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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Erik Alexandersson
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| | BMC Systems Biology, Volume 2 |
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Research article
 
Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways
Rajat K De, Mouli Das, Subhasis Mukhopadhyay
BMC Systems Biology 2008, 2:65 (18July2008)
[Abstract] [Provisional PDF]
Methodology article
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data
Zuyi (Jacky) Huang, Fatih Senocak, Arul Jayaraman, Juergen Hahn
BMC Systems Biology 2008, 2:64 (17July2008)
[Abstract] [Provisional PDF]
Methodology article
Multiway modeling and analysis in stem cell systems biology
Bulent Yener, Evrim Acar, Phaedra Agius, Kristin Bennett, Scott L Vandenberg, George E Plopper
BMC Systems Biology 2008, 2:63 (14July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
A systems approach to model natural variation in reactive properties of bacterial ribosomes
Julius H Jackson, Thomas M Schmidt, Patricia A Herring
BMC Systems Biology 2008, 2:62 (13July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Exhaustive identification of steady state cycles in large stoichiometric networks
Jeremiah Wright, Andreas Wagner
BMC Systems Biology 2008, 2:61 (11July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttila, Hannu Maaheimo
BMC Systems Biology 2008, 2:60 (9July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures
Joao M L Dias, Adrian Oehmen, Luisa S Serafim, Paulo C Lemos, Maria A M Reis, Rui Oliveira
BMC Systems Biology 2008, 2:59 (8July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Commentary
Short time-series microarray analysis: Methods and challenges
Xuewei Wang, Ming Wu, Zheng Li, Christina Chan
BMC Systems Biology 2008, 2:58 (7July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Seeded Bayesian Networks: Constructing genetic networks from microarray data
Amira Djebbari, John Quackenbush
BMC Systems Biology 2008, 2:57 (4July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets
Liang-Hui Chu, Bor-Sen Chen
BMC Systems Biology 2008, 2:56 (30June2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright, Andreas Wagner
BMC Systems Biology 2008, 2:55 (29June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The effects of protein interactions, gene essentiality and regulatory regions on expression variation
Linqi Zhou, Xiaotu Ma, Fengzhu Sun
BMC Systems Biology 2008, 2:54 (26June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Systematic reconstruction of TRANSPATH data into Cell System Markup Language
Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
BMC Systems Biology 2008, 2:53 (23June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A computational analysis of protein-protein interaction networks in neurodegenerative diseases
Joaqu n Go i, Francisco J Esteban, Nieves V lez de Mendiz bal, Jorge Sepulcre, Sergio Ardanza-Trevijano, Ion Agirrezabal, Pablo Villoslada
BMC Systems Biology 2008, 2:52 (20June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
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 (18June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Can single knockouts accurately single out gene functions?
David Deutscher, Isaac Meilijson, Stefan Schuster, Eytan Ruppin
BMC Systems Biology 2008, 2:50 (18June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion
XiaoDong Huang, Jean YJ Wang, Xin Lu
BMC Systems Biology 2008, 2:49 (13June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach
Najl V Valeyev, Declan G Bates, Pat Heslop-Harrison, Ian Postlethwaite, Nikolay V Kotov
BMC Systems Biology 2008, 2:48 (2June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Commentary
Optimization in computational systems biology
Julio R Banga
BMC Systems Biology 2008, 2:47 (28May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network
Susanne Reymann, J rgen Borlak
BMC Systems Biology 2008, 2:46 (22May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Defining a Modular Signalling Network from the Fly Interactome
Ana s Baudot, Jean-Baptiste Angelelli, Alain Gunoche, Bernard Jacq, Christine Brun
BMC Systems Biology 2008, 2:45 (19May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
William J Heuett, Daniel A Beard, Hong Qian
BMC Systems Biology 2008, 2:44 (15May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Mathematical modeling and analysis of insulin clearance in vivo
Markus Koschorreck, Ernst Dieter Gilles
BMC Systems Biology 2008, 2:43 (13May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A Dominated Coupling From The Past algorithm for the stochastic
simulation of networks of biochemical reactions
Martin Hemberg, Mauricio Barahona
BMC Systems Biology 2008, 2:42 (8May2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Extraction of elementary rate constants from global network analysis of E. coli central metabolism
Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko, Michael Ellison
BMC Systems Biology 2008, 2:41 (7May2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Exploiting the pathway structure of metabolism to reveal high-order epistasis
Marcin Imielinski, Calin Belta
BMC Systems Biology 2008, 2:40 (30April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Andreas Dr ger, Nadine Hassis, Jochen Supper, Adrian Schr der, Andreas Zell
BMC Systems Biology 2008, 2:39 (30April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
Julio Vera, Julie Bachmann, Andrea C Pfeifer, Verena Becker, Jose A Hormiga, Nestor V Torres Darias, Jens Timmer, Ursula Klingmller, Olaf Wolkenhauer
BMC Systems Biology 2008, 2:38 (25April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Phenotype prediction in regulated metabolic networks
Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich
BMC Systems Biology 2008, 2:37 (25April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A logic-based diagram of signalling pathways central to macrophage activation
Sobia Raza, Kevin A Robertson, Paul A Lacaze, David Page, Anton J Enright, Peter Ghazal, Tom C Freeman
BMC Systems Biology 2008, 2:36 (23April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Parameter optimization in S-system models
Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza R Vasconcelos, Eberhard O Voit, Jonas S Almeida
BMC Systems Biology 2008, 2:35 (16April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Using genetic markers to orient the edges in quantitative trait networks: The NEO software
