Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects (2009)
Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about...
Optimal drug combinations and minimal hitting sets (2009)
Abstract Background Identifying effective drug combinations that significantly improve over single agents is a challenging problem. Pairwise combinations already represent a huge screening effort....
An empirical framework for binary interactome mapping (2009)
Venkatesan, Kavitha, Rual, Jean-Francois, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets....
Data clustering, including problems such as finding network communities, can be put into a systematic framework by means of a Bayesian approach. The application of Bayesian approaches to real...
Population stratification using a statistical model on hypergraphs (2007)
Population stratification is a problem encountered in several areas of biology and public health. We tackle this problem by mapping a population and its elements attributes into a hypergraph, a...
Impact of non-Poisson activity patterns on spreading processes (2006)
Vazquez, Alexei, Balazs, Racz, Andras, Lukacs, Barabasi, Albert-Laszlo
Halting a computer or biological virus outbreak requires a detailed understanding of the timing of the interactions between susceptible and infected individuals. While current spreading models assume...
Epidemic outbreaks on structured populations (2006)
Our chances to halt epidemic outbreaks rely on how accurately we represent the population structure underlying the disease spread. When analyzing global epidemics this force us to consider...
Spreading of infectious diseases on heterogeneous populations: multi-type network approach (2006)
I study the spreading of infectious diseases on heterogeneous populations. I represent the population structure by a contact-graph where vertices represent agents and edges represent disease...
Impact of memory on human dynamics (2006)
Our experience of web access slowing down is a consequence of the aggregated web access pattern of web users. This is just one example among several human oriented services which are strongly...
Spreading dynamics on small-world networks with connectivity fluctuations and correlations (2006)
Infectious diseases and computer malwares spread among humans and computers through the network of contacts among them. These networks are characterized by wide connectivity fluctuations,...
Exact results for the Barabasi model of human dynamics (2005)
Human activity patterns display a bursty dynamics, with interevent times following a heavy tailed distribution. This behavior has been recently shown to be rooted in the fact that humans assign their...
Polynomial growth in age-dependent branching processes with diverging reproductive number (2005)
We study the spreading dynamics on graphs with a power law degree distribution p_k ~ k^-gamma with 2
The inhomogeneous evolution of subgraphs and cycles in complex networks (2005)
Vazquez, Alexei, Oliveira, Joao G., Barabasi, Albert-Laszlo
Subgraphs and cycles are often used to characterize the local properties of complex networks. Here we show that the subgraph structure of real networks is highly time dependent: as the network grows,...
Exploring networks with traceroute-like probes: theory and simulations (2004)
Dall'Asta, Luca, Alvarez-Hamelin, Ignacio, Barrat, Alain, Vazquez, Alexei, Vespignani, Alessandro
Mapping the Internet generally consists in sampling the network from a limited set of sources by using traceroute-like probes. This methodology, akin to the merging of different spanning trees to a...
Clustering coefficient without degree correlations biases (2004)
Soffer, Sara Nadiv, Vazquez, Alexei
The clustering coefficient quantifies how well connected are the neighbors of a vertex in a graph. In real networks it decreases with the vertex degree, which has been taken as a signature of the...
Distance-d covering problems in scale-free networks with degree correlations (2004)
Echenique, Pablo, Gomez-Gardenes, Jesus, Moreno, Yamir, Vazquez, Alexei
A number of problems in communication systems demand the distributed allocation of network resources in order to provide better services, sampling and distribution methods. The solution to these...
A statistical approach to the traceroute-like exploration of networks: theory and simulations (2004)
Dall'Asta, Luca, Alvarez-Hamelin, Ignacio, Barrat, Alain, Vazquez, Alexei, Vespignani, Alessandro
Mapping the Internet generally consists in sampling the network from a limited set of sources by using "traceroute"-like probes. This methodology, akin to the merging of different spanning trees to a...
Global protein function prediction from protein-protein interaction networks (2003)
Vazquez, Alexei, Flammini, Alessandro, Maritan, Amos, Vespignani, Alessandro
The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access gene's co-expression patterns...
