Mapping Complex Networks: Exploring Boolean Modeling of Signal Transduction Pathways (2009)
Bhardwaj, Gaurav, Wells, Christine P., Albert, Reka, Van Rossum, Damian B., Patterson, Randen L.
In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information....
Near linear time algorithm to detect community structures in large-scale networks (2007)
Raghavan, Usha Nandini, Albert, Reka, Kumara, Soundar
Community detection and analysis is an important methodology for understanding the organization of various real-world networks and has applications in problems as diverse as consensus formation in...
Modeling Systems-Level Regulation of Host Immune Responses (2007)
Juilee Thakar, Mylisa Pilione, Girish Kirimanjeswara, Eric T Harvill, Reka Albert
Many pathogens are able to manipulate the signaling pathways responsible for the generation of host immune responses. Here we examine and model a respiratory infection system in which disruption of...
Li, Song, Assmann, Sarah M., Albert, Reka
Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid...
Using graph concepts to understand the organization of complex systems (2006)
Christensen, Claire, Albert, Reka
Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has...
Methods of robustness analysis for Boolean models of gene control networks (2006)
Chaves, Madalena, Sontag, Eduardo D., Albert, Reka
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally...
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network (2006)
Chung, Wen-Yu, Albert, Reka, Albert, Istvan, Nekrutenko, Anton, Makova, Kateryna D
Abstract Background While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is...
Joo, Jaewook, Harvill, Eric, Albert, Reka
Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle...
Search in weighted complex networks (2005)
Thadakamalla, Hari P., Albert, Reka, Kumara, Soundar R. T.
We study trade-offs presented by local search algorithms in complex networks which are heterogeneous in edge weights and node degree. We show that search based on a network measure, local betweenness...
Gupta, Anshuman, Maranas, Costas D., Albert, Reka
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network...
Scale- free networks in cell biology (2005)
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory...
Bacteriophage-mediated competition in Bordetella bacteria (2005)
Joo, Jaewook, Gunny, Michelle, Cases, Marisa, Hudson, Peter, Albert, Reka, Harvill, Eric
Apparent competition between species is believed to be one of the principle driving forces that structure ecological communities, although the precise mecha nisms have yet to be characterized. Here...
Robustness and fragility of Boolean models for genetic regulatory networks (2005)
Chaves, Madalena, Albert, Reka, Sontag, Eduardo D.
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these...
Modeling Cascading Failures in the North American Power Grid (2004)
Kinney, Ryan, Crucitti, Paolo, Albert, Reka, Latora, Vito
The North American power grid is one of the most complex technological networks, and its interconnectivity allows both for long-distance power transmission and for the propagation of disturbances. We...
Conserved network motifs allow protein-protein interaction prediction (2004)
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by...
Structural Vulnerability of the North American Power Grid (2004)
Albert, Reka, Albert, Istvan, Nakarado, Gary L.
The magnitude of the August 2003 blackout affecting the United States has put the challenges of energy transmission and distribution into limelight. Despite all the interest and concerted effort, the...
Dynamic receptor team formation can explain the high signal transduction gain in E. coli (2003)
Albert, Reka, Chiu, Yu-wen, Othmer, Hans G.
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of...
Expression of the Drosophila segment polarity genes is initiated by a prepattern of pair-rule gene products and maintained by a network of regulatory interactions throughout several stages of...
Statistical mechanics of complex networks (2001)
Albert, Reka, Barabasi, Albert-Laszlo
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of...
Error and attack tolerance of complex networks (2000)
Albert, Reka, Jeong, Hawoong, Barabasi, Albert-Laszlo
Many complex systems, such as communication networks, display a surprising degree of robustness: while key components regularly malfunction, local failures rarely lead to the loss of the global...
Topology of evolving networks: local events and universality (2000)
Albert, Reka, Barabasi, Albert-Laszlo
Networks grow and evolve by local events, such as the addition of new nodes and links, or rewiring of links from one node to another. We show that depending on the frequency of these processes two...
Emergence of scaling in random networks (1999)
Barabasi, Albert-Laszlo, Albert, Reka
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a...
Mean-field theory for scale-free random networks (1999)
Barabasi, Albert-Laszlo, Albert, Reka, Jeong, Hawoong
Random networks with complex topology are common in Nature, describing systems as diverse as the world wide web or social and business networks. Recently, it has been demonstrated that most large...
The diameter of the world wide web (1999)
Albert, Reka, Jeong, Hawoong, Barabasi, Albert-Laszlo
Despite its increasing role in communication, the world wide web remains the least controlled medium: any individual or institution can create websites with unrestricted number of documents and...
Mean-Field Theory for Scale-Free Random Networks (1999)
Albert-László Barabási, Albert-laszlo Barabasi, Reka Albert, Hawoong Jeong
Random networks with complex topology are common in Nature, describing systems as diverse as the world wide web or social and business networks. Recently, it has been demonstrated that most large...
Albert, Reka, Barabasi, Albert-Laszlo, Carle, Nathan, Dougherty, Andrew
While there have been important theoretical advances in understanding the universality classes of interfaces moving in porous media, the developed tools cannot be directly applied to experiments....
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
Chung, Wen-Yu, Albert, Reka, Albert, Istvan, Nekrutenko, Anton, Makova, Kateryna D
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
Chung, Wen-Yu, Albert, Reka, Albert, Istvan, Nekrutenko, Anton, Makova, Kateryna D
Biological switches and clocks
Tyson, John J., Albert, Reka, Goldbeter, Albert, Ruoff, Peter, Sible, Jill
To introduce this special issue on biological switches and clocks, we review the historical development of mathematical models of bistability and oscillations in chemical reaction networks. In the...