Silvana Ilie

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MOTIVATION High-throughput sequencing technologies produce very large amounts of data and sequencing errors constitute one of the major problems in analyzing such data. Current algorithms for correcting these errors are not very accurate and do not automatically adapt to the given data. RESULTS We present HiTEC, an algorithm that provides a highly(More)
SUMMARY Multiple spaced seeds represent the current state-of-the-art for similarity search in bioinformatics, with applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present SpEED, a software program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude faster and(More)
MOTIVATION Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by(More)
The cost of solving an initial value problem for index-1 differential algebraic equations to accuracy ɛ is polynomial in ln(1/ɛ). This cost is obtained for an algorithm based on the Taylor series method for solving differential algebraic equations developed by Pryce. This result extends a recent result by Corless for solutions of ordinary differential(More)
DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms. We present a sound framework for evaluating the quality of seeds for oligonucleotide(More)
MOTIVATION Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for(More)
Complicated nonlinear systems of pde with constraints (called pdae) arise frequently in applications. Missing constraints arising by prolongation (differentiation) of the pdae need to be determined to consistently initialize and stabilize their numerical solution. In this article we review a fast prolongation method, a development of (explicit) symbolic(More)
Sensitivity analysis characterizes the dependence of a model's behaviour on system parameters. It is a critical tool in the formulation, characterization, and verification of models of biochemical reaction networks, for which confident estimates of parameter values are often lacking. In this paper, we propose a novel method for sensitivity analysis of(More)
Mathematical and computational modeling are key tools in analyzing important biological processes in cells and living organisms. In particular, stochastic models are essential to accurately describe the cellular dynamics, when the assumption of the thermodynamic limit can no longer be applied. However, stochastic models are computationally much more(More)