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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Tim Sands PhD
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 BMC Systems Biology, Volume 3
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Methodology article
 
BowTieBuilder: modeling signal transduction pathways
Jochen Supper, Lucia Spangenberg, Hannes Planatscher, Andreas Draeger, Adrian Schroeder, Andreas Zell
BMC Systems Biology 2009, 3:67 (30June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
A systematic design method for robust synthetic biology to satisfy design specifications
Bor-Sen Chen, Chih-Hung Wu
BMC Systems Biology 2009, 3:66 (30June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Clustered microRNAs' coordination in regulating protein-protein interaction network
Xiongying Yuan, Changning Liu, Pengcheng Yang, Shunmin He, Qi Liao, Shuli Kang, Yi Zhao
BMC Systems Biology 2009, 3:65 (26June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Stochastic simulation and analysis of biomolecular reaction networks
John M Frazier, Yaroslav Chushak, Brent Foy
BMC Systems Biology 2009, 3:64 (17June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M C novas, Jos M Peregr n-Alvarez
BMC Systems Biology 2009, 3:63 (16June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains
Patricia Buendia, Giri Narasimhan
BMC Systems Biology 2009, 3:62 (16June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Intervention in gene regulatory networks via greedy control policies based on long-run behavior
Xiaoning Qian, Ivan Ivanov, Noushin Ghaffari, Edward R Dougherty
BMC Systems Biology 2009, 3:61 (15June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
The mathematics of tanning
Josef Thingnes, Leiv Oyehaug, Eivind Hovig, Stig W Omholt
BMC Systems Biology 2009, 3:60 (9June2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"
Damion Nero, Gabriel Krouk, Daniel Tranchina, Gloria M Coruzzi
BMC Systems Biology 2009, 3:59 (6June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
Tom Helikar, Jim A Rogers
BMC Systems Biology 2009, 3:58 (6June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
LeishCyc: a biochemical pathways database for Leishmania major
Maria A Doyle, James I MacRae, David P De Souza, Eleanor C Saunders, Malcolm J McConville, Vladimir A Liki
BMC Systems Biology 2009, 3:57 (5June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Commentary
Computational disease modeling  fact or fiction?
Jesper N Tegnr, Albert Compte, Charles Auffray, Gary An, Gunnar Cedersund, Gilles Clermont, Boris Gutkin, Zoltn N Oltvai, Klaas Enno Stephan, Randy Thomas, Pablo Villoslada
BMC Systems Biology 2009, 3:56 (4June2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism
Jen-hwa Chu, Scott T Weiss, Vincent J Carey, Benjamin A Raby
BMC Systems Biology 2009, 3:55 (27May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Inference of gene pathways using mixture Bayesian networks
Younhee Ko, ChengXiang Zhai, Sandra Rodriguez-Zas
BMC Systems Biology 2009, 3:54 (19May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
Bj rn Goemann, Edgar Wingender, Anatolij P Potapov
BMC Systems Biology 2009, 3:53 (19May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi
Seth B Roberts, Jennifer L Robichaux, Arvind K Chavali, Patricio A Manque, Vladimir Lee, Ana M Lara, Jason A Papin, Gregory A Buck
BMC Systems Biology 2009, 3:52 (16May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems
Lan K Nguyen, Don Kulasiri
BMC Systems Biology 2009, 3:51 (11May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Systematic identifiability testing for unambiguous mechanistic modeling -
application to JAK-STAT, MAP kinase, and NF-kappaB signaling pathway models
Tom Quaiser, Martin Monnigmann
BMC Systems Biology 2009, 3:50 (9May2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
BMC Systems Biology 2009, 3:49 (7May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system
Jos Daz, Elena R Alvarez-Buylla
BMC Systems Biology 2009, 3:48 (5May2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
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