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		Methodology article Likelihood based observability analysis and confidence intervals for predictions of dynamic models Clemens Kreutz, Andreas Raue, Jens Timmer BMC Systems Biology 2012, 6:120 (5 September 2012) Abstract \| Full text \| PDF \| PubMed
		Research article An integer optimization algorithm for robust identification of non-linear gene regulatory networks Nishanth Chemmangattuvalappil, Keith Task, Ipsita Banerjee BMC Systems Biology 2012, 6:119 (2 September 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter BMC Systems Biology 2012, 6:118 (31 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs Jason E Shoemaker, Satoshi Fukuyama, Amie J Eisfeld, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Yukiko Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka BMC Systems Biology 2012, 6:117 (31 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Continuous time boolean modeling for biological signaling: application of Gillespie algorithm Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone BMC Systems Biology 2012, 6:116 (29 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer Giuseppe Facchetti, Mattia Zampieri, Claudio Altafini BMC Systems Biology 2012, 6:115 (29 August 2012) Abstract \| Provisional PDF \| PubMed
		Research article CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism Anja Karlstädt, Daniela Fliegner, Georgios Kararigas, Hugo Sanchez Ruderisch, Vera Regitz-Zagrosek, Hermann-Georg Holzhütter BMC Systems Biology 2012, 6:114 (29 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks Jinghang Liang, Jie Han BMC Systems Biology 2012, 6:113 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Methodology article Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study Mohammed Alshalalfa, Gary D Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj BMC Systems Biology 2012, 6:112 (28 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback Yonatan Savir, Nir Waysbort, Yaron E Antebi, Tsvi Tlusty, Nir Friedman BMC Systems Biology 2012, 6:111 (27 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Topological effects of data incompleteness of gene regulatory networks Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno BMC Systems Biology 2012, 6:110 (25 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike, Boris N Kholodenko BMC Systems Biology 2012, 6:109 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bimodal signaling response of individual cells in a population in response to stimulation need not imply a digital cellular response, but can arise from a combination of protein expression noise and negative feedback.
		Research article Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz, Lubomira Stateva BMC Systems Biology 2012, 6:108 (24 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner BMC Systems Biology 2012, 6:107 (22 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Flux variability scanning based on enforced objective flux for identifying gene amplification targets Jong Park, Hye Park, Won Kim, Hyun Kim, Tae Kim, Sang Lee BMC Systems Biology 2012, 6:106 (21 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang BMC Systems Biology 2012, 6:105 (20 August 2012) Abstract \| Full text \| PDF \| PubMed
		Software DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph BMC Systems Biology 2012, 6:104 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Designing optimal cell factories: integer programming couples elementary mode analysis with regulation Christian Jungreuthmayer, Jürgen Zanghellini BMC Systems Biology 2012, 6:103 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data Tzu-Hsien Yang, Wei-Sheng Wu BMC Systems Biology 2012, 6:102 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Integrating external biological knowledge in the construction of regulatory networks from time-series expression data Kenneth Lo, Adrian E Raftery, Kenneth M Dombek, Jun Zhu, Eric E Schadt, Roger E Bumgarner, Ka Yeung BMC Systems Biology 2012, 6:101 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak BMC Systems Biology 2012, 6:100 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article A variational approach to parameter estimation in ordinary differential equations Daniel Kaschek, Jens Timmer BMC Systems Biology 2012, 6:99 (14 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency Vijay Chickarmane, Victor Olariu, Carsten Peterson BMC Systems Biology 2012, 6:98 (13 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis Eduardo Tejera, João Bernardes, Irene Rebelo BMC Systems Biology 2012, 6:97 (8 August 2012) Abstract \| Full text \| PDF \| PubMed
		Software The Cell Collective: Toward an open and collaborative approach to systems biology Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers BMC Systems Biology 2012, 6:96 (7 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new web-based platform, The Cell Collective, allows scientists from across the globe to collaboratively build, analyze and simulate large-scale biological systems in real time enabling efficient transfer of laboratory data into models for complex networks.

