Search results for "Probability"
showing 10 items of 3417 documents
Reactome diagram viewer: data structures and strategies to boost performance
2017
Abstract Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partit…
Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients.
2018
AbstractFriedreich’s ataxia (FRDA; OMIM 229300), an autosomal recessive neurodegenerative mitochondrial disease, is the most prevalent hereditary ataxia. In addition, FRDA patients have shown additional non-neurological features such as scoliosis, diabetes, and cardiac complications. Hypertrophic cardiomyopathy, which is found in two thirds of patients at the time of diagnosis, is the primary cause of death in these patients. Here, we used small RNA-seq of microRNAs (miRNAs) purified from plasma samples of FRDA patients and controls. Furthermore, we present the rationale, experimental methodology, and analytical procedures for dataset analysis. This dataset will facilitate the identificatio…
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record [insert complete citation information here] is available online at: https://doi.org/10.1093/bioinformatics/btw038 [Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe , a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of S…
Gene-based and semantic structure of the Gene Ontology as a complex network
2012
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. This approach might be usefully complemented by a bottom-up approach based on the knowledge of relationships amongst genes. To this end, we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium and a gene-based …
L1-Penalized Censored Gaussian Graphical Model
2018
Graphical lasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. Typical examples are data generated by polymerase chain reactions and flow cytometer. The combination of censoring and high-dimensionality make inference of the underlying genetic networks from these data very challenging. In this article, we propose an $\ell_1$-penalized Gaussian graphical model for censored data and derive two EM-like algorithm…
Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks.
2016
Abstract Factorial Gaussian graphical Models (fGGMs) have recently been proposed for inferring dynamic gene regulatory networks from genomic high-throughput data. In the search for true regulatory relationships amongst the vast space of possible networks, these models allow the imposition of certain restrictions on the dynamic nature of these relationships, such as Markov dependencies of low order – some entries of the precision matrix are a priori zeros – or equal dependency strengths across time lags – some entries of the precision matrix are assumed to be equal. The precision matrix is then estimated by l 1-penalized maximum likelihood, imposing a further constraint on the absolute value…
Prioritizing covariates in the planning of future studies in the meta-analytic framework
2016
Science can be seen as a sequential process where each new study augments evidence to the existing knowledge. To have the best prospects to make an impact in this process, a new study should be designed optimally taking into account the previous studies and other prior information. We propose a formal approach for the covariate prioritization, i.e., the decision about the covariates to be measured in a new study. The decision criteria can be based on conditional power, change of the p-value, change in lower confidence limit, Kullback-Leibler divergence, Bayes factors, Bayesian false discovery rate or difference between prior and posterior expectation. The criteria can be also used for decis…
The adaptive value of tandem communication in ants:Insights from an agent-based model
2021
AbstractSocial animals often share information about the location of resources, such as a food source or a new nest-site. One well-studied communication strategy in ants is tandem running, whereby a leader guides a recruit to a resource. Tandem running is considered an example of animal teaching because a leader adjusts her behaviour and invests time to help another ant to learn the location of a resource more efficiently. Tandem running also has costs, such as waiting inside the nest for a leader and a reduced walking speed. Whether and when these costs outweigh the benefits of tandem running is not well understood. We developed an agent-based simulation model to investigate the conditions…
Identification and visualization of differential isoform expression in RNA-seq time series
2018
Abstract Motivation As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Results Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major …
A generalization of Kingman's model of selection and mutation and the Lenski experiment.
2017
Kingman’s model of selection and mutation studies the limit type value distribution in an asexual population of discrete generations and infinite size undergoing selection and mutation. This paper generalizes the model to analyze the long-term evolution of Escherichia. coli in Lenski experiment. Weak assumptions for fitness functions are proposed and the mutation mechanism is the same as in Kingman’s model. General macroscopic epistasis are designable through fitness functions. Convergence to the unique limit type distribution is obtained.