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		Methodology article Integrating systems biology models and biomedical ontologies Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook, Georgios V Gkoutos BMC Systems Biology 2011, 5:124 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle Olivia Eriksson, Tom Andersson, Yishao Zhou, Jesper Tegnér BMC Systems Biology 2011, 5:123 (7 August 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A retrosynthetic biology approach to metabolic pathway design for therapeutic production Pablo Carbonell, Anne-Gaëlle Planson, Davide Fichera, Jean-Loup Faulon BMC Systems Biology 2011, 5:122 (5 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Inferring causal genomic alterations in breast cancer using gene expression data Linh M Tran, Bin Zhang, Zhan Zhang, Chunsheng Zhang, Tao Xie, John R Lamb, Hongyue Dai, Eric E Schadt, Jun Zhu BMC Systems Biology 2011, 5:121 (1 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Systematic identification of causal copy number variations (CNVs) in breast cancer gene expression data using a wavelet based method to distinguish "driver genes" from "passenger genes" identifies known oncogenes and novel susceptibility genes.
		Research article Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling Osbaldo Resendis-Antonio, Magdalena Hernández, Emmanuel Salazar, Sandra Contreras, Gabriel Batallar, Yolanda Mora, Sergio Encarnación BMC Systems Biology 2011, 5:120 (29 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration Dorota Herman, Christopher M Thomas, Dov J Stekel BMC Systems Biology 2011, 5:119 (29 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Mechanisms of gap gene expression canalization in the Drosophila blastoderm Vitaly V Gursky, Lena Panok, Ekaterina M Myasnikova, Manu, Maria G Samsonova, John Reinitz, Alexander M Samsonov BMC Systems Biology 2011, 5:118 (28 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article An integrative approach to inferring biologically meaningful gene modules Ji-Hoon Cho, Kai Wang, David J Galas BMC Systems Biology 2011, 5:117 (26 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network Saheed Imam, Safak Yilmaz, Ugur Sohmen, Alexander S Gorzalski, Jennifer L Reed, Daniel R Noguera, Timothy J Donohue BMC Systems Biology 2011, 5:116 (21 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue Pernille Yde, Benedicte Mengel, Mogens H Jensen, Sandeep Krishna, Ala Trusina BMC Systems Biology 2011, 5:115 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis Nieves Vélez de Mendizábal, Jorge Carneiro, Ricard V Solé, Joaquín Goñi, Jean Bragard, Ivan Martinez-Forero, Sara Martinez-Pasamar, Jorge Sepulcre, Javier Torrealdea, Francesca Bagnato, Jordi Garcia-Ojalvo, Pablo Villoslada BMC Systems Biology 2011, 5:114 (15 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks Markus Durzinsky, Annegret Wagler, Wolfgang Marwan BMC Systems Biology 2011, 5:113 (15 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability XN Wei, BC Han, JX Zhang, XH Liu, CY Tan, YY Jiang, BC Low, B Tidor, YZ Chen BMC Systems Biology 2011, 5:112 (15 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli Daniel Madar, Erez Dekel, Anat Bren, Uri Alon BMC Systems Biology 2011, 5:111 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states Aarash Bordbar, Neema Jamshidi, Bernhard O Palsson BMC Systems Biology 2011, 5:110 (12 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles John Jack, John F Wambaugh, Imran Shah BMC Systems Biology 2011, 5:109 (11 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro Hai Fang, Wen Jin, Ying Yang, Ying Jin, Ji Zhang, Kankan Wang BMC Systems Biology 2011, 5:108 (6 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Combined logical and data-driven models for linking signalling pathways to cellular response Ioannis N Melas, Alexander Mitsos, Dimitris E Messinis, Thomas S Weiss, Leonidas G Alexopoulos BMC Systems Biology 2011, 5:107 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting Kaspar Valgepea, Kaarel Adamberg, Raivo Vilu BMC Systems Biology 2011, 5:106 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Construction of a computable cell proliferation network focused on non-diseased lung cells Jurjen W Westra, Walter K Schlage, Brian P Frushour, Stephan Gebel, Natalie L Catlett, Wanjiang Han, Sean F Eddy, Arnd Hengstermann, Andrea L Matthews, Carole Mathis, Rosemarie B Lichtner, Carine Poussin, Marja Talikka, Emilija Veljkovic, Aaron A Van Hooser, Benjamin Wong, Michael J Maria, Manuel C Peitsch, Renee Deehan, Julia Hoeng BMC Systems Biology 2011, 5:105 (2 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Is RNA-dependent RNA polymerase essential for transposon control? Anton Crombach, Paulien Hogeweg BMC Systems Biology 2011, 5:104 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article The coupling of pathways and processes through shared components Daniel D Seaton, J Krishnan BMC Systems Biology 2011, 5:103 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle Anthony C Smith, Alan J Robinson BMC Systems Biology 2011, 5:102 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
		Research article Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production Jong Park, Tae Kim, Sang Lee BMC Systems Biology 2011, 5:101 (28 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella Hyunjin Yoon, Charles Ansong, Jason E McDermott, Marina Gritsenko, Richard D Smith, Fred Heffron, Joshua N Adkins BMC Systems Biology 2011, 5:100 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

	All
		Methodology article Integrating systems biology models and biomedical ontologies Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook, Georgios V Gkoutos BMC Systems Biology 2011, 5:124 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle Olivia Eriksson, Tom Andersson, Yishao Zhou, Jesper Tegnér BMC Systems Biology 2011, 5:123 (7 August 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A retrosynthetic biology approach to metabolic pathway design for therapeutic production Pablo Carbonell, Anne-Gaëlle Planson, Davide Fichera, Jean-Loup Faulon BMC Systems Biology 2011, 5:122 (5 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Inferring causal genomic alterations in breast cancer using gene expression data Linh M Tran, Bin Zhang, Zhan Zhang, Chunsheng Zhang, Tao Xie, John R Lamb, Hongyue Dai, Eric E Schadt, Jun Zhu BMC Systems Biology 2011, 5:121 (1 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Systematic identification of causal copy number variations (CNVs) in breast cancer gene expression data using a wavelet based method to distinguish "driver genes" from "passenger genes" identifies known oncogenes and novel susceptibility genes.
