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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 2 |
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Methodology article
  
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure
Yunlei Li, Dick de Ridder, Marco JL de Groot, Marcel JT Reinders
BMC Systems Biology 2008, 2:111 (24December2008)
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Research article
Essential operating principles for tumor spheroid growth
Jesse A Engelberg, Glen EP Ropella, C Anthony Hunt
BMC Systems Biology 2008, 2:110 (23December2008)
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Research article
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
Karthik Raman, Kalidas Yeturu, Nagasuma Chandra
BMC Systems Biology 2008, 2:109 (19December2008)
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Research article
Signal duration and the time scale dependence of signal integration in biochemical pathways
Jason W Locasale
BMC Systems Biology 2008, 2:108 (17December2008)
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Research article
Modelling phagosomal lipid networks that regulate actin assembly
Mark K hnel, Luis S Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths, Jens Reich
BMC Systems Biology 2008, 2:107 (5December2008)
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Research article
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
Andr Fujita, Luciana Rodrigues Gomes, Jo o Ricardo Sato, Rui Yamaguchi, Carlos Eduardo Thomaz, Mari Cleide Sogayar, Satoru Miyano
BMC Systems Biology 2008, 2:106 (5December2008)
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Research article
RNA silencing can explain chlorotic infection patterns on plant leaves
Marian AC Groenenboom, Paulien Hogeweg
BMC Systems Biology 2008, 2:105 (30November2008)
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Software
Arena3D: visualization of biological networks in 3D
Georgios A Pavlopoulos, Se n I O'Donoghue, Venkata P Satagopam, Theodoros G Soldatos, Evangelos Pafilis, Reinhard Schneider
BMC Systems Biology 2008, 2:104 (28November2008)
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Research article
A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises
Bor-Sen Chen, Yu-Te Chang
BMC Systems Biology 2008, 2:103 (27November2008)
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Research article
From pathway to population  a multiscale model of juxtacrine EGFR-MAPK signalling
DC Walker, NT Georgopoulos, J Southgate
BMC Systems Biology 2008, 2:102 (26November2008)
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Research article
Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks
Christopher R Bauer, Andrew M Epstein, Sarah J Sweeney, Daniela C Zarnescu, Giovanni Bosco
BMC Systems Biology 2008, 2:101 (25November2008)
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Research article
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles
Pawel Durek, Dirk Walther
BMC Systems Biology 2008, 2:100 (25November2008)
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Research article
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks
Gwenael Kervizic, Laurent Corcos
BMC Systems Biology 2008, 2:99 (24November2008)
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Research article
Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model
Mariana Ben tez, Carlos Espinosa-Soto, Pablo Padilla-Longoria, Elena R Alvarez-Buylla
BMC Systems Biology 2008, 2:98 (17November2008)
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Research article
Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: Modeling and experiments reveal hierarchy in glucose repression
Vinay Prasad, KV Venkatesh
BMC Systems Biology 2008, 2:97 (17November2008)
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Research article
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans
I King Jordan, Lee S Katz, Dee R Denver, J Todd Streelman
BMC Systems Biology 2008, 2:96 (13November2008)
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Methodology article
Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Angela P Presson, Eric M Sobel, Jeanette C Papp, Charlyn J Suarez, Toni Whistler, Mangalathu S Rajeevan, Suzanne D Vernon, Steve Horvath
BMC Systems Biology 2008, 2:95 (6November2008)
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Research article
Genetic noise control via protein oligomerization
Cheol-Min Ghim, Eivind Almaas
BMC Systems Biology 2008, 2:94 (3November2008)
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Research article
An in silico method for detecting overlapping functional modules from composite biological networks
Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos
BMC Systems Biology 2008, 2:93 (1November2008)
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Research article
Dynamics of receptor and protein transducer homodimerisation
Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer
BMC Systems Biology 2008, 2:92 (31October2008)
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Software
ALC: automated reduction of rule-based models
Markus Koschorreck, Ernst Dieter Gilles
BMC Systems Biology 2008, 2:91 (31October2008)
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Research article
From protein interactions to functional annotation: graph alignment in Herpes
Michal Kol , Michael L ssig, Johannes Berg
BMC Systems Biology 2008, 2:90 (28October2008)
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Research article
Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli
Jiangjun Cui, Jaap A Kaandorp, Catherine M Lloyd
BMC Systems Biology 2008, 2:89 (24October2008)
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Research article
Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle
Ashley J Waardenberg, Antonio Reverter, Christine A Wells, Brian P Dalrymple
BMC Systems Biology 2008, 2:88 (22October2008)
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Research article
A quantitative estimation of the global translational activity in logarithmically growing yeast cells
Tobias von der Haar
BMC Systems Biology 2008, 2:87 (16October2008)
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Research article
Robust simplifications of multiscale biochemical networks
Ovidiu Radulescu, Alexander N Gorban, Andrei Zinovyev, Alain Lilienbaum
BMC Systems Biology 2008, 2:86 (14October2008)
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Research article
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
Maxime Durot, Fran ois Le F vre, Vronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schachter
BMC Systems Biology 2008, 2:85 (7October2008)
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Methodology article
Network evaluation from the consistency of the graph structure with the measured data
Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
BMC Systems Biology 2008, 2:84 (1October2008)
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Research article
Parameter estimation and determinability analysis applied to Drosophila gap gene circuits
Maksat Ashyraliyev, Johannes Jaeger, Joke G Blom
BMC Systems Biology 2008, 2:83 (25September2008)
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Research article
Origin of structural difference in metabolic networks with respect to temperature
Kazuhiro Takemoto, Tatsuya Akutsu
BMC Systems Biology 2008, 2:82 (22September2008)
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Research article
Employing conservation of co-expression to improve functional inference
Carsten O Daub, Erik LL Sonnhammer
BMC Systems Biology 2008, 2:81 (22September2008)
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Research article
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks
Michael Hsing, Kendall Grant Byler, Artem Cherkasov
BMC Systems Biology 2008, 2:80 (16September2008)
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Research article
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Juan Nogales, Bernhard  Palsson, Ines Thiele
BMC Systems Biology 2008, 2:79 (16September2008)
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Methodology article
Exact model reduction of combinatorial reaction networks
Holger Conzelmann, Dirk Fey, Ernst D Gilles
BMC Systems Biology 2008, 2:78 (28August2008)
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Research article
A compartment model of VEGF distribution in blood, healthy and diseased tissues
Marianne O Stefanini, Florence TH Wu, Feilim Mac Gabhann, Aleksander S Popel
BMC Systems Biology 2008, 2:77 (19August2008)
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Software
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle
Derek Ruths, Luay Nakhleh, Prahlad T Ram
BMC Systems Biology 2008, 2:76 (19August2008)
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Research article
