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A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of ‘elementary flux modes’ provides a mathematical tool to define and comprehensivelyExpand
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Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
Rational metabolic engineering requires powerful theoretical methods such as pathway analysis, in which the topology of metabolic networks is considered. All metabolic capabilities in steady statesExpand
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Identifying functional modules in protein–protein interaction networks: an integrated exact approach
TLDR
We propose a new additive score with two desirable properties: (i) it is scalable by a statistically interpretable parameter and (ii) it allows a smooth integration of data from various sources. Expand
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5.8S-28S rRNA interaction and HMM-based ITS2 annotation.
The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate forExpand
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4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
TLDR
An algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. Expand
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Distinguishing species.
Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laboriousExpand
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ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments
TLDR
ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments-using PNJ with manual or iterative and automatic profile definition. Expand
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The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses
TLDR
The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Expand
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The ITS2 Database II: homology modelling RNA structure for molecular systematics
TLDR
An increasing number of phylogenetic analyses are based on the internal transcribed spacer 2 (ITS2). Expand
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BioNet: an R-Package for the functional analysis of biological networks
TLDR
We present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules. Expand
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