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Empirical systems biology Section edited by Matteo Pellegrini

This section covers the conduct of experiments or use of empirical data to improve the understanding of the structure and function of biological systems.

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1.

Research article   Open Access

JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis

Prashant K Srivastava, Richard P Hull, Jacques Behmoaras, Enrico Petretto, Timothy J Aitman BMC Systems Biology 2013, 7:93 (22 September 2013)

Abstract | Full text | PDF | PubMed

2.

Research article   Open Access

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

Saheed Imam, Daniel R Noguera, Timothy J Donohue BMC Systems Biology 2013, 7:89 (13 September 2013)

Abstract | Full text | PDF | PubMed

3.

Research article   Open Access

Modularity and evolutionary constraints in a baculovirus gene regulatory network

Juliana Oliveira, Anderson de Brito, Carla Braconi, Caio de Melo Freire, Atila Iamarino, Paolo de Andrade Zanotto BMC Systems Biology 2013, 7:87 (4 September 2013)

Abstract | Full text | PDF | PubMed

4.

Research article   Open Access

Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

Treenut Saithong, Oratai Rongsirikul, Saowalak Kalapanulak, Porntip Chiewchankaset, Wanatsanan Siriwat, Supatcharee Netrphan, Malinee Suksangpanomrung, Asawin Meechai, Supapon Cheevadhanarak BMC Systems Biology 2013, 7:75 (10 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Methodology article   Open Access

Identification of yeast cell cycle regulated genes based on genomic features

Chao Cheng, Yao Fu, Linsheng Shen, Mark Gerstein BMC Systems Biology 2013, 7:70 (29 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Research article   Open Access Highly Accessed

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Nicolas Tchitchek, Amie J Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, Lisa E Gralinski, Christophe Bécavin, Susan C Tilton, Bobbie-Jo Webb-Robertson, Martin T Ferris, Allison L Totura, Chengjun Li, Gabriele Neumann, Thomas O Metz, Richard D Smith, Katrina M Waters, Ralph Baric, Yoshihiro Kawaoka, Michael G Katze BMC Systems Biology 2013, 7:69 (29 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

7.

Research article   Open Access

Modeling heterogeneous responsiveness of intrinsic apoptosis pathway

Hsu Ooi, Lan Ma BMC Systems Biology 2013, 7:65 (23 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Research article   Open Access

Transient oscillatory dynamics of interferon beta signaling in macrophages

Inna Pertsovskaya, Elena Abad, Núria Domedel-Puig, Jordi Garcia-Ojalvo, Pablo Villoslada BMC Systems Biology 2013, 7:59 (9 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

9.

Research article   Open Access

Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast

Gaël Yvert, Shinsuke Ohnuki, Satoru Nogami, Yasutaka Imanaga, Steffen Fehrmann, Joseph Schacherer, Yoshikazu Ohya BMC Systems Biology 2013, 7:54 (3 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

10.

Research article   Open Access Highly Accessed

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

Katherine Lawler, Kim Hammond-Kosack, Alvis Brazma, Richard MR Coulson BMC Systems Biology 2013, 7:52 (27 June 2013)

Abstract | Full text | PDF | PubMed

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