Search results for "Statistics"

Simulation-based estimation of branching models for LTR retrotransposons

2017

Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …

On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory

2017

Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a v…

Evolutionary distances corrected for purifying selection and ancestral polymorphisms.

2019

Abstract Evolutionary distance formulas that take into account effects due to ancestral polymorphisms and purifying selection are obtained on the basis of the full solution of Jukes–Cantor and Kimura DNA substitution models. In the case of purifying selection two different methods are developed. It is shown that avoiding the dimensional reduction implicitly carried out in the conventional model solving is instrumental to incorporate the quoted effects into the formalism. The problem of estimating the numerical values of the model parameters, as well as those of the correction terms, is not addressed.

REGGAE : a novel approach for the identification of key transcriptional regulators

2019

Abstract Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines assoc…

Multiplicity- and dependency-adjusted p-values for control of the family-wise error rate

2016

Abstract Under the multiple testing framework, we propose the multiplicity- and dependency-adjustment method (MADAM) which transforms test statistics into adjusted p -values for control of the family-wise error rate. For demonstration, we apply the MADAM to data from a genetic association study.

bookdown: Authoring Books and Technical Documents with R Markdown

2018

Pitfalls of hypothesis tests and model selection on bootstrap samples: Causes and consequences in biometrical applications

2015

The bootstrap method has become a widely used tool applied in diverse areas where results based on asymptotic theory are scarce. It can be applied, for example, for assessing the variance of a statistic, a quantile of interest or for significance testing by resampling from the null hypothesis. Recently, some approaches have been proposed in the biometrical field where hypothesis testing or model selection is performed on a bootstrap sample as if it were the original sample. P-values computed from bootstrap samples have been used, for example, in the statistics and bioinformatics literature for ranking genes with respect to their differential expression, for estimating the variability of p-v…

Competing species system as a qualitative model of radiation therapy

2016

To examine complex features of tumor dynamics we analyze a competing-species lattice model that takes into account the competition for nutrients or space as well as interaction with therapeutic factors such as drugs or radiation. Our model might be interpreted as a certain prey–predator system having three trophic layers: (i) the basal species that might be interpreted as nutrients; (ii) normal and tumor cells that consume nutrients, and (iii) therapeutic factors that might kill either nutrient, normal or tumor cells. Using a wide spectrum of parameters we examined survival of our species and tried to identify the corresponding dynamical regimes. It was found that the radiotherapy influence…

Collective Cell Migration in a Fibrous Environment: A Hybrid Multiscale Modelling Approach

2021

International audience; The specific structure of the extracellular matrix (ECM), and in particular the density and orientation of collagen fibres, plays an important role in the evolution of solid cancers. While many experimental studies discussed the role of ECM in individual and collective cell migration, there are still unanswered questions about the impact of nonlocal cell sensing of other cells on the overall shape of tumour aggregation and its migration type. There are also unanswered questions about the migration and spread of tumour that arises at the boundary between different tissues with different collagen fibre orientations. To address these questions, in this study we develop …

In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes

2018

Abstract Motivation Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy. Therefore, an important issue is to understand if, and to what extent, the structural differences in the chromatin organization between in vit…