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| 2. |
- Eriksen, K. A., et al.
(författare)
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Visualization of large-scale correlations in gene expressions
- 2004
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Ingår i: Functional & Integrative Genomics. - : Springer Science and Business Media LLC. - 1438-793X .- 1438-7948. ; 4:4, s. 241-245
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale expression data are today measured for several thousands of genes simultaneously. Furthermore, most genes are being categorized according to their properties. This development has been followed by an exploration of theoretical tools to integrate these diverse data types. A key problem is the large noise-level in the data. Here, we investigate ways to extract the remaining signals within these noisy data sets. We find large-scale correlations within data from Saccharomyces cerevisiae with respect to properties of the encoded proteins. These correlations are visualized in a way that is robust to the underlying noise in the measurement of the individual gene expressions. In particular, for S. cerevisiae we observe that the proteins corresponding to the 400 highest expressed genes typically are localized to the cytoplasm. These most expressed genes are not essential for cell survival.
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| 3. |
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| 4. |
- Aurell, Erik, et al.
(författare)
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Epigenetics as a first exit problem
- 2002
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 88:4
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Tidskriftsartikel (refereegranskat)abstract
- We develop a framework to discuss the stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the A prophage. The formalism defines a quantitative measure of robustness of inherited states.
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| 5. |
- Aurell, Erik, et al.
(författare)
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Stability puzzles in phage lambda
- 2002
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 65:5
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Tidskriftsartikel (refereegranskat)abstract
- In the absence of RecA-mediated cleavage of the repressor, the X prophage is exceptionally stable. We. develop a stochastic model that predicts the stability of such epigenetic states from affinities of the molecular components. We find that the stability, in particular, depends on the maximum possible cI protein production. and on the number of translated cro proteins per transcribed mRNA. We apply the model to the behavior of recently published mutants of O-R and find, in particular, that a mutant that overexpress cro behaves in a different way than what was predicted, thus suggesting that the current view of the O-R switch is incomplete. The approach described here should be generally applicable to the stability of expressed states.
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| 6. |
- Maslov, S, et al.
(författare)
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Upstream plasticity and downstream robustness in evolution of molecular networks
- 2004
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein interactions and transcriptional regulations allow us to assess the effect of gene duplication on robustness and plasticity of these molecular networks. Results: We demonstrate that the transcriptional regulation of duplicated genes in baker's yeast Saccharomyces cerevisiae diverges fast so that on average they lose 3% of common transcription factors for every 1% divergence of their amino acid sequences. The set of protein-protein interaction partners of their protein products changes at a slower rate exhibiting a broad plateau for amino acid sequence similarity above 70%. The stability of functional roles of duplicated genes at such relatively low sequence similarity is further corroborated by their ability to substitute for each other in single gene knockout experiments in yeast and RNAi experiments in a nematode worm Caenorhabditis elegans. We also quantified the divergence rate of physical interaction neighborhoods of paralogous proteins in a bacterium Helicobacter pylori and a fly Drosophila melanogaster. However, in the absence of system-wide data on transcription factors' binding in these organisms we could not compare this rate to that of transcriptional regulation of duplicated genes. Conclusions: For all molecular networks studied in this work we found that even the most distantly related paralogous proteins with amino acid sequence identities around 20% on average have more similar positions within a network than a randomly selected pair of proteins. For yeast we also found that the upstream regulation of genes evolves more rapidly than downstream functions of their protein products. This is in accordance with a view which puts regulatory changes as one of the main driving forces of the evolution. In this context a very important open question is to what extent our results obtained for homologous genes within a single species (paralogs) carries over to homologous proteins in different species (orthologs).
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| 7. |
- Simonsen, I, et al.
(författare)
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Diffusion on complex networks: a way to probe their large-scale topological structures
- 2004
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Ingår i: Proceedings of the XVIII Max Born Symposium @'Statistical Physics outside Physics@' (Physica A: Statistical Mechanics and its Applications). - : Elsevier BV. - 0378-4371. ; 336:1-2, s. 163-173
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Konferensbidrag (refereegranskat)abstract
- A diffusion process on complex networks is introduced in order to uncover their large-scale topological structures. This is achieved by focusing on the slowest decaying diffusive modes of the network. The proposed procedure is applied to real-world networks like a friendship network of known modular structure, and an Internet routing network. For the friendship network, its known structure is well reproduced. In case of the Internet, where the structure is far less well known, one indeed finds a modular structure, and modules can roughly be associated with individual countries. Quantitatively, the modular structure of the Internet manifests itself in an approximately 10 times larger participation ratio of its slowest decaying modes as compared to the null model-a random scale-free network. The extreme edges of the Internet are found to correspond to Russian and US military sites. (C) 2004 Elsevier B.V. All rights reserved.
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| 8. |
- Sneppen, K, et al.
(författare)
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Analyzing molecular networks
- 2004
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Ingår i: Proceedings of the Idea-Finding Symposium for the Frankfurt Institute.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 9. |
- Sneppen, K., et al.
(författare)
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Structures in molecular networks
- 2004
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Ingår i: Forces, growth and form in soft condensed matter: at the interface. - 1402023383 ; NATO science series. 2, mathematics, physics and chemistry; 160, s. 181-193
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 10. |
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