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Proteinortho: Detection of (Co-)orthologs in large-scale analysis
BackgroundOrthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequenceExpand
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The p53-p21-DREAM-CDE/CHR pathway regulates G2/M cell cycle genes
The tumor suppressor p53 functions predominantly as a transcription factor by activating and downregulating gene expression, leading to cell cycle arrest or apoptosis. p53 was shown to indirectlyExpand
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The transcription factor p53: Not a repressor, solely an activator
The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognitionExpand
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A Global Genome Segmentation Method for Exploration of Epigenetic Patterns
Current genome-wide ChIP-seq experiments on different epigenetic marks aim at unraveling the interplay between their regulation mechanisms. Published evaluation tools, however, allow testing forExpand
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Analyzing Chromatin Using Tiled Binned Scatterplot Matrices
Background: Over the last years, more and more biological data became available. Besides the pure amount of new data, also its dimensionality - the number of different attributes per data point -Expand
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Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation.
Chromatin-related mechanisms, as e.g. histone modifications, are known to be involved in regulatory switches within the transcriptome. Only recently, mathematical models of these mechanisms have beenExpand
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Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin.
Epigenetic mechanisms play an important role in regulating and stabilizing functional states of living cells. However, in spite of an increasing amount of experimental data, models of transcriptionalExpand
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Pitfalls of ascertainment biases in genome annotations—computing comparable protein domain distributions in eukarya
Most investigations into the large-scale patterns of protein evolution are based on gene annotations that have been compiled in reference databases. The use of these resources for quantitativeExpand
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Cost effectiveness and application of online monitoring in reinforced concrete structures
The annual costs for the maintenance of the Swiss national road networks amount to SFr. 560-640 millions [1]. Due to the limited means and the large number of engineering structures at the criticalExpand
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