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- Gina Cannarozzi, Nicol N. Schraudolph, Mahamadou Faty, Peter von Rohr, Markus T. Friberg, Alexander C. Roth +3 others
- 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)

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)

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)

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)

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)

This paper describes QuickSched, a compact and efficient Open-Source C-language library for task-based shared-memory parallel programming. QuickSched extends the standard dependency-only scheme of task-based programming with the concept of task conflicts, i.e. sets of tasks that can be executed in any order, yet not concurrently. These conflicts are… (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)

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)

The most critical component of any adaptive numerical quadrature routine is the estimation of the integration error. Since the publication of the first algorithms in the 1960s, many error estimation schemes have been presented, evaluated, and discussed. This article presents a review of existing error estimation techniques and discusses their differences… (More)