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		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 \| Provisional PDF
		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 \| Provisional PDF
		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 \| Provisional PDF \| PubMed
		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 \| Provisional PDF \| PubMed
		Research article Model composition through model reduction: a combined model of CD95 and NF-kappaB signaling pathways Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov BMC Systems Biology 2013, 7:13 (15 February 2013) Abstract \| Provisional PDF \| 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 \| Provisional 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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, Dezs¿ Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Bek¿, Katalin Lenti, Illés J Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros BMC Systems Biology 2013, 7:7 (18 January 2013) Abstract \| Provisional 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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

	All
		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 \| Provisional PDF
		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 \| Provisional PDF
		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 \| Provisional PDF \| PubMed
		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 \| Provisional PDF \| PubMed
		Research article Model composition through model reduction: a combined model of CD95 and NF-kappaB signaling pathways Elena Kutumova, Andrei Zinovyev, Ruslan Sharipov, Fedor Kolpakov BMC Systems Biology 2013, 7:13 (15 February 2013) Abstract \| Provisional PDF \| 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 \| Provisional 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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, Dezs¿ Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Bek¿, Katalin Lenti, Illés J Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros BMC Systems Biology 2013, 7:7 (18 January 2013) Abstract \| Provisional 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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 \| Provisional PDF \| 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