Search results for "algorithms"
showing 10 items of 1716 documents
Splitting the dynamics of large biochemical interaction networks
2003
This article is inscribed in the general motivation of understanding the dynamics on biochemical networks including metabolic and genetic interactions. Our approach is continuous modeling by differential equations. We address the problem of the huge size of those systems. We present a mathematical tool for reducing the size of the model, master-slave synchronization, and fit it to the biochemical context.
Comprehensive estimation of input signals and dynamics in biochemical reaction networks
2012
Abstract Motivation: Cellular information processing can be described mathematically using differential equations. Often, external stimulation of cells by compounds such as drugs or hormones leading to activation has to be considered. Mathematically, the stimulus is represented by a time-dependent input function. Parameters such as rate constants of the molecular interactions are often unknown and need to be estimated from experimental data, e.g. by maximum likelihood estimation. For this purpose, the input function has to be defined for all times of the integration interval. This is usually achieved by approximating the input by interpolation or smoothing of the measured data. This procedu…
ballaxy: web services for structural bioinformatics.
2014
Abstract Motivation: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. Results: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large …
On a set of data for the membrane potential in a neuron
2006
We consider a set of data where the membrane potential in a pyramidal neuron is measured almost continuously in time, under varying experimental conditions. We use nonparametric estimates for the diffusion coefficient and the drift in view to contribute to the discussion which type of diffusion process is suitable to model the membrane potential in a neuron (more exactly: in a particular type of neuron under particular experimental conditions).
Tests for Differentiation in Gene Expression Using a Data-Driven Order or Weights for Hypotheses
2005
In the analysis of gene expression by microarrays there are usually few subjects, but high-dimensional data. By means of techniques, such as the theory of spherical tests or with suitable permutation tests, it is possible to sort the endpoints or to give weights to them according to specific criteria determined by the data while controlling the multiple type I error rate. The procedures developed so far are based on a sequential analysis of weighted p-values (corresponding to the endpoints), including the most extreme situation of weighting leading to a complete order of p-values. When the data for the endpoints have approximately equal variances, these procedures show good power properties…
CARE: context-aware sequencing read error correction.
2020
Abstract Motivation Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes. Results We present CARE—an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors ar…
A parallel and sensitive software tool for methylation analysis on multicore platforms.
2015
Abstract Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. Results: We present a new software tool, called HPG-Methyl, which efficiently maps bis…
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model.
2006
Abstract Motivation: The general-time-reversible (GTR) model is one of the most popular models of nucleotide substitution because it constitutes a good trade-off between mathematical tractability and biological reality. However, when it is applied for inferring evolutionary distances and/or instantaneous rate matrices, the GTR model seems more prone to inapplicability than more restrictive time-reversible models. Although it has been previously noted that the causes for intractability are caused by the impossibility of computing the logarithm of a matrix characterised by negative eigenvalues, the issue has not been investigated further. Results: Here, we formally characterize the mathematic…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…