Genome Biology

official impact factor 6.89

Open Access

An evolutionary and functional assessment of regulatory network motifs

Aurélien Mazurie, Samuel Bottani* and Massimo Vergassola

Genome Biology 2005, 6:R35 doi:10.1186/gb-2005-6-4-r35

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BioMed Central: 12 citations

Research article   Open Access

Evolvability of feed-forward loop architecture biases its abundance in transcription networks

Stefanie Widder, Ricard Solé, Javier Macía BMC Systems Biology 2012, 6:7 (19 January 2012)

Research article   Open Access

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test

Chao Wu, Fan Zhang, Xia Li, Shihua Zhang, Jiang Li, Fei Su, Kongning Li, Yuqing Yan BMC Systems Biology 2010, 4:82 (10 June 2010)

Research article   Open Access Highly Accessed

Integrated cellular network of transcription regulations and protein-protein interactions

Yu-Chao Wang, Bor-Sen Chen BMC Systems Biology 2010, 4:20 (8 March 2010)

Methodology article   Open Access Highly Accessed

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks

Björn Goemann, Edgar Wingender, Anatolij P Potapov BMC Systems Biology 2009, 3:53 (19 May 2009)

Research article   Open Access

Simple molecular networks that respond optimally to time-periodic stimulation

Axel Cournac, Jacques-Alexandre Sepulchre BMC Systems Biology 2009, 3:29 (3 March 2009)

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Protein evolution on a human signaling network

Qinghua Cui, Enrico O Purisima, Edwin Wang BMC Systems Biology 2009, 3:21 (18 February 2009)

Research   Open Access Highly Accessed

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach

Julio A Freyre-González, José A Alonso-Pavón, Luis G Treviño-Quintanilla, Julio Collado-Vides Genome Biology 2008, 9:R154 (27 October 2008)

The E. coli transcriptional regulatory network is shown to have a nonpyramidal architecture of independent modules governed by transcription factors, whose responses are integrated by intermodular genes.

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Efficiency of the immunome protein interaction network increases during evolution

Csaba Ortutay, Mauno Vihinen Immunome Research 2008, 4:4 (22 April 2008)

Research article   Open Access

Modeling protein network evolution under genome duplication and domain shuffling

Kirill Evlampiev, Hervé Isambert BMC Systems Biology 2007, 1:49 (13 November 2007)

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Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

Ofer Meshi, Tomer Shlomi, Eytan Ruppin BMC Systems Biology 2007, 1:1 (8 January 2007)

Contrary to widespread belief, simple network patterns that are over-represented in yeast are not associated with any particular biological functions, and those patterns that are functionally enriched mainly involve recently evolved genes.

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The effects of incomplete protein interaction data on structural and evolutionary inferences

Eric de Silva, Thomas Thorne, Piers Ingram, Ino Agrafioti, Jonathan Swire, Carsten Wiuf, Michael PH Stumpf BMC Biology 2006, 4:39 (3 November 2006)

The properties of protein interaction networks are profoundly altered by sampling biases and by noise within available datasets, a finding that must be borne in mind when drawing structural or evolutionary inferences.

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Design principles of molecular networks revealed by global comparisons and composite motifs

Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein Genome Biology 2006, 7:R55 (19 July 2006)

A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles.