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When studying their systemic nature many modeling approaches focus on identifying simple, but prominent, structural components, as such components are easier to understand, and, once identified, can be used as building blocks to succinctly describe the network.<\/jats:p><jats:p>Results: In recent social network studies, exponential random graph models have been used extensively to model global social network structure as a function of their \u2018local features\u2019. Starting from those studies, we describe the exponential random graph models and demonstrate their utility in modeling the architecture of biological networks as a function of the prominence of local features. We argue that the flexibility, in terms of the number of available local feature choices, and scalability, in terms of the network sizes, make this approach ideal for statistical modeling of biological networks. We illustrate the modeling on both genetic and metabolic networks and provide a novel way of classifying biological networks based on the prevalence of their local features.<\/jats:p><jats:p>Contact: \u00a0saul@cs.ucdavis.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm370","type":"journal-article","created":{"date-parts":[[2007,7,21]],"date-time":"2007-07-21T00:34:25Z","timestamp":1184978065000},"page":"2604-2611","source":"Crossref","is-referenced-by-count":66,"title":["Exploring biological network structure using exponential random graph models"],"prefix":"10.1093","volume":"23","author":[{"given":"Zachary M.","family":"Saul","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA"}]},{"given":"Vladimir","family":"Filkov","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,7,20]]},"reference":[{"key":"2023041208441005100_","doi-asserted-by":"crossref","first-page":"5234","DOI":"10.1103\/PhysRevLett.85.5234","article-title":"Topology of evolving networks: local events and universality","volume":"85","author":"Albert","year":"2000","journal-title":"Phys. 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