8,560 research outputs found
A model of large-scale proteome evolution
The next step in the understanding of the genome organization, after the
determination of complete sequences, involves proteomics. The proteome includes
the whole set of protein-protein interactions, and two recent independent
studies have shown that its topology displays a number of surprising features
shared by other complex networks, both natural and artificial. In order to
understand the origins of this topology and its evolutionary implications, we
present a simple model of proteome evolution that is able to reproduce many of
the observed statistical regularities reported from the analysis of the yeast
proteome. Our results suggest that the observed patterns can be explained by a
process of gene duplication and diversification that would evolve proteome
networks under a selection pressure, favoring robustness against failure of its
individual components
Comparative genomic analysis of novel Acinetobacter symbionts : A combined systems biology and genomics approach
Acknowledgements This work was supported by University of Delhi, Department of Science and Technology- Promotion of University Research and Scientific Excellence (DST-PURSE). V.G., S.H. and U.S. gratefully acknowledge the Council for Scientific and Industrial Research (CSIR), University Grant Commission (UGC) and Department of Biotechnology (DBT) for providing research fellowship.Peer reviewedPublisher PD
Wavelet analysis on symbolic sequences and two-fold de Bruijn sequences
The concept of symbolic sequences play important role in study of complex
systems. In the work we are interested in ultrametric structure of the set of
cyclic sequences naturally arising in theory of dynamical systems. Aimed at
construction of analytic and numerical methods for investigation of clusters we
introduce operator language on the space of symbolic sequences and propose an
approach based on wavelet analysis for study of the cluster hierarchy. The
analytic power of the approach is demonstrated by derivation of a formula for
counting of {\it two-fold de Bruijn sequences}, the extension of the notion of
de Bruijn sequences. Possible advantages of the developed description is also
discussed in context of applied
Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data
We present two complementary approaches for the interpretation of clusters of
co-regulated genes, such as those obtained from DNA chips and related methods.
Starting from a cluster of genes with similar expression profiles, two basic
questions can be asked:
1. Which mechanism is responsible for the coordinated transcriptional response
of the genes? This question is approached by extracting motifs that are shared
between the upstream sequences of these genes. The motifs extracted are putative
cis-acting regulatory elements.
2. What is the physiological meaning for the cell to express together these
genes? One way to answer the question is to search for potential metabolic
pathways that could be catalyzed by the products of the genes. This can be
done by selecting the genes from the cluster that code for enzymes, and trying
to assemble the catalyzed reactions to form metabolic pathways.
We present tools to answer these two questions, and we illustrate their use with
selected examples in the yeast Saccharomyces cerevisiae. The tools are available
on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/;
http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)
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