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Editor-in-Chief Melissa Norton, MD
Biology Editor Penelope Webb, PhD
In-house Editor Tim Sands PhD
Welcome to BMC Systems Biology published by BioMed Central
BMC Systems Biology is an open access journal publishing original peer-reviewed research articles in experimental and theoretical aspects of the function of biological systems at the molecular, cellular or organismal level, in particular those addressing the engineering of biological systems, network modeling, quantitative analyses and the integration of different levels of information.
BMC Systems Biology (ISSN 1752-0509) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.
BMC Systems Biology 2009, 3 :103
ReTrace finds branching pathways in atom-level representations of genome-scale metabolic networks by considering combinations of the shortest linear pathways, scaling better than constraint-based modeling and avoiding shortfalls of graph-theoretic approaches.
BMC Systems Biology 2009, 3 :97
A Boolean network model for liver cells has four stable system states, two for survival and two for apoptosis, and is validated by successful predictions of the outcome of viral infection and varying growth substrate signals in the presence of FasL.
BMC Systems Biology 2009, 3 :90
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.
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Methodology article
Using the ratio of means as the effect size measure in combining results of microarray experiments Pingzhao Hu, Celia MT Greenwood, Joseph Beyene BMC Systems Biology 2009, 3 :106 (5 [Abstract ] [Provisional PDF ]
Research article
A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides Mark AJ Roberts, Elias August, Abdullah Hamadeh, Philip K Maini, Patrick E McSharry, Judith P Armitage, Antonis Papachristodoulou BMC Systems Biology 2009, 3 :105 (31 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose Paula Jouhten, Esa Pitkanen, Tiina Pakula, Markku Saloheimo, Merja Penttila, Hannu Maaheimo BMC Systems Biology 2009, 3 :104 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Methodology article
Inferring branching pathways in genome-scale metabolic networks Esa Pitkanen, Paula Jouhten, Juho Rousu BMC Systems Biology 2009, 3 :103 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ] [Cited on BioMed Central ]
Research article
How to identify essential genes from molecular networks? Gabriel del Rio, Dirk Kosch BMC Systems Biology 2009, 3 :102 (13 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Research article
Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments Ramon Grima BMC Systems Biology 2009, 3 :101 (8 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway Richard J Orton, Michiel E Adriaens, Amelie Gormand, Oliver E Sturm, Walter Kolch, David R Gilbert BMC Systems Biology 2009, 3 :100 (5 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Software
An editor for pathway drawing and data visualization in the Biopathways Workbench Robert W Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam BMC Systems Biology 2009, 3 :99 (2 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Methodology article
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling Dominik M Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A Lauffenburger, Steffen Klamt, Fabian J Theis BMC Systems Biology 2009, 3 :98 (28 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Research article
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar BMC Systems Biology 2009, 3 :97 (22 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Research article
Elucidation of functional consequences of signalling pathway interactions Adaoha E C Ihekwaba, Phuong T Nguyen, Corrado Priami BMC Bioinformatics 2009, 10 :370 (6 [Abstract ] [Provisional PDF ]
Research
Proteins related to lipoprotein profile were identified using a pharmaco-proteomic approach as markers for growth response to growth hormone (GH) treatment in short prepubertal children Bjorn Andersson, Gunnel Hellgren, Andreas F.M Nierop, Ze'ev Hochberg, Kerstin Albertsson-Wikland Proteome Science 2009, 7 :40 (2 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research
Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi Analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10 :R121 (2 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells Yi Zhang, Lee Opresko, Harish Shankaran, William B. Chrisler, H. Steven Wiley, Haluk Resat BMC Cell Biology 2009, 10 :78 (31 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research
TinkerCell: modular CAD tool for synthetic biology Deepak Chandran, Frank T Bergmann, Herbert M Sauro Journal of Biological Engineering 2009, 3 :19 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research
Changes in timber haul emissions in the context of shifting forest management and infrastructure Sean P Healey, Jock A Blackard, Todd A Morgan, Dan Loeffler, Greg Jones, Jon Songster, Jason P Brandt, Gretchen G Moisen, Larry T DeBlander Carbon Balance and Management 2009, 4 :9 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Research article
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy Zheng Rong Yang BMC Bioinformatics 2009, 10 :361 (29 [Abstract ] [Provisional PDF ] [PubMed ] [Related articles ]
Editorial
Welcome to Automated Experimentation: a new open access journal David Robertson, Siu-wai Leung, Dietlind Gerloff Automated Experimentation 2009, 1 :1 (29 [Abstract ] [Provisional PDF ]
Methodology article
Analysis and comparison of very large metagenomes with fast clustering and functional annotation Weizhong Li BMC Bioinformatics 2009, 10 :359 (28 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
Software
Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB Aristotelis Chatziioannou, Panagiotis Moulos, Fragiskos N Kolisis BMC Bioinformatics 2009, 10 :354 (27 [Abstract ] [Full text ] [PDF ] [PubMed ] [Related articles ]
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