Author
M. Carmen Romano
Other affiliations: University of Potsdam, King's College, Aberdeen
Bio: M. Carmen Romano is an academic researcher from University of Aberdeen. The author has contributed to research in topics: Translation (biology) & Transfer RNA. The author has an hindex of 25, co-authored 49 publications receiving 4197 citations. Previous affiliations of M. Carmen Romano include University of Potsdam & King's College, Aberdeen.
Papers
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TL;DR: The aim of this work is to provide the readers with the know how for the application of recurrence plot based methods in their own field of research, and detail the analysis of data and indicate possible difficulties and pitfalls.
2,993 citations
TL;DR: In this article, the authors estimate the errors due to observational noise on the recurrence quantification analysis (RQA) based on this estimation, and present ways to minimize these errors.
229 citations
TL;DR: It is shown that—under some conditions—it is possible to reconstruct an attractor from the recurrence plot, at least topologically, which means that all relevant dynamical information is contained in the plot.
134 citations
TL;DR: This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency, and reveals that translation output is governed both by initiation efficiency and elongation dynamics.
Abstract: To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function.
127 citations
TL;DR: In this paper, a new approach to calculate recurrence plots of multivariate time series, based on joint recurrences in phase space, was proposed, which allows to estimate dynamical invariants of the whole system, like the joint Renyi entropy of second order.
127 citations
Cited by
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TL;DR: The aim of this work is to provide the readers with the know how for the application of recurrence plot based methods in their own field of research, and detail the analysis of data and indicate possible difficulties and pitfalls.
2,993 citations
TL;DR: It is shown that the full set of hydromagnetic equations admit five more integrals, besides the energy integral, if dissipative processes are absent, which made it possible to formulate a variational principle for the force-free magnetic fields.
Abstract: where A represents the magnetic vector potential, is an integral of the hydromagnetic equations. This -integral made it possible to formulate a variational principle for the force-free magnetic fields. The integral expresses the fact that motions cannot transform a given field in an entirely arbitrary different field, if the conductivity of the medium isconsidered infinite. In this paper we shall show that the full set of hydromagnetic equations admit five more integrals, besides the energy integral, if dissipative processes are absent. These integrals, as we shall presently verify, are I2 =fbHvdV, (2)
1,858 citations
1,620 citations
Journal Article•
TL;DR: In this paper, a genotypic screen was developed to identify a heterozygous recessive mutation at the URA3 locus, which was introduced by targeted mutagenesis, homologous integration of transforming DNA, to avoid introduction of extraneous mutations.
1,595 citations