Jason E Aten, Tova F Fuller, Aldons J Lusis, Steve Horvath
BMC Systems Biology 2008, 2:34 (15April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Extracting expression modules from perturbational gene expression compendia
Steven Maere, Patrick Van Dijck, Martin Kuiper
BMC Systems Biology 2008, 2:33 (10April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis
Hannah Schmidt-Glenewinkel, Ivayla Vacheva, Daniela Hoeller, Ivan Dikic, Roland Eils
BMC Systems Biology 2008, 2:32 (7April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
Karen E Thum, Michael J Shin, Rodrigo A Gutirrez, Indrani Mukherjee, Manpreet S Katari, Damion Nero, Dennis Shasha, Gloria M Coruzzi
BMC Systems Biology 2008, 2:31 (4April2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
Youfang Cao, Jie Liang
BMC Systems Biology 2008, 2:30 (29March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification
Tae Hoon Yang, Oliver Frick, Elmar Heinzle
BMC Systems Biology 2008, 2:29 (26March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The dynamics and efficacy of antiviral RNA silencing: A model study
Marian AC Groenenboom, Paulien Hogeweg
BMC Systems Biology 2008, 2:28 (26March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency
Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nystrom, Milton H Saier Jr, Vic Norris
BMC Systems Biology 2008, 2:27 (25March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Hybrid optimization method with general switching strategy for parameter estimation
Eva Balsa-Canto, Martin Peifer, Julio R Banga, Jens Timmer, Christian Fleck
BMC Systems Biology 2008, 2:26 (24March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
One hub-one process: a tool based view on regulatory network topology
Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen
BMC Systems Biology 2008, 2:25 (4March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
OptCircuit: An optimization based method for computational design of genetic circuits
Madhukar S Dasika, Costas D Maranas
BMC Systems Biology 2008, 2:24 (3March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Interactive analysis of systems biology molecular expression data
Mingwu Zhang, Qi Ouyang, Alan Stephenson, Michael D Kane, David E Salt, Sunil Prabhakar, John Burgner, Charles Buck, Xiang Zhang
BMC Systems Biology 2008, 2:23 (29February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Global parameter search reveals design principles of the mammalian circadian clock
James CW Locke, P l O Westermark, Achim Kramer, Hanspeter Herzel
BMC Systems Biology 2008, 2:22 (29February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response
Areejit Samal, Sanjay Jain
BMC Systems Biology 2008, 2:21 (29February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
Anne Goelzer, Fadia Bekkal Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessi res, Stphane Aymerich, Vincent Fromion
BMC Systems Biology 2008, 2:20 (26February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility
Divyaswetha Peddinti, Bindu Nanduri, Abdullah Kaya, Jean M Feugang, Shane C Burgess, Erdogan Memili
BMC Systems Biology 2008, 2:19 (22February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Dissecting the logical types of network control in gene expression profiles
Carsten Marr, Marcel Geertz, Marc-Thorsten Htt, Georgi Muskhelishvili
BMC Systems Biology 2008, 2:18 (19February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
Ana Paula Oliveira, Kiran Raosaheb Patil, Jens Nielsen
BMC Systems Biology 2008, 2:17 (8February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants
David J Weston, Lee E Gunter, Alistair Rogers, Stan D Wullschleger
BMC Systems Biology 2008, 2:16 (4February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Equilibrium model selection: dTTP induced R1 dimerization
Tomas Radivoyevitch
BMC Systems Biology 2008, 2:15 (4February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Three factors underlying incorrect in silico predictions of essential metabolic genes
Scott A Becker, Bernhard O Palsson
BMC Systems Biology 2008, 2:14 (4February2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae
Lev Guzmn-Vargas, Moiss Santilln
BMC Systems Biology 2008, 2:13 (31January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
On cycles in the transcription network of Saccharomyces cerevisiae
Jieun Jeong, Piotr Berman
BMC Systems Biology 2008, 2:12 (31January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Evidence of probabilistic behaviour in protein interaction networks
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
BMC Systems Biology 2008, 2:11 (31January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of gene interactions associated with disease from gene expression data using synergy networks
John Watkinson, Xiaodong Wang, Tian Zheng, Dimitris Anastassiou
BMC Systems Biology 2008, 2:10 (30January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Dynamical pathway analysis
Hao Xiong, Yoonsuck Choe
BMC Systems Biology 2008, 2:9 (27January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Regulatory network reconstruction using an integral additive model with flexible kernel functions
Eugene Novikov, Emmanuel Barillot
BMC Systems Biology 2008, 2:8 (24January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Impact of the solvent capacity constraint on E. coli metabolism
Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-Lszl Barabsi, Lszl G Boros, Zoltn N Oltvai
BMC Systems Biology 2008, 2:7 (23January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression
Dov J Stekel, Dafyd J Jenkins
BMC Systems Biology 2008, 2:6 (18January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Commentary
Biomolecular network querying: a promising approach in systems biology
Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
BMC Systems Biology 2008, 2:5 (18January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction
Raimo Franke, Melanie Mller, Nicole Wundrack, Ernst-Dieter Gilles, Steffen Klamt, Thilo Khne, Michael Naumann
BMC Systems Biology 2008, 2:4 (14January2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Annotating novel genes by integrating synthetic lethals and genomic information
Daniel Schner, Markus Kalisch, Christian Leisner, Lukas Meier, Marc Sohrmann, Mahamadou Faty, Yves Barral, Matthias Peter, Wilhelm Gruissem, Peter Bhlmann
BMC Systems Biology 2008, 2:3 (14January |
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