Proposal for an enzyme redesign method to improve production rates in Aspergillus niger

Relating sequence properties to protein secretion

Aspergillus niger is widely used for industrial enzyme production. Knowledge on high-level protein secretion could be useful to improve production rates. We used sequencebased classification methods to identify important properties<br/>for successful high-level secretion, which will be used to redesign proteins for improved secretion.

GATA3 Expression Is Decreased in Psoriasis and during Epidermal Regeneration: Induction by Narrow-Band UVB and IL-4

Psoriasis is characterized by hyperproliferation of keratinocytes and by infiltration of activated Th1 and Th17 cells in the (epi)dermis. By expression microarray, we previously found the GATA3 transcription factor significantly downregulated in lesional psoriatic skin. Since GATA3 serves as a key switch in both epidermal and T helper cell...

Correlating the topology of a metabolic network with its growth capacity

Metabolic network destruction: Relating topology to robustness

Biological networks exhibit intriguing topological properties such as small-worldness. In this paper, we investigate whether the topology of a metabolic network is related to its robustness. We do so by perturbing a metabolic system in silico, one reaction at a time and studying the correlations between growth, as predicted by flux balance...

Integrating genome assemblies with MAIA

De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for...

Metabolite and reaction inference based on enzyme specificities

Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this paper, we propose to model enzyme aspecificity by...

Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks

In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by...

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the...

Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction

In recent years, more and more high-throughput data sources useful for protein complex prediction have become available (e.g., gene sequence, mRNA expression, and interactions). The integration of these different data sources can be challenging. Recently, it has been recognized that kernel-based classifiers are well suited for this task. However...

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Adaptive methods of image processing

A new measure for the effect of sharpening and smoothing filters on images

A quantitative measure for the perception of sharpening and smoothing in images

A weight set decorrelating algorithm for neural network interpretation and symmetry breaking