Explaining oscillations and variability in the p53-Mdm2 system
Carole J Proctor, Douglas A Gray
BMC Systems Biology 2008, 2:75 (18August2008)
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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 (12August2008)
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Research article
On the origin of distribution patterns of motifs in biological networks
Arun S Konagurthu, Arthur M Lesk
BMC Systems Biology 2008, 2:73 (12August2008)
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Research article
Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang
BMC Systems Biology 2008, 2:72 (10August2008)
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Research article
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana
BMC Systems Biology 2008, 2:71 (7August2008)
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Research article
An enzyme-centric approach for modelling non-linear biological complexity
Chin-Rang Yang
BMC Systems Biology 2008, 2:70 (1August2008)
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Research article
Structural similarity of genetically interacting proteins
Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J Wolfson, Roded Sharan
BMC Systems Biology 2008, 2:69 (31July2008)
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Methodology article
Modeling cellular deformations using the level set formalism
Liu Yang, Janet C Effler, Brett L Kutscher, Sarah E Sullivan, Douglas N Robinson, Pablo A Iglesias
BMC Systems Biology 2008, 2:68 (24July2008)
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Methodology article
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer K nig
BMC Systems Biology 2008, 2:67 (24July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GridCell: a stochastic particle-based biological system simulator
Laurier Boulianne, Sevin Al Assaad, Michel Dumontier, Warren J Gross
BMC Systems Biology 2008, 2:66 (23July2008)
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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)
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Methodology article
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data
Zuyi Huang, Fatih Senocak, Arul Jayaraman, Juergen Hahn
BMC Systems Biology 2008, 2:64 (17July2008)
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Methodology article
Multiway modeling and analysis in stem cell systems biology
Blent Yener, Evrim Acar, Pheadra Aguis, Kristin Bennett, Scott L Vandenberg, George E Plopper
BMC Systems Biology 2008, 2:63 (14July2008)
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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)
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Methodology article
Exhaustive identification of steady state cycles in large stoichiometric networks
Jeremiah Wright, Andreas Wagner
BMC Systems Biology 2008, 2:61 (11July2008)
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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 Penttil, Hannu Maaheimo
BMC Systems Biology 2008, 2:60 (9July2008)
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Research article
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures
Joo ML Dias, Adrian Oehmen, Lusa S Serafim, Paulo C Lemos, Maria AM Reis, Rui Oliveira
BMC Systems Biology 2008, 2:59 (8July2008)
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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] [Cited on BioMed Central]
Research article
Seeded Bayesian Networks: Constructing genetic networks from microarray data
Amira Djebbari, John Quackenbush
BMC Systems Biology 2008, 2:57 (4July2008)
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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)
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Software
The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright, Andreas Wagner
BMC Systems Biology 2008, 2:55 (29June2008)
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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)
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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)
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Research article
A computational analysis of protein-protein interaction networks in neurodegenerative diseases
Joaqun Go i, Francisco J Esteban, Nieves Vlez de Mendizbal, Jorge Sepulcre, Sergio Ardanza-Trevijano, Ion Agirrezabal, Pablo Villoslada
BMC Systems Biology 2008, 2:52 (20June2008)
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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)
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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)
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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)
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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)
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Commentary
Optimization in computational systems biology
Julio R Banga
BMC Systems Biology 2008, 2:47 (28May2008)
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Research article
Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network
Susanne Reymann, Jrgen Borlak
BMC Systems Biology 2008, 2:46 (22May2008)
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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)
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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)
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Research article
Mathematical modeling and analysis of insulin clearance in vivo
Markus Koschorreck, Ernst Dieter Gilles
BMC Systems Biology 2008, 2:43 (13May2008)
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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)
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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)
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Methodology article
Exploiting the pathway structure of metabolism to reveal high-order epistasis
Marcin Imielinski, Calin Belta
BMC Systems Biology 2008, 2:40 (30April2008)
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Software
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Andreas Drger, Nadine Hassis, Jochen Supper, Adrian Schrder, Andreas Zell
BMC Systems Biology 2008, 2:39 (30April2008)
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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)
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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)
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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)
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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)
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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)
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Methodology article
Extracting expression modules from perturbational gene expression compendia
Steven Maere, Patrick Van Dijck, Martin Kuiper
BMC Systems Biology 2008, 2:33 (10April2008)
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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)
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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] [Cited on BioMed Central]
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)
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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)
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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] [Cited on BioMed Central]
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)
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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)
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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)
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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)
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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)
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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)
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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 Bessires, Stphane Aymerich, Vincent Fromion
BMC Systems Biology 2008, 2:20 (26February2008)
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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)
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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)
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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)
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