References of "Aurell, Erik"
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See detailDynamic insights on transcription initiation and RNA processing during bacterial adaptation
Lacoux, Caroline; Fouquier d'Hérouël, Aymeric UL; Wessner- Le Bohec, Françoise et al

in RNA (2020)

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental ... [more ▼]

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σE system in E. coli was coupled to our previously-described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5’ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity; i) constant and independent of RNA levels, ii) increased once RNA has accumulated, and iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes, and can serve as blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control. [less ▲]

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See detailAn observation of circular RNAs in bacterial RNA-seq data
Innocenti, Nicolas; Nguyen, Hoang-Son; Fouquier d'Hérouël, Aymeric UL et al

E-print/Working paper (2016)

Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed ... [more ▼]

Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from Enterococcus faecalis and Escherichia coli in a way similar to previous studies performed on eukaryotes. We report observations of circRNAs in RNA-seq data that are reproducible across multiple experiments performed with different protocols or growth conditions. [less ▲]

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See detailWhole genome mapping of 5' ends in bacteria by tagged sequencing: A comprehensive view in Enterococcus faecalis
Innocenti, Nicolas; Golumbeanu, Monica; Fouquier d'Hérouël, Aymeric UL et al

in RNA (New York, N.Y.) (2015), 21(5), 1018-1030

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See detailLocal search methods based on variable focusing for random K-satisfiability
Lemoy, Rémi UL; Alava, Mikko; Aurell, Erik

in PHYSICAL REVIEW E (2015), 91(1), 013305-6

We introduce variable focused local search algorithms for satisfiabiliity problems. Usual approaches focus uniformly on unsatisfied clauses. The methods described here work by focusing on random variables ... [more ▼]

We introduce variable focused local search algorithms for satisfiabiliity problems. Usual approaches focus uniformly on unsatisfied clauses. The methods described here work by focusing on random variables in unsatisfied clauses. Variants are considered where variables are selected uniformly and randomly or by introducing a bias towards picking variables participating in several unsatistified clauses. These are studied in the case of the random 3-SAT problem, together with an alternative energy definition, the number of variables in unsatisfied constraints. The variable-based focused Metropolis search (V-FMS) is found to be quite close in performance to the standard clause-based FMS at optimal noise. At infinite noise, instead, the threshold for the linearity of solution times with instance size is improved by picking preferably variables in several UNSAT clauses. Consequences for algorithmic design are discussed. [less ▲]

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