	All
		Methodology article Likelihood based observability analysis and confidence intervals for predictions of dynamic models Clemens Kreutz, Andreas Raue, Jens Timmer BMC Systems Biology 2012, 6:120 (5 September 2012) Abstract \| Full text \| PDF \| PubMed
		Research article An integer optimization algorithm for robust identification of non-linear gene regulatory networks Nishanth Chemmangattuvalappil, Keith Task, Ipsita Banerjee BMC Systems Biology 2012, 6:119 (2 September 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter BMC Systems Biology 2012, 6:118 (31 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs Jason E Shoemaker, Satoshi Fukuyama, Amie J Eisfeld, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Yukiko Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka BMC Systems Biology 2012, 6:117 (31 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Continuous time boolean modeling for biological signaling: application of Gillespie algorithm Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone BMC Systems Biology 2012, 6:116 (29 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer Giuseppe Facchetti, Mattia Zampieri, Claudio Altafini BMC Systems Biology 2012, 6:115 (29 August 2012) Abstract \| Provisional PDF \| PubMed
		Research article CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism Anja Karlstädt, Daniela Fliegner, Georgios Kararigas, Hugo Sanchez Ruderisch, Vera Regitz-Zagrosek, Hermann-Georg Holzhütter BMC Systems Biology 2012, 6:114 (29 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks Jinghang Liang, Jie Han BMC Systems Biology 2012, 6:113 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Methodology article Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study Mohammed Alshalalfa, Gary D Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj BMC Systems Biology 2012, 6:112 (28 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback Yonatan Savir, Nir Waysbort, Yaron E Antebi, Tsvi Tlusty, Nir Friedman BMC Systems Biology 2012, 6:111 (27 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Topological effects of data incompleteness of gene regulatory networks Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno BMC Systems Biology 2012, 6:110 (25 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike, Boris N Kholodenko BMC Systems Biology 2012, 6:109 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bimodal signaling response of individual cells in a population in response to stimulation need not imply a digital cellular response, but can arise from a combination of protein expression noise and negative feedback.
		Research article Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae Thomas Williamson, Delali Adiamah, Jean-Marc Schwartz, Lubomira Stateva BMC Systems Biology 2012, 6:108 (24 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner BMC Systems Biology 2012, 6:107 (22 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Flux variability scanning based on enforced objective flux for identifying gene amplification targets Jong Park, Hye Park, Won Kim, Hyun Kim, Tae Kim, Sang Lee BMC Systems Biology 2012, 6:106 (21 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang BMC Systems Biology 2012, 6:105 (20 August 2012) Abstract \| Full text \| PDF \| PubMed
		Software DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph BMC Systems Biology 2012, 6:104 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Designing optimal cell factories: integer programming couples elementary mode analysis with regulation Christian Jungreuthmayer, Jürgen Zanghellini BMC Systems Biology 2012, 6:103 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data Tzu-Hsien Yang, Wei-Sheng Wu BMC Systems Biology 2012, 6:102 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Integrating external biological knowledge in the construction of regulatory networks from time-series expression data Kenneth Lo, Adrian E Raftery, Kenneth M Dombek, Jun Zhu, Eric E Schadt, Roger E Bumgarner, Ka Yeung BMC Systems Biology 2012, 6:101 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak BMC Systems Biology 2012, 6:100 (16 August 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article A variational approach to parameter estimation in ordinary differential equations Daniel Kaschek, Jens Timmer BMC Systems Biology 2012, 6:99 (14 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency Vijay Chickarmane, Victor Olariu, Carsten Peterson BMC Systems Biology 2012, 6:98 (13 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis Eduardo Tejera, João Bernardes, Irene Rebelo BMC Systems Biology 2012, 6:97 (8 August 2012) Abstract \| Full text \| PDF \| PubMed
		Software The Cell Collective: Toward an open and collaborative approach to systems biology Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers BMC Systems Biology 2012, 6:96 (7 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new web-based platform, The Cell Collective, allows scientists from across the globe to collaboratively build, analyze and simulate large-scale biological systems in real time enabling efficient transfer of laboratory data into models for complex networks.