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BMC Systems Biology

ISSN: 1752--0509
Publisher: BioMed Central


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An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis PDF available

Author(s): Li Ru-Dong | Li Yuan-Yuan | Lu Ling-Yi | Ren Cong | Li Yi-Xue | Liu Lei
Volume: 5
Issue: Suppl 1
Year: 2011
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction PDF available

Author(s): Si Jingna | Zhang Zengming | Lin Biaoyang | Schroeder Michael | Huang Bingding
Volume: 5
Issue: Suppl 1
Year: 2011
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression PDF available

Author(s): Zhou Huarong | Saito Shigeru | Piao Guanying | Liu Zhi-Ping | Wang Jiguang | Horimoto Katsuhisa | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger PDF available

Author(s): Omony Jimmy | de Graaff Leo | van Straten Gerrit | van Boxtel Anton
Volume: 5
Issue: Suppl 1
Year: 2011
Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells PDF available

Author(s): Saito Shigeru | Onuma Yasuko | Ito Yuzuru | Tateno Hiroaki | Toyoda Masashi | Hidenori Akutsu | Nishino Koichiro | Chikazawa Emi | Fukawatase Yoshihiro | Miyagawa Yoshitaka | Okita Hajime | Kiyokawa Nobutaka | Shimma Yohichi | Umezawa Akihiro | Hirabayashi Jun | Horimoto Katsuhisa | Asashima Makoto
Volume: 5
Issue: Suppl 1
Year: 2011
Network target for screening synergistic drug combinations with application to traditional Chinese medicine PDF available

Author(s): Li Shao | Zhang Bo | Zhang Ningbo
Volume: 5
Issue: Suppl 1
Year: 2011
A trigger model of apoptosis induced by tumor necrosis factor signaling PDF available

Author(s): Gu Chang | Zhang Junjie | Chen Yingyu | Lei Jinzhi
Volume: 5
Issue: Suppl 1
Year: 2011
Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context PDF available

Author(s): Wang Yong-Cui | Wang Yong | Yang Zhi-Xia | Deng Nai-Yang
Volume: 5
Issue: Suppl 1
Year: 2011
Functional pathway mapping analysis for hypoxia-inducible factors PDF available

Author(s): Chuang Chia-Sheng | Pai Tun-Wen | Hu Chin-Hua | Tzou Wen-Shyong | Dah-Tsyr Chang Margaret | Chang Hao-Teng | Chen Chih-Chia
Volume: 5
Issue: Suppl 1
Year: 2011
Integrating multiple types of data to predict novel cell cycle-related genes PDF available

Author(s): Wang Lin | Hou Lin | Qian Minping | Li Fangting | Deng Minghua
Volume: 5
Issue: Suppl 1
Year: 2011
DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts PDF available

Author(s): Li Zhenhua | Wong Limsoon | Li Jinyan
Volume: 5
Issue: Suppl 1
Year: 2011
Conditional random field approach to prediction of protein-protein interactions using domain information PDF available

Author(s): Hayashida Morihiro | Kamada Mayumi | Song Jiangning | Akutsu Tatsuya
Volume: 5
Issue: Suppl 1
Year: 2011
Regulatory link mapping between organisms PDF available

Author(s): Sharma Rachita | Evans Patricia | Bhavsar Virendrakumar
Volume: 5
Issue: Suppl 1
Year: 2011
Computational systems biology: integration of sequence, structure, network, and dynamics PDF available

Author(s): Wang Yong | Zhang Xiang-Sun | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Multi-equilibrium property of metabolic networks: SSI module PDF available

Author(s): Lei Hong-Bo | Zhang Ji-Feng | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Two-stage flux balance analysis of metabolic networks for drug target identification PDF available

Author(s): Li Zhenping | Wang Rui-Sheng | Zhang Xiang-Sun
Volume: 5
Issue: Suppl 1
Year: 2011
Interactions among oscillatory pathways in NF-kappa B signaling

Author(s): Wang Yunjiao | Paszek Pawel | Horton Caroline | Kell Douglas | White Michael | Broomhead David | Muldoon Mark
Volume: 5
Issue: 1
Year: 2011
A protein network-guided screen for cell cycle regulators in Drosophila

