies. However, the performance of LMMs in
non-randomly ascertained case-control studies deteriorates with increasing
sample size. We propose a framework called LEAP (Liability Estimator As a
Phenotype, https://github.com/omerwe/LEAP) that tests for association with
estimated latent values corresponding to severity of phenotype, and demonstrate
that this can lead to a substantial power increase
Fregene: Simulation of realistic sequence-level data in populations and ascertained samples
Background: FREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, and recombination to be modelled simultaneously. Detailed tracking of sites under selection is implemented in FREGENE and provides the opportunity to test theoretical predictions and gain new insights into mechanisms of selection. We describe here main functionalities of both FREGENE and SAMPLE, a companion program that can replicate association study datasets.Results: We report detailed analyses of six large simulated datasets that we have made publicly available. Three demographic scenarios are modelled: one panmictic, one substructured with migration, and one complex scenario that mimics the principle features of genetic variation in major worldwide human populations. For each scenario there is one neutral simulation, and one with a complex pattern of selection.Conclusion: FREGENE and the simulated datasets will be valuable for assessing the validity of models for selection, demography and population genetic parameters, as well as the efficacy of association studies. Its principle advantages are modelling flexibility and computational efficiency. It is open source and object-oriented. As such, it can be customised and the range of models extended
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