The linear preferential attachment hypothesis has been shown to be quite successful to explain the existence of networks with power-law degree distributions. It is then quite important to determine...
Disease Spreading in Structured Scale-Free Networks (2002)
Moreno, Yamir, Vazquez, Alexei
We study the spreading of a disease on top of structured scale-free networks recently introduced. By means of numerical simulations we analyze the SIS and the SIR models. Our results show that when...
Resilience to damage of graphs with degree correlations (2002)
Vazquez, Alexei, Moreno, Yamir
The existence or not of a percolation threshold on power law correlated graphs is a fundamental question for which a general criterion is lacking. In this work we investigate the problems of site and...
Topology and correlations in structured scale-free networks (2002)
Vazquez, Alexei, Boguna, Marian, Moreno, Yamir, Pastor-Satorras, Romualdo, Vespignani, Alessandro
We study a recently introduced class of scale-free networks showing a high clustering coefficient and non-trivial connectivity correlations. We find that the connectivity probability distribution...
Computational complexity arising from degree correlations in networks (2002)
Vazquez, Alexei, Weigt, Martin
We apply a Bethe-Peierls approach to statistical-mechanics models defined on random networks of arbitrary degree distribution and arbitrary correlations between the degrees of neighboring vertices....
The Bak-Sneppen model on scale-free networks (2002)
Moreno, Yamir, Vazquez, Alexei
We investigate by numerical simulations and analytical calculations the Bak-Sneppen model for biological evolution in scale-free networks. By using large scale numerical simulations, we study the...
Large-scale topological and dynamical properties of Internet (2001)
Vazquez, Alexei, Pastor-Satorras, Romualdo, Vespignani, Alessandro
We study the large-scale topological and dynamical properties of real Internet maps at the autonomous system level, collected in a three years time interval. We find that the connectivity structure...
The Bak-Sneppen Model on Scale-Free Networks (2001)
Moreno, Yamir, Vazquez, Alexei
We investigate by numerical simulations and analytical calculations the Bak-Sneppen model for biological evolution in scale-free networks. By using large scale numerical simulations, we study the...
Dynamical and correlation properties of the Internet (2001)
Pastor-Satorras, Romualdo, Vazquez, Alexei, Vespignani, Alessandro
The description of the Internet topology is an important open problem, recently tackled with the introduction of scale-free networks. In this paper we focus on the topological and dynamical...
Statistics of citation networks (2001)
The out-degree distribution of citation networks is investigated. Statistical data of the number of papers cited within a paper (out-degree) for different journals in the period 1991-1999 is...
Self-organization in populations of competing agents (2000)
A population of heterogenous agents compeeting through a minority rule is investigated. Agents which frequently loose are selected for evolution by changing their strategies. The stationary...
Non conservative Abelian sandpile model with BTW toppling rule (2000)
A non conservative Abelian sandpile model with BTW toppling rule introduced in [Tsuchiya and Katori, Phys. Rev. E {\bf 61}, 1183 (2000)] is studied. Using a scaling analysis of the different energy...
Knowing a network by walking on it: emergence of scaling (2000)
A model for growing networks is introduced, having as a main ingredient that new nodes are attached to the network through one existing node and then explore the network through the links of the...
Numerical simulations of directed sandpile models (2000)
Directed sandpile models with different toppling rules are studied by means of numerical simulations in two dimensions, with the purpose of determining the different universality classes. It is...
Constant rate linear interface depinning and self organized criticality (1999)
Vazquez, Alexei, Sotolongo-Costa, Oscar
The precise determination of the universality classes in self-organized critical phenomena (SOC) is still an unsolved problem. Different SOC models like sandpile, linear interface depinning, and the...
Universality in self-organized critical slope models (1999)
Vazquez, Alexei, Sotolongo-Costa, Oscar
The dynamics of critical slope self-organized critical models is studied, using a previous mapping into a linear interface depinning model dragged at one end. The model is solved obtaining the...
Force fluctuations in granular materials (1999)
Vazquez, Alexei, Marin-Antuña, Jose, Sotolongo-Costa, O.
