Search results for "computational"
showing 10 items of 5884 documents
Clarkson-McCarthy inequalities with unitary and isometry orbits
2020
Abstract A refinement of a trace inequality of McCarthy establishing the uniform convexity of the Schatten p-classes for p > 2 is proved: if A , B are two n-by-n matrices, then there exists some pair of n-by-n unitary matrices U , V such that U | A + B 2 | p U ⁎ + V | A − B 2 | p V ⁎ ≤ | A | p + | B | p 2 . A similar statement holds for compact Hilbert space operators. Another improvement of McCarthy's inequality is given via the new operator parallelogramm law, | A + B | 2 ⊕ | A − B | 2 = U 0 ( | A | 2 + | B | 2 ) U 0 ⁎ + V 0 ( | A | 2 + | B | 2 ) V 0 ⁎ for some pair of 2n-by-n isometry matrices U 0 , V 0 .
TWO-LANE TRAFFIC WITH PLACES OF OBSTRUCTION TO TRAFFIC
2004
As the Nagel–Schreckenberg model (NaSch model) became known as a realistic approach to describe traffic flow on single-lane streets, this model was extended to two-lane traffic by several groups. On the base of our two-lane model, we will now investigate the impact of a place of obstruction, e.g., because of road works, on partial fractions, densities and mean velocities.
Learning the structure of HMM's through grammatical inference techniques
2002
A technique is described in which all the components of a hidden Markov model are learnt from training speech data. The structure or topology of the model (i.e. the number of states and the actual transitions) is obtained by means of an error-correcting grammatical inference algorithm (ECGI). This structure is then reduced by using an appropriate state pruning criterion. The statistical parameters that are associated with the obtained topology are estimated from the same training data by means of the standard Baum-Welch algorithm. Experimental results showing the applicability of this technique to speech recognition are presented. >
Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods
2019
The biogenesis of RNAs is a multi-layered and highly regulated process that involves a diverse set of players acting in an orchestrated manner throughout the transcription cycle. Transcription initiation, elongation and termination factors act on RNA polymerases to modulate their movement along the DNA template in a very precise manner, more complex than previously anticipated. Genome-scale run-on-based methodologies have been developed to study in detail the position of transcriptionally-engaged RNA polymerases. Genomic run-on (GRO), and its many variants and refinements made over the years, are helping the community to address an increasing amount of scientific questions, spanning an incr…
Genomics of mRNA turnover
2007
Most studies on eukaryotic gene regulation have focused on mature mRNA levels. Nevertheless, the steady-state mRNA level is the result of two opposing biological processes: transcription and degradation, both of which can be important points to regulate gene expression. It is now possible to determine the transcription and degradation rates (TR and DR), as well as the mRNA amount, for each gene using DNA chip technologies. In this way, each individual contribution to gene expression can be analysed. This review will deal with the techniques used for the genomic evaluation of TR and DR developed for the yeast Saccharomyces cerevisiae. They will be described in detail and their potential draw…
TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
2020
AbstractAlternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3’end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3’end maturation is closely linked to transcription, RNA processing, and even epigenetic (histone/DNA/RNA) modifications. Here we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging…
Detection, validation, and downstream analysis of allelic variation in gene expression.
2009
AbstractCommon sequence variants within a gene often generate important differences in expression of corresponding mRNAs. This high level of local (allelic) control—or cis modulation—rivals that produced by gene targeting, but expression is titrated finely over a range of levels. We are interested in exploiting this allelic variation to study gene function and downstream consequences of differences in expression dosage. We have used several bioinformatics and molecular approaches to estimate error rates in the discovery of cis modulation and to analyze some of the biological and technical confounds that contribute to the variation in gene expression profiling. Our analysis of SNPs and alter…
Genome-wide analysis of factors regulating gene expression in liver
2007
In recent decades, multiple individual genes have been studied with respect to their level of expression in liver tissue and in many cases substantial progress has been made in identifying individual factors promoting gene expression in liver. However, the overall picture is still undefined and general rules or factors regulating gene expression in liver have not yet been established. Thus, a genome-wide screen for factors regulating gene expression in liver is of high interest, as it may reveal common regulatory mechanisms for most genes highly expressed in liver. These factors represent potential new targets in liver disease associated with differential gene expression. Using a novel bioi…
Annotation of microsporidian genomes using transcriptional signals
2012
EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-asso…
A genomic view of mRNA turnover in yeast
2011
The steady-state mRNA level is the result of two opposing processes: transcription and degradation; both of which can provide important points to regulate gene expression. In the model organism yeast Saccharomyces cerevisiae, it is now possible to determine, at the genomic level, the transcription and degradation rates, as well as the mRNA amount, using DNA chip or parallel sequencing technologies. In this way, the contribution of both rates to individual and global gene expressions can be analysed. Here we review the techniques used for the genomic evaluation of the transcription and degradation rates developed for this yeast, and we discuss the integration of the data obtained to fully an…