Related papers: Moment based gene set tests
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
We seek to identify genes involved in Parkinson's Disease (PD) by combining information across different experiment types. Each experiment, taken individually, may contain too little information to distinguish some important genes from…
Entropy metrics are nonlinear measures to quantify the complexity of time series. Among them, permutation entropy is a common metric due to its robustness and fast computation. Multivariate entropy metrics techniques are needed to analyse…
Permutations of correlated sequences of random variables appear naturally in a variety of applications such as graph matching and asynchronous communications. In this paper, the asymptotic statistical behavior of such permuted sequences is…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…
Permutation entropy measures the complexity of deterministic time series via a data symbolic quantization consisting of rank vectors called ordinal patterns or just permutations. The reasons for the increasing popularity of this entropy in…
The increasing observation of mutual exclusivity correlations among cancer gene mutations is a key component for identifying driver events or pathways in cancer genome analysis. Here we report a rigorous statistical method to compute an…
Early detection of person-to-person transmission of emerging infectious diseases such as avian influenza is crucial for containing pandemics. We developed a simple permutation test and its refined version for this purpose. A simulation…
In this paper we study the parameterized complexity of two well-known permutation group problems which are NP-complete. 1. Given a permutation group G=<S>, subgroup of $S_n$, and a parameter $k$, find a permutation $\pi$ in G such that…
Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities…
Genomic studies face a vast hypothesis space, while interventions such as gene perturbations remain costly and time-consuming. To accelerate such experiments, gene perturbation models predict the transcriptional outcome of interventions.…
We study properties of two resampling scenarios: Conditional Randomisation and Conditional Permutation schemes, which are relevant for testing conditional independence of discrete random variables $X$ and $Y$ given a random variable $Z$.…
It is conventionally believed that a permutation test should ideally use all permutations. If this is computationally unaffordable, it is believed one should use the largest affordable Monte Carlo sample or (algebraic) subgroup of…
The two-phase sampling design is a cost-efficient way of collecting expensive covariate information on a judiciously selected subsample. It is natural to apply such a strategy for collecting genetic data in a subsample enriched for exposure…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
Gene set analysis, a popular approach for analysing high-throughput gene expression data, aims to identify sets of genes that show enriched expression patterns between two conditions. In addition to the multitude of methods available for…
The identification of predefined groups of genes ("gene-sets") which are differentially expressed between two conditions ("gene-set analysis", or GSA) is a very popular analysis in bioinformatics. GSA incorporates biological knowledge by…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
When multiple hypotheses are tested, interest is often in ensuring that the proportion of false discoveries (FDP) is small with high confidence. In this paper, confidence upper bounds for the FDP are constructed, which are simultaneous over…