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		Research article Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway Kevin Gonzales, Ömür Kayikçi, David G Schaeffer, Paul M Magwene BMC Systems Biology 2013, 7:40 (17 May 2013) Abstract \| Provisional PDF \| PubMed
		Methodology article Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics Luca Salerno, Carlo Cosentino, Alessio Merola, Declan G Bates, Francesco Amato BMC Systems Biology 2013, 7:39 (17 May 2013) Abstract \| Provisional PDF \| PubMed
		Research article Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis Emily Greenfest-Allen, Jeffrey Malik, James Palis, Christian J Stoeckert BMC Systems Biology 2013, 7:38 (15 May 2013) Abstract \| Provisional PDF \| PubMed
		Research article Dynamic modeling of yeast meiotic initiation Debjit Ray, Yongchun Su, Ping Ye BMC Systems Biology 2013, 7:37 (1 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen BMC Systems Biology 2013, 7:36 (30 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Dynamic cross-regulation of antigen-specific effector and regulatory T cell subpopulations and microglia in brain autoimmunity Sara Martinez-Pasamar, Elena Abad, Beatriz Moreno, Nieves Velez de Mendizabal, Ivan Martinez-Forero, Jordi Garcia-Ojalvo, Pablo Villoslada BMC Systems Biology 2013, 7:34 (26 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Reviewer acknowledgement Annual acknowledgement of reviewers Tim Sands BMC Systems Biology 2013, 7:35 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A metabolite-centric view on flux distributions in genome-scale metabolic models S Riemer, René Rex, Dietmar Schomburg BMC Systems Biology 2013, 7:33 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Construction and analysis of the protein-protein interaction network related to essential hypertension Jihua Ran, Hui Li, Jianfeng Fu, Ling Liu, Yanchao Xing, Xiumei Li, Hongming Shen, Yan Chen, Xiaofang Jiang, Yan Li, Huiwu Li BMC Systems Biology 2013, 7:32 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Optimization of personalized therapies for anticancer treatment Alexei Vazquez BMC Systems Biology 2013, 7:31 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia Kyungchul Noh, Kyung Soon Shin, Dongkwan Shin, Jae Yeon Hwang, June Sic Kim, Joon Hwan Jang, Chun Kee Chung, Jun Soo Kwon, Kwang-Hyun Cho BMC Systems Biology 2013, 7:30 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Probabilistic strain optimization under constraint uncertainty Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun BMC Systems Biology 2013, 7:29 (29 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li, Yi Pan BMC Systems Biology 2013, 7:28 (28 March 2013) Abstract \| Full text \| PDF \| PubMed
		Research article The last generation of bacterial growth in limiting nutrient Anat Bren, Yuval Hart, Erez Dekel, Daniel Koster, Uri Alon BMC Systems Biology 2013, 7:27 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response William A Bryant, Michael JE Sternberg, John W Pinney BMC Systems Biology 2013, 7:26 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla Favera, Raul Rabadan BMC Systems Biology 2013, 7:25 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Muzi Falconi, Daniela Besozzi, Paolo Plevani BMC Systems Biology 2013, 7:24 (20 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs Alexandra Pokhilko, Paloma Mas, Andrew J Millar BMC Systems Biology 2013, 7:23 (19 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article Novel semantic similarity measure improves an integrative approach to predicting gene functional associations Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter, Igor Jurisica BMC Systems Biology 2013, 7:22 (14 March 2013) Abstract \| Provisional PDF \| PubMed
		Methodology article Cluster and propensity based approximation of a network John Michael Ranola, Peter Langfelder, Kenneth Lange, Steve Horvath BMC Systems Biology 2013, 7:21 (14 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Function and design of the Nox1 system in vascular smooth muscle cells Weiwei Yin, Eberhard O Voit BMC Systems Biology 2013, 7:20 (11 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling Sven EF Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind Jakobsen, Per Bruheim, Trond E Ellingsen, Jens Nielsen, Svein Valla BMC Systems Biology 2013, 7:19 (11 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Genome-scale metabolic modelling and chemostat experiments identify the genomic features in Pseudomonas fluorescens necessary to develop highly productive strains and optimal conditions for the industrial production of the important polysaccharide gel alginate, currently produced from seaweed.