Force fluctuations in granular materials are investigated. A continuum equation is derived starting from a discrete model proposed in the literature. The influence of boundary conditions is...
On the equivalence between the Barkhausen effect and directed Abelian sandpile models (1999)
Vazquez, Alexei, Sotolongo-Costa, Oscar
The existence of self-organized criticality in the Barkhausen effect and its analogy with sandpile models is investigated. It is demonstrated that a model recently introduced to describe the dynamics...
Aging and Levy distributions in sandpiles (1999)
Sotolongo-Costa, Oscar, Vazquez, Alexei, Antoranz, J. C.
Aging in complex systems is studied via the sandpile model. Relaxation of avalanches in sandpiles is observed to depend on the time elapsed since the begining of the relaxation. Levy behavior is...
Domain wall dynamics in soft magnetic materials (1998)
Vazquez, Alexei, Sotolongo-Costa, Oscar
The dynamics of a domain wall in magnetostrictive materials is investigated. The domain wall is modeled by a d-dimensional interface moving in a d+1-dimensional environment. Long-range...
Universality classes in the random-storage sandpile model (1998)
Vazquez, Alexei, Sotolongo-Costa, O.
The avalanche statistics in a stochastic sandpile model where toppling takes place with a probability p is investigated. The limiting case p=1 corresponds to the Bak-Tang-Wiesenfeld (BTW) model with...
Self-organized criticality in linear interface depinning and sandpile models (1998)
Vazquez, Alexei, Sotolongo-Costa, Oscar
The dynamics of an elastic interface profile h(x,t) under a driving force increasing at rate c, a restored force -epsilon h, and disorder is investigated. Using perturbation theory and functional...
Self-organized criticality and directed percolation (1998)
Vazquez, Alexei, Sotolongo-Costa, Oscar
A sandpile model with stochastic toppling rule is studied. The control parameters and the phase diagram are determined through a MF approach, the subcritical and critical regions are analyzed. The...
Fractal approach to the beta relaxation in supercooled liquids (1998)
Vazquez, Alexei, Sotolongo-Costa, Oscar
In the present work we present a fractal model for the beta relaxation in supercooled liquids. The macroscopic dynamics is obtained by superposition of relaxation of independent mesoscopic regions...
A Bethe lattice representation for sandpiles (1998)
Sotolongo-Costa, Oscar, Vazquez, Alexei, Antoranz, J. C.
Avalanches in sandpiles are represented throughout a process of percolation in a Bethe lattice with a feedback mechanism. The results indicate that the frequency spectrum and probability distribution...
Diffusion regimes in Levy flights with trapping (1998)
Vazquez, Alexei, Costa, Oscar Sotolongo, Brouers, Francois
The diffusion of a walk in the presence of traps is investigated. Different diffusion regimes are obtained considering the magnitude of the fluctuations in waiting times and jump distances. A...
Avalanche dynamics and nonexponential relaxation (1998)
Vazquez, Alexei, Costa, Oscar Sotolongo, Antoranz, Carlos
The theory of SOC, and related avalanche dynamics, is proposed as the origin of the ubiquitous nonexponential relaxation observed in complex systems. Introducing some scaling laws and relations we...
Epstein–Barr virus and virus human protein interaction maps
Calderwood, Michael A., Venkatesan, Kavitha, Xing, Li, Chase, Michael R., Vazquez, Alexei, Holthaus, Amy M., ...
A comprehensive mapping of interactions among Epstein–Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on...
Impact of the solvent capacity constraint on E. coli metabolism
Vazquez, Alexei, Beg, Qasim K, DeMenezes, Marcio A, Ernst, Jason, Bar-Joseph, Ziv, Barabási, Albert-László, ...
Vazquez, Alexei, De Menezes, Marcio A., Barabási, Albert-László, Oltvai, Zoltan N.
The cell's cytoplasm is crowded by its various molecular components, resulting in a limited solvent capacity for the allocation of new proteins, thus constraining various cellular processes such as...