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- Gina Cannarozzi, Nicol N. Schraudolph, +6 authors Yves Barral
- Cell
- 2010

The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is… (More)

- Pedro Gonnet, Frédérique Lisacek
- Bioinformatics
- 2002

MOTIVATION
Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc.) characteristics of a signal or pattern to be detected. The results produced are based on the… (More)

The aim of the present study was to assess the stimulating effects of bright light (BL) on subjective and objective alertness. Eight subjects were exposed to either bright light or dim light (DL) during a 24-h constant routine (0900-0900). Bright light failed to modify either the 24-h course or the level of body temperature. Compared to DL, BL delayed the… (More)

- Pedro Gonnet, Kenneth E Rudd, Frédérique Lisacek
- Proteomics
- 2004

A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each other and to ensure a stable definition of… (More)

Protein translation is a rapid and accurate process, which has been optimized by evolution. Recently, it has been shown that tRNA reusage influences translation speed. We present the tRNA Pairing Index (TPI), a novel index to measure the degree of tRNA reusage in any gene. We describe two variants of the index, how to combine various such indices to a… (More)

- Pedro Gonnet, Stefan Güttel, Lloyd N. Trefethen
- SIAM Review
- 2013

Padé approximation is considered from the point of view of robust methods of numerical linear algebra, in particular, the singular value decomposition. This leads to an algorithm for practical computation that bypasses most problems of solution of nearly-singular systems and spurious pole-zero pairs caused by rounding errors, for which a MATLAB code is… (More)

- Pedro Gonnet
- Journal of Computational Chemistry
- 2007

Cell lists are ubiquitous in molecular dynamics simulations--be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary… (More)

- F. Lisacek, C. Chichester, +7 authors R. Appel
- Comparative and functional genomics
- 2004

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since… (More)

- Ricardo Pachón, Pedro Gonnet, Joris Van Deun
- SIAM J. Numerical Analysis
- 2012

A new method for interpolation by rational functions of prescribed numerator and denominator degrees is presented. When the interpolation nodes are roots of unity or Chebyshev points, the algorithm is particularly simple and relies on discrete Fourier transform matrices, which results in a fast implementation using the Fast Fourier Transform. The method is… (More)

- Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Jörg Stelling
- BMC Systems Biology
- 2011

Dynamic mathematical models in the form of systems of ordinary differential equations (ODEs) play an important role in systems biology. For any sufficiently complex model, the speed and accuracy of solving the ODEs by numerical integration is critical. This applies especially to systems identification problems where the parameter sensitivities must be… (More)