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9 papers found.
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Memory-efficient RNA energy landscape exploration

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches...

Inferring chemical reaction patterns using rule composition in graph grammars

Background Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to...

Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete

Background A classical problem in metabolic design is to maximize the production of a desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the flux cone. The prior construction of the flux cone is computationally expensive and no...

Evolution of metabolic networks: a computational frame-work

Christoph Flamm Alexander Ullrich 0 Heinz Ekker Martin Mann Daniel Hgerl Markus Rohrschneider Sebastian Sauer Gerik Scheuermann Konstantin Klemm 0 Ivo L Hofacker Peter F Stadler 0 0 Bioinformatics

Determination of thermodynamic parameters for HIV DIS type loop–loop kissing complexes

The HIV-1 type dimerization initiation signal (DIS) loop was used as a starting point for the analysis of the stability of Watson–Crick (WC) base pairs in a tertiary structure context. We used ultraviolet melting to determine thermodynamic parameters for loop–loop tertiary interactions and compared them with regular secondary structure RNA helices of the same sequences. In 1 M Na...

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks

The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of...

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation

Background Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems. Results Metabolic networks are naturally represented as directed hypergraphs in such a way...

The expansion of the metazoan microRNA repertoire

Background MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their...

Automatic detection of conserved RNA structure elements in complete RNA virus genomes

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of ∼10 sequences, efficiently exploiting the information contained in the...