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In this article we give an in depth overview of the recent advances in the field of equilibrium networks. After outlining this topic, we provide a novel way of defining equilibrium graph (network) ensembles. We illustrate this concept on the classical random graph model and then survey a large variety of recently studied network models. Next, we analyze the structural properties of the graphs in these ensembles in terms of both local and global characteristics, such as degrees, degree-degree correlations, component sizes, and spectral properties. We conclude with topological phase transitions and show examples for both continuous and discontinuous transitions., Comment: 25 pages, 10 figures. Lecture Notes in Physics: "Networks: structure, dynamics, and function", ed by E. Ben-Naim, H. Frauenfelder, and Z. Toroczkai Springer, in press (2004)

We analyse growing networks ranging from collaboration graphs of scientists to the network of similarities defined among the various transcriptional profiles of living cells. For the explicit demonstration of the scale-free nature and hierarchical organization of these graphs, a deterministic construction is also used. We demonstrate the use of determining the eigenvalue spectra of sparse random graph models for the categorization of small measured networks., Comment: 12 pages, 5 figures, last figure color

We critically discuss the concept of ``synchronized flow'' from a historical, empirical, and theoretical perspective. Problems related to the measurement of vehicle data are highlighted, and questionable interpretations are identified. Moreover, we propose a quantitative and consistent theory of the empirical findings based on a phase diagram of congested traffic states, which is universal for all conventional traffic models having the same instability diagram and a fundamental diagram. New empirical and simulation data supporting this approach are presented as well. We also give a short overview of the various phenomena observed in panicking pedestrian crowds relevant from the point of evacuation of buildings, ships, and stadia. Some of these can be applied to the optimization of production processes, e.g. the ``slower-is-faster effect''., Comment: To appear in: M. Fukui, Y. Sugiyama, M. Schreckenberg, and D.E. Wolf (eds.) Traffic and Granular Flow '01 (Springer, Berlin)

MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene activity coupled with the assessment of perturbed transcriptome (i. e., global mRNA expression) patterns represents one approach toward this goal, and may provide a backbone into which other measurements can be later integrated. RESULT: We use microarray data on 287 single gene deletion Saccharomyces cerevisiae mutant strains to elucidate generic relationships among perturbed transcriptomes. Their comparison with a method that preferentially recognizes distinct expression subpatterns allows us to pair those transcriptomes that share localized similarities. Analyses of the resulting transcriptome similarity network identify a continuum hierarchy among the deleted genes, and in the frequency of local similarities that establishes the links among their reorganized transcriptomes. We also find a combinatorial utilization of shared expression subpatterns within individual links, with increasing quantitative similarity among those that connect transcriptome states induced by the deletion of functionally related gene products. This suggests a distinct hierarchical and combinatorial organization of the S. cerevisiae transcriptional activity, and may represent a pattern that is generic to the transcriptional organization of all eukaryotic organisms. AVAILABILITY: Detailed analyses of the comparison method and free software are available from the authors and at http://angel.elte.hu/bioinf, Comment: 23 pages (include 4 composite figures), corrections added http://angel.elte.hu/bioinf