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Proteinortho: Detection of (Co-)orthologs in large-scale analysis
TLDR
We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. Expand
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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
TLDR
We present a tool called TiBi-Scatter enabling correlation analysis of large multidimensional biological data sets. 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
TLDR
We observe that statistics derived from different computational gene annotation procedure show dramatic discrepancies, and even qualitative changes from negative to positive correlation, when compared to statistics obtained from annotation databases. Expand
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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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