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	1. 7850 Accesses	Research article An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver Linglin Xie, Brent Weichel, Joyce Ohm, Ke Zhang BMC Systems Biology 2011, 5(Suppl 3):S4 (23 December 2011) Abstract \| Full text \| PDF \| 3 comments
	2. 6465 Accesses	Database AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka BMC Systems Biology 2012, 6:52 (30 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary AlzPathway is a publicly available database collating known Alzheimer's disease intra, inter and extra cellular signalling pathways into a comprehensive pathway map, providing a useful resource in deciphering Alzheimer's disease pathogenesis.
	3. 5362 Accesses	Research article Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks Daniel C Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M Burke, Douglas A Lauffenburger, Peter K Sorger BMC Systems Biology 2012, 6:29 (1 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	4. 5136 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
	5. 5092 Accesses	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
	6. 4931 Accesses	Research article Understanding network concepts in modules Jun Dong, Steve Horvath BMC Systems Biology 2007, 1:24 (4 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	7. 4394 Accesses	Research article Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui BMC Systems Biology 2012, 6:68 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	8. 4299 Accesses	Methodology article Computational codon optimization of synthetic gene for protein expression Bevan Chung, Dong-Yup Lee BMC Systems Biology 2012, 6:134 (20 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method for codon usage optimization in artificial gene synthesis, optimizing use of both individual codon usage and codon context approaches, is predicted to lead to improved in vitro heterologous protein expression in biotechnology applications.
	9. 4290 Accesses	Research article Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker BMC Systems Biology 2012, 6:55 (4 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10. 4262 Accesses	Research article Low-complexity regions within protein sequences have position-dependent roles Alain Coletta, John W Pinney, David Solís, James Marsh, Steve R Pettifer, Teresa K Attwood BMC Systems Biology 2010, 4:43 (13 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	11. 3961 Accesses	Research article Time-resolved metabolomics reveals metabolic modulation in rice foliage Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita BMC Systems Biology 2008, 2:51 (18 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	12. 3895 Accesses	Research article Crosstalk between transcription factors and microRNAs in human protein interaction network Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang BMC Systems Biology 2012, 6:18 (13 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	13. 3881 Accesses	Research article A reconfigurable NAND/NOR genetic logic gate Angel Goñi-Moreno, Martyn Amos BMC Systems Biology 2012, 6:126 (18 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel genetic circuit is proposed and computationally tested that can be dynamically reconfigured to serve as either a NAND or NOR genetic logic gate in either single cells or cell populations.
	14. 3833 Accesses	Methodology article A general co-expression network-based approach to gene expression analysis: comparison and applications Jianhua Ruan, Angela K Dean, Weixiong Zhang BMC Systems Biology 2010, 4:8 (2 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	15. 3770 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
	16. 3721 Accesses	Research article Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen BMC Systems Biology 2012, 6:24 (4 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new genome-scale metabolic model of the industrially important yeast species Pichia stipitis and Pichia pastoris enables the modeling of growth on xylose, which is essential to optimising the production of ethanol from biomass.
	17. 3579 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 \| Cited on BioMed Central
	18. 3512 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
	19. 3489 Accesses	Research article A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen Galina Lebedeva, Azusa Yamaguchi, Simon P Langdon, Kenneth Macleod, David J Harrison BMC Systems Biology 2012, 6:138 (8 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A minimal mechanistic model of estrogen receptor alpha-dependent gene expression, predicts complex non-linear effects in transcriptional response to natural hormone 17 beta-estradiol and its external competitor tamoxifen under a range of biologically plausible parameter values.
	20. 3383 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
	21. 3278 Accesses	Software CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel Goncalves, Melody K Morris, Martijn van Iersel, Douglas A Lauffenburger, Julio Saez-Rodriguez BMC Systems Biology 2012, 6:133 (18 October 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Cited on BioMed Central \| Editor’s summary CellNOptR is an R based software package for the training of signaling networks extracted from prior knowledge using experimental data, which extends the existing CellNetOptimizer MATLAB package with further logical formalisms.
	22. 3276 Accesses	Methodology article Improving metabolic flux predictions using absolute gene expression data Dave Lee, Kieran Smallbone, Warwick B Dunn, Ettore Murabito, Catherine L Winder, Douglas B Kell, Pedro Mendes, Neil Swainston BMC Systems Biology 2012, 6:73 (19 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23. 3268 Accesses	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.
	24. 3265 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 \| Cited on BioMed Central
	25. 3226 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