		Research article Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling Osbaldo Resendis-Antonio, Magdalena Hernández, Emmanuel Salazar, Sandra Contreras, Gabriel Batallar, Yolanda Mora, Sergio Encarnación BMC Systems Biology 2011, 5:120 (29 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration Dorota Herman, Christopher M Thomas, Dov J Stekel BMC Systems Biology 2011, 5:119 (29 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Mechanisms of gap gene expression canalization in the Drosophila blastoderm Vitaly V Gursky, Lena Panok, Ekaterina M Myasnikova, Manu, Maria G Samsonova, John Reinitz, Alexander M Samsonov BMC Systems Biology 2011, 5:118 (28 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article An integrative approach to inferring biologically meaningful gene modules Ji-Hoon Cho, Kai Wang, David J Galas BMC Systems Biology 2011, 5:117 (26 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network Saheed Imam, Safak Yilmaz, Ugur Sohmen, Alexander S Gorzalski, Jennifer L Reed, Daniel R Noguera, Timothy J Donohue BMC Systems Biology 2011, 5:116 (21 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue Pernille Yde, Benedicte Mengel, Mogens H Jensen, Sandeep Krishna, Ala Trusina BMC Systems Biology 2011, 5:115 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis Nieves Vélez de Mendizábal, Jorge Carneiro, Ricard V Solé, Joaquín Goñi, Jean Bragard, Ivan Martinez-Forero, Sara Martinez-Pasamar, Jorge Sepulcre, Javier Torrealdea, Francesca Bagnato, Jordi Garcia-Ojalvo, Pablo Villoslada BMC Systems Biology 2011, 5:114 (15 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks Markus Durzinsky, Annegret Wagler, Wolfgang Marwan BMC Systems Biology 2011, 5:113 (15 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability XN Wei, BC Han, JX Zhang, XH Liu, CY Tan, YY Jiang, BC Low, B Tidor, YZ Chen BMC Systems Biology 2011, 5:112 (15 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli Daniel Madar, Erez Dekel, Anat Bren, Uri Alon BMC Systems Biology 2011, 5:111 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states Aarash Bordbar, Neema Jamshidi, Bernhard O Palsson BMC Systems Biology 2011, 5:110 (12 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles John Jack, John F Wambaugh, Imran Shah BMC Systems Biology 2011, 5:109 (11 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro Hai Fang, Wen Jin, Ying Yang, Ying Jin, Ji Zhang, Kankan Wang BMC Systems Biology 2011, 5:108 (6 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Combined logical and data-driven models for linking signalling pathways to cellular response Ioannis N Melas, Alexander Mitsos, Dimitris E Messinis, Thomas S Weiss, Leonidas G Alexopoulos BMC Systems Biology 2011, 5:107 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting Kaspar Valgepea, Kaarel Adamberg, Raivo Vilu BMC Systems Biology 2011, 5:106 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Construction of a computable cell proliferation network focused on non-diseased lung cells Jurjen W Westra, Walter K Schlage, Brian P Frushour, Stephan Gebel, Natalie L Catlett, Wanjiang Han, Sean F Eddy, Arnd Hengstermann, Andrea L Matthews, Carole Mathis, Rosemarie B Lichtner, Carine Poussin, Marja Talikka, Emilija Veljkovic, Aaron A Van Hooser, Benjamin Wong, Michael J Maria, Manuel C Peitsch, Renee Deehan, Julia Hoeng BMC Systems Biology 2011, 5:105 (2 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Is RNA-dependent RNA polymerase essential for transposon control? Anton Crombach, Paulien Hogeweg BMC Systems Biology 2011, 5:104 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article The coupling of pathways and processes through shared components Daniel D Seaton, J Krishnan BMC Systems Biology 2011, 5:103 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle Anthony C Smith, Alan J Robinson BMC Systems Biology 2011, 5:102 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
		Research article Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production Jong Park, Tae Kim, Sang Lee BMC Systems Biology 2011, 5:101 (28 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella Hyunjin Yoon, Charles Ansong, Jason E McDermott, Marina Gritsenko, Richard D Smith, Fred Heffron, Joshua N Adkins BMC Systems Biology 2011, 5:100 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central