Biomedical subjects

Tamás Vicsek

Publications and source records attributed to Tamás Vicsek.

11 recordsLinked to original sources

PubMed2006

CFinder: locating cliques and overlapping modules in biological networks.

UNLABELLED: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs. AVAILABILITY: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering. SUPPLEMENTARY INFORMATION: Supplementary data are available on Bioinformatics online.

Biology↗

PubMed2005

Uncovering the overlapping community structure of complex networks in nature and society.

Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of communities, we apply an efficient technique for exploring overlapping communities on a large scale. We find that overlaps are significant, and the distributions we introduce reveal universal features of networks. Our studies of collaboration, word-association and protein interaction graphs show that the web of communities has non-trivial correlations and specific scaling properties.

Community Networks↗

PubMed2005

Clique percolation in random networks.

The notion of k-clique percolation in random graphs is introduced, where k is the size of the complete subgraphs whose large scale organizations are analytically and numerically investigated. For the Erdos-Rényi graph of N vertices we obtain that the percolation transition of k-cliques takes place when the probability of two vertices being connected by an edge reaches the threshold p(c) (k) = [(k - 1)N](-1/(k - 1)). At the transition point the scaling of the giant component with N is highly nontrivial and depends on k. We discuss why clique percolation is a novel and efficient approach to the identification of overlapping communities in large real networks.

Community Networks↗

PubMed2005

Dystroglycan is involved in laminin-1-stimulated motility of Müller glial cells: combined velocity and directionality analysis.

We investigate the role of dystroglycan, a major laminin-1 receptor and central member of the dystrophin-glycoprotein complex, in the laminin-1 induced motility of cultured Muller glial cells. Binding of laminin-1 to dystroglycan was prevented by IIH6, a function-blocking monoclonal antibody against alpha-dystroglycan. As an alternative means of inhibition, we used heparin to mask the dystroglycan binding site of the laminin-1, known to overlap with heparin binding sites. Cell motility was characterized in a two-dimensional motility assay based on computer-controlled videomicroscopy and statistical analysis of cellular trajectories. We obtained data on both the cell velocity and the diffusion index, a measure of direction-changing frequency. Both means of inhibition of dystroglycan function led to a significant decrease in the ability of laminin-1 to stimulate cell migration. At the same time, dystroglycan function does not appear to be involved in laminin-1-dependent increase in process dynamism and direction-changing activity.

Animals↗

PubMed2004

Reverse engineering of linking preferences from network restructuring.

We provide a method to deduce the preferences governing the restructuring dynamics of a network from the observed rewiring of the edges. Our approach is applicable for systems in which the preferences can be formulated in terms of a single-vertex energy function with f (k) being the contribution of a node of degree k to the total energy, and the dynamics obeys the detailed balance. The method is first tested by Monte Carlo simulations of restructuring graphs with known energies; then it is used to study variations of real network systems ranging from the coauthorship network of scientific publications to the asset graphs of the New York Stock Exchange. The empirical energies obtained from the restructuring can be described by a universal function f (k) approximately -k ln k , which is consistent with and justifies the validity of the preferential attachment rule proposed for growing networks.

Journal Article↗

PubMed2004

Statistical mechanics of topological phase transitions in networks.

We provide a phenomenological theory for topological transitions in restructuring networks. In this statistical mechanical approach energy is assigned to the different network topologies and temperature is used as a quantity referring to the level of noise during the rewiring of the edges. The associated microscopic dynamics satisfies the detailed balance condition and is equivalent to a lattice gas model on the edge-dual graph of a fully connected network. In our studies-based on an exact enumeration method, Monte Carlo simulations, and theoretical considerations-we find a rich variety of topological phase transitions when the temperature is varied. These transitions signal singular changes in the essential features of the global structure of the network. Depending on the energy function chosen, the observed transitions can be best monitored using the order parameters Phi(s)=s(max)/M, i.e., the size of the largest connected component divided by the number of edges, or Phi(k)=k(max)/M, the largest degree in the network divided by the number of edges. If, for example, the energy is chosen to be E=-s(max), the observed transition is analogous to the percolation phase transition of random graphs. For this choice of the energy, the phase diagram in the ( ,T) plane is constructed. Single-vertex energies of the form E= summation operator (i)f(k(i)), where k(i) is the degree of vertex i, are also studied. Depending on the form of f(k(i)), first-order and continuous phase transitions can be observed. In case of f(k(i))=-(k(i)+alpha)ln(k(i)), the transition is continuous, and at the critical temperature scale-free graphs can be recovered. Finally, by abruptly decreasing the temperature, nonequilibrium processes (e.g., nucleation and growth of particular topological phases) can also be interpreted by the present approach.

Journal Article↗

PubMed2003

Protein-induced morphological transitions in KCl crystal growth.

