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	1. 4736 Accesses	Methodology article Rule-based multi-level modeling of cell biological systems Carsten Maus, Stefan Rybacki, Adelinde M Uhrmacher BMC Systems Biology 2011, 5:166 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ML-Rules is a formal modeling language for implementing rule-based modeling of biochemical systems at multiple levels with bidirectional causation between them, simplifying construction of hierarchical multi-level models for general users.
	2. 4507 Accesses	Research article A deterministic map of Waddington's epigenetic landscape for cell fate specification Sudin Bhattacharya, Qiang Zhang, Melvin E Andersen BMC Systems Biology 2011, 5:85 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A visualization of Conrad Waddington’s classic "epigenetic landscape" is derived from a gene regulatory network controlling cell fate, and is presented as a quasi-potential surface that provides a predictive model of cellular differentiation.
	3. 4025 Accesses	Research article The smallest chemical reaction system with bistability Thomas Wilhelm BMC Systems Biology 2009, 3:90 (8 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The smallest bistable system contains just two reactants and four irreversible reactions, and it reveals that the necessary conditions for bistability are positive feedback, filtering out small stimuli, and a mechanism to prevent 'explosion' of the system.
	4. 3805 Accesses	Research article A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili BMC Systems Biology 2011, 5:180 (31 October 2011) Abstract \| Full text \| PDF \| PubMed
	5. 3787 Accesses	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 \| 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.
	6. 3474 Accesses	Research article Initial characterization of the human central proteome Thomas R Burkard, Melanie Planyavsky, Ines Kaupe, Florian P Breitwieser, Tilmann Bürckstümmer, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge BMC Systems Biology 2011, 5:17 (26 January 2011) Abstract \| Full text \| PDF \| PubMed
	7. 3352 Accesses	Review A review of imaging techniques for systems biology Armen R Kherlopian, Ting Song, Qi Duan, Mathew A Neimark, Ming J Po, John K Gohagan, Andrew F Laine BMC Systems Biology 2008, 2:74 (12 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	8. 3248 Accesses	Research article Biological interaction networks are conserved at the module level Guy E Zinman, Shan Zhong, Ziv Bar-Joseph BMC Systems Biology 2011, 5:134 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	9. 3187 Accesses	Research article Critical assessment of human metabolic pathway databases: a stepping stone for future integration Miranda D Stobbe, Sander M Houten, Gerbert A Jansen, Antoine HC van Kampen, Perry D Moerland BMC Systems Biology 2011, 5:165 (14 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10. 3117 Accesses	Research article The evolution of metabolic networks of E. coli David J Baumler, Roman G Peplinski, Jennifer L Reed, Jeremy D Glasner, Nicole T Perna BMC Systems Biology 2011, 5:182 (1 November 2011) Abstract \| Full text \| PDF \| PubMed
	11. 3076 Accesses	Research article Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 Caroline B Milne, James A Eddy, Ravali Raju, Soroush Ardekani, Pan-Jun Kim, Ryan S Senger, Yong-Su Jin, Hans P Blaschek, Nathan D Price BMC Systems Biology 2011, 5:130 (16 August 2011) Abstract \| Full text \| PDF \| PubMed
	12. 3043 Accesses	Software TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks Paul A Jensen, Kyla A Lutz, Jason A Papin BMC Systems Biology 2011, 5:147 (23 September 2011) Abstract \| Full text \| PDF \| PubMed
	13. 3027 Accesses	Research article Proteomic patterns of cervical cancer cell lines, a network perspective Juan Higareda-Almaraz, María Enríquez-Gasca, Magdalena Hernández-Ortiz, Osbaldo Resendis-Antonio, Sergio Encarnación-Guevara BMC Systems Biology 2011, 5:96 (22 June 2011) Abstract \| Full text \| PDF \| PubMed
	14. 2999 Accesses	Research article Receptor downregulation and desensitization enhance the information processing ability of signalling receptors Harish Shankaran, H Steven Wiley, Haluk Resat BMC Systems Biology 2007, 1:48 (9 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Downregulation and desensitization of cell surface receptors creates a strong link between variation in ligands over time and cell signaling; in an engineering analogy, this is an overdamped oscillator, with receptor attenuation stabilizing the system.
	15. 2983 Accesses	Research article A Novel microRNA and transcription factor mediated regulatory network in schizophrenia An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao BMC Systems Biology 2010, 4:10 (15 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16. 2942 Accesses	Research article Integrative network analysis reveals active microRNAs and their functions in gastric cancer Chien-Wei Tseng, Chen-Ching Lin, Chiung-Nien Chen, Hsuan-Cheng Huang, Hsueh-Fen Juan BMC Systems Biology 2011, 5:99 (26 June 2011) Abstract \| Full text \| PDF \| PubMed
	17. 2856 Accesses	Research article targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis Karthik Raman, Kalidas Yeturu, Nagasuma Chandra BMC Systems Biology 2008, 2:109 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18. 2808 Accesses	Report Network target for screening synergistic drug combinations with application to traditional Chinese medicine Shao Li, Bo Zhang, Ningbo Zhang BMC Systems Biology 2011, 5(Suppl 1):S10 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Medicine \| F1000 Biology
	19. 2756 Accesses	Research article Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian J Theis BMC Systems Biology 2011, 5:21 (31 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	20. 2704 Accesses	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 \| 1 comment
	21. 2663 Accesses	Research article Network analysis of microRNAs and their regulation in human ovarian cancer Sebastian Schmeier, Ulf Schaefer, Magbubah Essack, Vladimir B Bajic BMC Systems Biology 2011, 5:183 (3 November 2011) Abstract \| Full text \| PDF \| PubMed
	22. 2656 Accesses	Research article Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis Carola Huthmacher, Andreas Hoppe, Sascha Bulik, Hermann-Georg Holzhütter BMC Systems Biology 2010, 4:120 (31 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23. 2653 Accesses	Research article A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory Juan Nogales, Bernhard Ø Palsson, Ines Thiele BMC Systems Biology 2008, 2:79 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24. 2634 Accesses	Research article Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii Nanette R Boyle, John A Morgan BMC Systems Biology 2009, 3:4 (7 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25. 2596 Accesses	Research article The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions Ottar Rolfsson, Bernhard Ø Palsson, Ines Thiele BMC Systems Biology 2011, 5:155 (1 October 2011) Abstract \| Full text \| PDF \| PubMed