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Systems as diverse as genetic networks or the World Wide
Web are best described as networks with complex topology. A commonproperty of many large networks is that the vertex connectivitiesfollow a scale-free power-law distribution. This feature was foundto
be a consequence of two generic mechanisms: (i) networks expandcontinuously by the addition of new vertices, and (ii) new verticesattach preferentially to sites that are already well connected.A model
based on these two ingredients reproduces the observedstationary
scale-free distributions, which indicates that thedevelopment of large
networks is governed by robust self-organizingphenomena that go beyond
the particulars of the individual systems.
Department of Physics, University of Notre Dame, Notre Dame, IN
46556, USA.
*
To whom correspondence should be addressed. E-mail: alb{at}nd.edu
Gene expression dynamics in the macrophage exhibit criticality.
M. Nykter, N. D. Price, M. Aldana, S. A. Ramsey, S. A. Kauffman, L. E. Hood, O. Yli-Harja, and I. Shmulevich (2008)
PNAS
105, 1897-1900
|Abstract »|Full Text »|PDF »
Encephalization, Emergent Properties, and Psychiatry: A Minicolumnar Perspective.
M. F. Casanova and C. R. Tillquist (2008)
Neuroscientist
14, 101-118
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Cardioinductive Network Guiding Stem Cell Differentiation Revealed by Proteomic Cartography of Tumor Necrosis Factor {alpha}-Primed Endodermal Secretome.
D. K. Arrell, N. J. Niederlander, R. S. Faustino, A. Behfar, and A. Terzic (2008)
Stem Cells
26, 387-400
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The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication.
A. Presser, M. B. Elowitz, M. Kellis, and R. Kishony (2008)
PNAS
105, 950-954
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Estimating node degree in bait-prey graphs.
D. Scholtens, T. Chiang, W. Huber, and R. Gentleman (2008)
Bioinformatics
24, 218-224
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Comparative Approaches for Assessing Network Vulnerability.
T. H. Grubesic, T. C. Matisziw, A. T. Murray, and D. Snediker (2008)
International Regional Science Review
31, 88-112
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How Directional Translocation is Regulated in a DNA Helicase Motor.
Bubble Continuous Positive Airway Pressure Enhances Lung Volume and Gas Exchange in Preterm Lambs.
J. J. Pillow, N. Hillman, T. J. M. Moss, G. Polglase, G. Bold, C. Beaumont, M. Ikegami, and A. H. Jobe (2007)
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Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network.
V. Vermeirssen, M. I. Barrasa, C. A. Hidalgo, J. A. B. Babon, R. Sequerra, L. Doucette-Stamm, A.-L. Barabasi, and A. J.M. Walhout (2007)
Genome Res.
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Hydrophobic, Hydrophilic, and Charged Amino Acid Networks within Protein.
Epstein-Barr virus and virus human protein interaction maps.
M. A. Calderwood, K. Venkatesan, L. Xing, M. R. Chase, A. Vazquez, A. M. Holthaus, A. E. Ewence, N. Li, T. Hirozane-Kishikawa, D. E. Hill, et al. (2007)
PNAS
104, 7606-7611
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Genome-Wide Network Analysis Reveals the Global Properties of IFN-beta Immediate Transcriptional Effects in Humans.
G. H. Fernald, S. Knott, A. Pachner, S. J. Caillier, K. Narayan, J. R. Oksenberg, P. Mousavi, and S. E. Baranzini (2007)
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From the Cover: Emergence of tempered preferential attachment from optimization.
R. M. D'Souza, C. Borgs, J. T. Chayes, N. Berger, and R. D. Kleinberg (2007)
PNAS
104, 6112-6117
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Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: Comparison with high-throughput experimental data.
Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits.
J. Tegner, J. Skogsberg, and J. Bjorkegren (2007)
J. Lipid Res.
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Biological network comparison using graphlet degree distribution.
Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes.
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target.
S. Horvath, B. Zhang, M. Carlson, K. V. Lu, S. Zhu, R. M. Felciano, M. F. Laurance, W. Zhao, S. Qi, Z. Chen, et al. (2006)
PNAS
103, 17402-17407
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Colloquium Papers: Genomic analysis of the hierarchical structure of regulatory networks.
Self-Organization of Surface Transportation Networks.
D. Levinson and B. Yerra (2006)
Transportation Science
40, 179-188
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Large-scale identification of protein-protein interaction of Escherichia coli K-12.
M. Arifuzzaman, M. Maeda, A. Itoh, K. Nishikata, C. Takita, R. Saito, T. Ara, K. Nakahigashi, H.-C. Huang, A. Hirai, et al. (2006)
Genome Res.
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Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.
N. Przulj, D. G. Corneil, and I. Jurisica (2006)
Bioinformatics
22, 974-980
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Conflict and Cooperation in an Actors' Network of Chechnya Based on Event Data.
A. Hammerli, R. Gattiker, and R. Weyermann (2006)
Journal of Conflict Resolution
50, 159-175
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Connection and coordination: the interplay between architecture and dynamics in evolved model pattern generators..
Herpesviral Protein Networks and Their Interaction with the Human Proteome.
P. Uetz, Y.-A. Dong, C. Zeretzke, C. Atzler, A. Baiker, B. Berger, S. V. Rajagopala, M. Roupelieva, D. Rose, E. Fossum, et al. (2006)
Science
311, 239-242
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From The Cover: A simple physical model for scaling in protein-protein interaction networks.
A Resilient, Low-Frequency, Small-World Human Brain Functional Network with Highly Connected Association Cortical Hubs.
S. Achard, R. Salvador, B. Whitcher, J. Suckling, and E. Bullmore (2006)
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Topological and Functional Discovery in a Gene Coexpression Meta-Network of Gastric Cancer.
A. Aggarwal, D. Li Guo, Y. Hoshida, S. Tsan Yuen, K.-M. Chu, S. So, A. Boussioutas, X. Chen, D. Bowtell, H. Aburatani, et al. (2006)
Cancer Res.
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Replication Methods for Load Balancing on Distributed Storagesin P2P Networks.
H. YAMAMOTO, D. MARUTA, and Y. OIE (2006)
IEICE Trans D: Information
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|Abstract »|PDF »
Protein Function, Connectivity, and Duplicability in Yeast.
A. Prachumwat and W.-H. Li (2006)
Mol. Biol. Evol.
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|Abstract »|