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		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
		Methodology article Precise generation of systems biology models from KEGG pathways Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell BMC Systems Biology 2013, 7:15 (21 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A new method allows the construction of correct BioPAX and SBML models based on data from the KEGG database, correcting KGML content and augmenting it with data from other sources to generate complete pathway models.
		Methodology article Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini BMC Systems Biology 2013, 7:14 (19 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov BMC Systems Biology 2013, 7:13 (15 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework Gaurav Kumar, Edmond J Breen, Shoba Ranganathan BMC Systems Biology 2013, 7:12 (6 February 2013) Abstract \| Full text \| PDF \| PubMed
		Research article A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns Anna Bershteyn, Philip A Eckhoff BMC Systems Biology 2013, 7:11 (4 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells Hyunju Cho, Ming Wu, Linxia Zhang, Ryan Thompson, Aritro Nath, Christina Chan BMC Systems Biology 2013, 7:9 (22 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials Jennifer E Dent, Christine Nardini BMC Systems Biology 2013, 7:10 (22 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels, Mats Jirstrand BMC Systems Biology 2013, 7:8 (19 January 2013) Abstract \| Provisional PDF \| PubMed
		Database SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks Dávid Fazekas, Mihály Koltai, Dénes Türei, Dezső Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Bekő, Katalin Lenti, Illés J Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros BMC Systems Biology 2013, 7:7 (18 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Dynamics of the quorum sensing switch: stochastic and non-stationary effects Marc Weber, Javier Buceta BMC Systems Biology 2013, 7:6 (16 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Disentangling function from topology to infer the network properties of disease genes Dario Ghersi, Mona Singh BMC Systems Biology 2013, 7:5 (16 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Software EnRICH: Extraction and Ranking using Integration and Criteria Heuristics Xia Zhang, M Heather West Greenlee, Jeanne M Serb BMC Systems Biology 2013, 7:4 (15 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT Ulf W Liebal, Thomas Millat, Jon Marles-Wright, Richard J Lewis, Olaf Wolkenhauer BMC Systems Biology 2013, 7:3 (15 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article A kinetic model for RNA-interference of focal adhesions Max Hoffmann, Ulrich S Schwarz BMC Systems Biology 2013, 7:2 (12 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0 Michael Weber, Sebastian G Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J van Zoelen, Dominik Driesch BMC Systems Biology 2013, 7:1 (2 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Metabolic Flux-Based Modularity using Shortest Retroactive distances Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee BMC Systems Biology 2012, 6:155 (27 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee BMC Systems Biology 2012, 6:154 (15 December 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE Yuliang Wang, James A Eddy, Nathan D Price BMC Systems Biology 2012, 6:153 (13 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li BMC Systems Biology 2012, 6:152 (10 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? Luisa Ana B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade, Walter M van Gulik BMC Systems Biology 2012, 6:151 (7 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach Ali Navid, Eivind Almaas BMC Systems Biology 2012, 6:150 (6 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, Vitor Martins dos Santos, Víctor de Lorenzo BMC Systems Biology 2012, 6:149 (6 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski BMC Systems Biology 2012, 6:148 (30 November 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt BMC Systems Biology 2012, 6:147 (29 November 2012) Abstract \| Full text \| PDF \| PubMed

	All
		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
		Methodology article Precise generation of systems biology models from KEGG pathways Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell BMC Systems Biology 2013, 7:15 (21 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A new method allows the construction of correct BioPAX and SBML models based on data from the KEGG database, correcting KGML content and augmenting it with data from other sources to generate complete pathway models.
		Methodology article Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini BMC Systems Biology 2013, 7:14 (19 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov BMC Systems Biology 2013, 7:13 (15 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework Gaurav Kumar, Edmond J Breen, Shoba Ranganathan BMC Systems Biology 2013, 7:12 (6 February 2013) Abstract \| Full text \| PDF \| PubMed
		Research article A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns Anna Bershteyn, Philip A Eckhoff BMC Systems Biology 2013, 7:11 (4 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells Hyunju Cho, Ming Wu, Linxia Zhang, Ryan Thompson, Aritro Nath, Christina Chan BMC Systems Biology 2013, 7:9 (22 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials Jennifer E Dent, Christine Nardini BMC Systems Biology 2013, 7:10 (22 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels, Mats Jirstrand BMC Systems Biology 2013, 7:8 (19 January 2013) Abstract \| Provisional PDF \| PubMed
		Database SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks Dávid Fazekas, Mihály Koltai, Dénes Türei, Dezső Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Bekő, Katalin Lenti, Illés J Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros BMC Systems Biology 2013, 7:7 (18 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Dynamics of the quorum sensing switch: stochastic and non-stationary effects Marc Weber, Javier Buceta BMC Systems Biology 2013, 7:6 (16 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Disentangling function from topology to infer the network properties of disease genes Dario Ghersi, Mona Singh BMC Systems Biology 2013, 7:5 (16 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Software EnRICH: Extraction and Ranking using Integration and Criteria Heuristics Xia Zhang, M Heather West Greenlee, Jeanne M Serb BMC Systems Biology 2013, 7:4 (15 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT Ulf W Liebal, Thomas Millat, Jon Marles-Wright, Richard J Lewis, Olaf Wolkenhauer BMC Systems Biology 2013, 7:3 (15 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research article A kinetic model for RNA-interference of focal adhesions Max Hoffmann, Ulrich S Schwarz BMC Systems Biology 2013, 7:2 (12 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology article Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0 Michael Weber, Sebastian G Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J van Zoelen, Dominik Driesch BMC Systems Biology 2013, 7:1 (2 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research article Metabolic Flux-Based Modularity using Shortest Retroactive distances Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee BMC Systems Biology 2012, 6:155 (27 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee BMC Systems Biology 2012, 6:154 (15 December 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE Yuliang Wang, James A Eddy, Nathan D Price BMC Systems Biology 2012, 6:153 (13 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li BMC Systems Biology 2012, 6:152 (10 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? Luisa Ana B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade, Walter M van Gulik BMC Systems Biology 2012, 6:151 (7 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach Ali Navid, Eivind Almaas BMC Systems Biology 2012, 6:150 (6 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, Vitor Martins dos Santos, Víctor de Lorenzo BMC Systems Biology 2012, 6:149 (6 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski BMC Systems Biology 2012, 6:148 (30 November 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt BMC Systems Biology 2012, 6:147 (29 November 2012) Abstract \| Full text \| PDF \| PubMed