		Software BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Zinovyev BMC Systems Biology 2013, 7:18 (1 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary ¹³C flux analysis Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol, Aljoscha Wahl BMC Systems Biology 2013, 7:17 (28 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis Kamil Erguler, Myrtani Pieri, Constantinos Deltas BMC Systems Biology 2013, 7:16 (21 February 2013) Abstract \| Provisional PDF \| PubMed

	All
		Research article Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway Kevin Gonzales, Ömür Kayikçi, David G Schaeffer, Paul M Magwene BMC Systems Biology 2013, 7:40 (17 May 2013) Abstract \| Provisional PDF \| PubMed
		Methodology article Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics Luca Salerno, Carlo Cosentino, Alessio Merola, Declan G Bates, Francesco Amato BMC Systems Biology 2013, 7:39 (17 May 2013) Abstract \| Provisional PDF \| PubMed
		Research article Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis Emily Greenfest-Allen, Jeffrey Malik, James Palis, Christian J Stoeckert BMC Systems Biology 2013, 7:38 (15 May 2013) Abstract \| Provisional PDF \| PubMed
		Research article Dynamic modeling of yeast meiotic initiation Debjit Ray, Yongchun Su, Ping Ye BMC Systems Biology 2013, 7:37 (1 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen BMC Systems Biology 2013, 7:36 (30 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Dynamic cross-regulation of antigen-specific effector and regulatory T cell subpopulations and microglia in brain autoimmunity Sara Martinez-Pasamar, Elena Abad, Beatriz Moreno, Nieves Velez de Mendizabal, Ivan Martinez-Forero, Jordi Garcia-Ojalvo, Pablo Villoslada BMC Systems Biology 2013, 7:34 (26 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Reviewer acknowledgement Annual acknowledgement of reviewers Tim Sands BMC Systems Biology 2013, 7:35 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A metabolite-centric view on flux distributions in genome-scale metabolic models S Riemer, René Rex, Dietmar Schomburg BMC Systems Biology 2013, 7:33 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Construction and analysis of the protein-protein interaction network related to essential hypertension Jihua Ran, Hui Li, Jianfeng Fu, Ling Liu, Yanchao Xing, Xiumei Li, Hongming Shen, Yan Chen, Xiaofang Jiang, Yan Li, Huiwu Li BMC Systems Biology 2013, 7:32 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Optimization of personalized therapies for anticancer treatment Alexei Vazquez BMC Systems Biology 2013, 7:31 (12 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia Kyungchul Noh, Kyung Soon Shin, Dongkwan Shin, Jae Yeon Hwang, June Sic Kim, Joon Hwan Jang, Chun Kee Chung, Jun Soo Kwon, Kwang-Hyun Cho BMC Systems Biology 2013, 7:30 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Probabilistic strain optimization under constraint uncertainty Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun BMC Systems Biology 2013, 7:29 (29 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li, Yi Pan BMC Systems Biology 2013, 7:28 (28 March 2013) Abstract \| Full text \| PDF \| PubMed
		Research article The last generation of bacterial growth in limiting nutrient Anat Bren, Yuval Hart, Erez Dekel, Daniel Koster, Uri Alon BMC Systems Biology 2013, 7:27 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response William A Bryant, Michael JE Sternberg, John W Pinney BMC Systems Biology 2013, 7:26 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla Favera, Raul Rabadan BMC Systems Biology 2013, 7:25 (25 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Muzi Falconi, Daniela Besozzi, Paolo Plevani BMC Systems Biology 2013, 7:24 (20 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs Alexandra Pokhilko, Paloma Mas, Andrew J Millar BMC Systems Biology 2013, 7:23 (19 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article Novel semantic similarity measure improves an integrative approach to predicting gene functional associations Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter, Igor Jurisica BMC Systems Biology 2013, 7:22 (14 March 2013) Abstract \| Provisional PDF \| PubMed
		Methodology article Cluster and propensity based approximation of a network John Michael Ranola, Peter Langfelder, Kenneth Lange, Steve Horvath BMC Systems Biology 2013, 7:21 (14 March 2013) Abstract \| Provisional PDF \| PubMed
		Research article Function and design of the Nox1 system in vascular smooth muscle cells Weiwei Yin, Eberhard O Voit BMC Systems Biology 2013, 7:20 (11 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling Sven EF Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind Jakobsen, Per Bruheim, Trond E Ellingsen, Jens Nielsen, Svein Valla BMC Systems Biology 2013, 7:19 (11 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Genome-scale metabolic modelling and chemostat experiments identify the genomic features in Pseudomonas fluorescens necessary to develop highly productive strains and optimal conditions for the industrial production of the important polysaccharide gel alginate, currently produced from seaweed.
		Software BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Zinovyev BMC Systems Biology 2013, 7:18 (1 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary ¹³C flux analysis Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol, Aljoscha Wahl BMC Systems Biology 2013, 7:17 (28 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis Kamil Erguler, Myrtani Pieri, Constantinos Deltas BMC Systems Biology 2013, 7:16 (21 February 2013) Abstract \| Provisional PDF \| PubMed