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Article
Open AccessGenome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce t...
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Article
Open AccessPhage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection
Excessive usage of antibiotics threatens the bacterial diversity in the microbiota of animals. An alternative to antibiotics that has been suggested to not disturb the microbiota is (bacterio)phage therapy. In...
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Article
Open AccessParameter inference for enzyme and temperature constrained genome-scale models
The metabolism of all living organisms is dependent on temperature, and therefore, having a good method to predict temperature effects at a system level is of importance. A recently developed Bayesian computat...
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Article
Open AccesscsdR, an R package for differential co-expression analysis
Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networ...
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Complex Network Analysis in Microbial Systems: Theory and Examples
A central driver for the field of systems biology is to develop an understanding of how interactions between components affect the functioning of a system as a whole. Network analysis is an approach that is uniqu...
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Article
Open AccessRobust bacterial co-occurence community structures are independent of r- and K-selection history
Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural...
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Article
Open AccessCorrection to: Containing pandemics through targeted testing of households
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Open AccessContaining pandemics through targeted testing of households
While invasive social distancing measures have proven efficient to control the spread of pandemics failing wide-scale deployment of vaccines, they carry vast societal costs. The development of a diagnostic met...
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Article
Open AccessCorrection to: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
An amendment to this paper has been published and can be accessed via the original article.
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Open AccessAutomatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA seque...
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Article
Open AccessAddressing uncertainty in genome-scale metabolic model reconstruction and analysis
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype map** to solving bio...
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Article
Open AccessGREM1 is associated with metastasis and predicts poor prognosis in ER-negative breast cancer patients
In breast cancer, activation of bone morphogenetic protein (BMP) signaling and elevated levels of BMP-antagonists have been linked to tumor progression and metastasis. However, the simultaneous upregulation of...
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Article
Open AccessModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of compu...
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Article
Open AccessAssessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
For more than a decade, gene expression data sets have been used as basis for the construction of co-expression networks used in systems biology investigations, leading to many important discoveries in a wide ...
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Article
Open AccessAutomated generation of genome-scale metabolic draft reconstructions based on KEGG
Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale...
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Article
Open AccesswTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool
Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exi...
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Article
Open AccessRobust Analysis of Fluxes in Genome-Scale Metabolic Pathways
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal ...
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Article
Open AccessHypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability
Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer geneti...
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Article
Open AccessStrategies for structuring interdisciplinary education in Systems Biology: an European perspective
Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and...
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Article
Open AccessGenome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach
Constraint-based computational approaches, such as flux balance analysis (FBA), have proven successful in modeling genome-level metabolic behavior for conditions where a set of simple cellular objectives can b...