We investigated the formation of KCl crystals on a glass surface by phase contrast, fluorescent, and atomic force microscopy on the micrometer scale and observed interesting morphological transitions as a function of the experimental conditions. The presence of proteins in the solution from which the salt crystals grow during the drying up leads to complex microscopic patterns of crystals, some of which are analogous to those commonly observed on the macroscopic scale. We tested the effect of tubulin, FITC-labeled albumin, and IgG on the morphology of crystals grown either slowly or fast. A rich variety of protein-specific and concentration-dependent morphologies was found and described by a morphological diagram. We give a phenomenological interpretation, which can explain the growth of complex patterns. Fluorescent images prove that a protein layer covers the surface of the KCl structures. We propose that this layer reduces the anisotropy of the effective surface tension during growth. The tip splitting fractal regime is attributed to the decrease of anisotropy. Further possible mechanisms, which can cause a morphological transition, are also discussed. We found elongated saw-toothed crystals induced by proteins, especially IgG, and identified their structure.

Animals↗

PubMed2002

Synchronization of oscillators with long range interaction: Phase transition and anomalous finite size effects.

Synchronization in a lattice of a finite population of phase oscillators with algebraically decaying, non-normalized coupling is studied by numerical simulations. A critical level of decay is found, below which full locking takes place if the population contains a sufficiently large number of elements. For large number of oscillators and small coupling constant, numerical simulations and analytical arguments indicate that a phase transition separating synchronization from incoherence appears at a decay exponent value equal to the number of dimensions of the lattice. In contrast with earlier results on similar systems with normalized coupling, we have indications that for the decay exponent less than the dimensions of the lattice and for large populations, synchronization is possible even if the coupling is arbitarily weak. This finding suggests that in organisms interacting through slowly decaying signals such as light or sound, collective oscillations can always be established if the population is sufficiently large.

Journal Article↗

PubMed2002

Segregation of granular binary mixtures by a ratchet mechanism.

We report on a segregation scheme for granular binary mixtures, where the segregation is performed by a ratchet mechanism realized by a vertically shaken asymmetric sawtooth-shaped base in a quasi-two-dimensional box. We have studied this system by computer simulations and found that most binary mixtures can be segregated using an appropriately chosen ratchet, even when the particles in the two components have the same size and differ only in their normal restitution coefficient or friction coefficient. These results suggest that the components of otherwise nonsegregating granular mixtures may be separated using our method.

Journal Article↗

PubMed2002

Laminin-1 increases motility, path-searching, and process dynamism of rat and mouse Muller glial cells in vitro: implication of relationship between cell behavior and formation of retinal morphology.

Spatial correlation was observed between the localization of laminin-1 at the inner limiting membrane (ILM) and extensive Muller glial process arborization in the same area, as demonstrated by immunolabeling of Muller glial processes and laminin-1 in rat retinae in situ. To test if this spatial correlation is due to a functional relationship, we investigated the impact of laminin-1 on the motility of cultured primary rat and mouse retinal Muller glial cells by statistical analysis of computer-controlled videomicroscopic time-lapse images. We demonstrate that laminin-1 increases motility and path-searching activity of Muller cells in vitro and it also enhances the cells' process formation/withdrawal dynamism. The increase in path-searching activity and cell process dynamism indicates that there is a functional relationship between laminin-1 and Muller glial cells presumably involving signaling towards the cytoskeleton. We hypothesize that laminin-1 is involved in process arborization of Muller cells at the vitread border of the retina resulting in the formation of the functional barrier made up of Muller glial endfeet.

Animals↗

PubMedDate not supplied

Irradiation and Taxol treatment result in non-monotonous, dose-dependent changes in the motility of glioblastoma cells.

OBJECTIVE: Three-dimensional conformal radiotherapy, stereotactic radiosurgery and concurrent chemoradiotherapy are among the most important postoperative therapeutic measures in the treatment of malignant gliomas. We investigated in vitro how these modalities affect cell motility, a key factor in tumor invasiveness and malignancy. METHODS: A highly motile glioblastoma cell line was exposed to clinically relevant (2-20 Gy) radiation doses. Some cultures were also subjected to radiosensitizing treatment, in which 5 and 10 nM Taxol was added to the medium for 2 h before the irradiation. The surviving cell fraction was continuously monitored during a 3 day-long time period using an automatized scanning videomicroscope system. Cell motility on a two-dimensional substrate was analyzed by following a large population of cells in each culture. Average velocities, their distribution within the population and persistence of migration were calculated from the cell trajectories. RESULTS: Irradiation increases both the persistence of migration and the heterogeneity of the cell population. Moreover, it results in a non-monotonous alteration of cell motility: While > 10 Gy doses impair motion, exposure to 2 Gy increases velocities by 20%. Taxol treatment reduced the motility of irradiated cells, while slightly increased the velocities of non-irradiated cells. We thus show that - at least for certain glioblastoma cells - both irradiation and Taxol treatment can substantially and synergistically influence cell motility. CONCLUSIONS: High grade gliomas are characterized by bad prognosis and poor response to therapy. The unexpected motogenic effect of low-dose radiation and paclitaxel treatments highlight the importance of similar investigations to develop more effective clinical treatments.

Actins↗