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	1. 1141 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 \| Provisional PDF \| PubMed
	2. 791 Accesses	Research article A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud, David J Sherman BMC Systems Biology 2012, 6:35 (4 May 2012) Abstract \| Provisional PDF \| PubMed
	3. 714 Accesses	Research article Gene regulation is governed by a core network in hepatocellular carcinoma Zuguang Gu, Chenyu Zhang, Jin Wang BMC Systems Biology 2012, 6:32 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	4. 677 Accesses	Research article Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network Rachel S Koh, Mary J Dunlop BMC Systems Biology 2012, 6:47 (20 May 2012) Abstract \| Provisional PDF \| PubMed
	5. 645 Accesses	Research article Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico Michael J McAnulty, Jiun Y Yen, Benjamin G Freedman, Ryan S Senger BMC Systems Biology 2012, 6:42 (14 May 2012) Abstract \| Provisional PDF \| PubMed
	6. 595 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 \| Provisional PDF \| 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.
	7. 592 Accesses	Research article Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert-Streib BMC Systems Biology 2012, 6:38 (14 May 2012) Abstract \| Provisional PDF \| PubMed
	8. 578 Accesses	Software FluxMap: a VANTED Add-on for the visual exploration of flux distributions in biological networks Hendrik Rohn, Anja Hartmann, Astrid Junker, Björn H Junker, Falk Schreiber BMC Systems Biology 2012, 6:33 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	9. 578 Accesses	Research article From Networks of Protein Interactions to Networks of Functional Dependencies Davide Luciani, Gianfranco Bazzoni BMC Systems Biology 2012, 6:44 (20 May 2012) Abstract \| Provisional PDF \| PubMed
	10. 576 Accesses	Research article A Network Perspective on Metabolic Inconsistency Nikolaus Sonnenschein, José Felipe Golib Dzib, Annick Lesne, Sebastian Eilebrecht, Sheerazed Boulkroun, Maria-Christina Zennaro, Arndt Benecke, Marc-Thorsten Hütt BMC Systems Biology 2012, 6:41 (14 May 2012) Abstract \| Provisional PDF \| PubMed
	11. 553 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 \| 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.
	12. 540 Accesses	Software STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies Iain Hepburn, Weiliang Chen, Stefan Wils, Erik De Schutter BMC Systems Biology 2012, 6:36 (10 May 2012) Abstract \| Provisional PDF \| PubMed
	13. 538 Accesses	Research article Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease Arvind K Chavali, Anna S Blazier, Jose L Tlaxca, Paul A Jensen, Richard D Pearson, Jason A Papin BMC Systems Biology 2012, 6:27 (27 April 2012) Abstract \| Provisional PDF \| PubMed
	14. 509 Accesses	Research article The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions Philipp Thomas, Arthur V Straube, Ramon Grima BMC Systems Biology 2012, 6:39 (14 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new method, called the slow-scale linear noise approximation (ssLNA), provides a simple and accurate means of performing stochastic model reduction under timescale separation conditions, giving more accurate noise estimates that the heuristic stochastic simulation algorithm.
	15. 502 Accesses	Research article Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions Jeffrey D Orth, Bernhard Ø Palsson BMC Systems Biology 2012, 6:30 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	16. 499 Accesses	Research article Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells Scott B Crown, Woo Suk Ahn, Maciek R Antoniewicz BMC Systems Biology 2012, 6:43 (16 May 2012) Abstract \| Provisional PDF \| PubMed
	17. 498 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
	18. 498 Accesses	Research article Morphogengineering roots: comparing mechanisms of morphogen gradient formation Veronica A. Grieneisen, Ben Scheres, Paulien Hogeweg, Athanasius F. M. Maree BMC Systems Biology 2012, 6:37 (14 May 2012) Abstract \| Provisional PDF \| PubMed
	19. 471 Accesses	Research article Revisiting the variation of clustering coefficient of biological networks suggests new modular structure Dapeng Hao, Cong Ren, ChuanXing Li BMC Systems Biology 2012, 6:34 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	20. 447 Accesses	Methodology article A Specialized ODE Integrator for Efficient Computation of Parameter Sensitivities Pedro Gonnet, Sotiris Dimopoulos, Lukas Widmer, Joerg Stelling BMC Systems Biology 2012, 6:46 (20 May 2012) Abstract \| Provisional PDF \| PubMed
	21. 425 Accesses	Research article Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis Jason E McDermott, Deborah L Diamond, Courtney Corley, Angela L Rasmussen, Michael G Katze, Katrina M Waters BMC Systems Biology 2012, 6:28 (30 April 2012) Abstract \| Provisional PDF \| PubMed
	22. 396 Accesses	Research article Redox balance is key to explaining full vs. partial switching to low-yield metabolism Milan JA van Hoek, Roeland MH Merks BMC Systems Biology 2012, 6:22 (24 March 2012) Abstract \| Provisional PDF \| PubMed
	23. 391 Accesses	Research article Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster Man-Sun Kim, Jeong-Rae Kim, Dongsan Kim, Arthur D. Lander, Kwang-Hyun Cho BMC Systems Biology 2012, 6:31 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	24. 374 Accesses	Research article Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth Seung Bum Sohn, Tae Yong Kim, Jay H. Lee, Sang Yup Lee BMC Systems Biology 2012, 6:49 (25 May 2012) Abstract \| Provisional PDF \| PubMed
	25. 367 Accesses	Research article Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling Jan Schellenberger, Daniel C Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A Scott, Jennifer L Reed, Andrei L Osterman, Bernhard ∅ Palsson BMC Systems Biology 2012, 6:9 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new Monte Carlo sampling algorithm determines the capability of 13C labeling experiments to resolve fluxes in metabolic networks, and is demonstrated on an E. coli isotopomer model to determine reaction fluxes.