Author(s): Guest Stephen | Yu Jingkai | Liu Dongmei | Hines Julie | Kashat Maria | Finley Russell
Volume: 5
Issue: 1
Year: 2011
A transfer function approach to measuring cell inheritance

Author(s): Rees Paul | Brown M Rowan | Summers Huw | Holton Mark | Errington Rachel | Chappell Sally | Smith Paul
Volume: 5
Issue: 1
Year: 2011
Initial characterization of the human central proteome

Author(s): Burkard Thomas | Planyavsky Melanie | Kaupe Ines | Breitwieser Florian | Bürckstümmer Tilmann | Bennett Keiryn | Superti-Furga Giulio | Colinge Jacques
Volume: 5
Issue: 1
Year: 2011
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

Author(s): Durzinsky Markus | Wagler Annegret | Marwan Wolfgang
Volume: 5
Issue: 1
Year: 2011
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

Author(s): Krumsiek Jan | Suhre Karsten | Illig Thomas | Adamski Jerzy | Theis Fabian
Volume: 5
Issue: 1
Year: 2011
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

Author(s): Yoon Hyunjin | Ansong Charles | McDermott Jason | Gritsenko Marina | Smith Richard | Heffron Fred | Adkins Joshua
Volume: 5
Issue: 1
Year: 2011
Genotype networks, innovation, and robustness in sulfur metabolism

Author(s): Matias Rodrigues João | Wagner Andreas
Volume: 5
Issue: 1
Year: 2011
Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells

Author(s): Jennen Danyel | Ruiz-Aracama Ainhoa | Magkoufopoulou Christina | Peijnenburg Ad | Lommen Arjen | van Delft Joost | Kleinjans Jos
Volume: 5
Issue: 1
Year: 2011
Optimality and evolution of transcriptionally regulated gene expression

Author(s): Poelwijk Frank | Heyning Philip | de Vos Marjon | Kiviet Daniel | Tans Sander
Volume: 5
Issue: 1
Year: 2011
Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products

Author(s): Carinhas Nuno | Bernal Vicente | Teixeira Ana | Carrondo Manuel | Alves Paula | Oliveira Rui
Volume: 5
Issue: 1
Year: 2011
Expanding a dynamic flux balance model of yeast fermentation to genome-scale

Author(s): Vargas Felipe | Pizarro Francisco | Pérez-Correa J Ricardo | Agosin Eduardo
Volume: 5
Issue: 1
Year: 2011
Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance

Author(s): Svensson J Peter | Pesudo Laia | Fry Rebecca | Adeleye Yeyejide | Carmichael Paul | Samson Leona
Volume: 5
Issue: 1
Year: 2011
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Author(s): Overton Ian | Graham Shirley | Gould Katherine | Hinds Jason | Botting Catherine | Shirran Sally | Barton Geoffrey | Coote Peter
Volume: 5
Issue: 1
Year: 2011
Parameter estimation in systems biology models using spline approximation

Author(s): Zhan Choujun | Yeung Lam
Volume: 5
Issue: 1
Year: 2011
Computational modelling elucidates the mechanism of ciliary regulation in health and disease

Author(s): Kotov Nikolay | Bates Declan | Gizatullina Antonina | Gilaziev Bulat | Khairullin Rustem | Chen Michael | Drozdov Ignat | Umezawa Yoshinori | Hundhausen Christian | Aleksandrov Alexey | Yan Xing-gang | Spurgeon Sarah | Smales C Mark | Valeyev Najl
Volume: 5
Issue: 1
Year: 2011
Is RNA-dependent RNA polymerase essential for transposon control?

Author(s): Crombach Anton | Hogeweg Paulien
Volume: 5
Issue: 1
Year: 2011
Fluxomers: a new approach for 13C metabolic flux analysis

Author(s): Srour Orr | Young Jamey | Eldar Yonina
Volume: 5
Issue: 1
Year: 2011
MEMOSys: Bioinformatics platform for genome-scale metabolic models

Author(s): Pabinger Stephan | Rader Robert | Agren Rasmus | Nielsen Jens | Trajanoski Zlatko
Volume: 5
Issue: 1
Year: 2011
Transcriptional robustness and protein interactions are associated in yeast

Author(s): Bekaert Michaël | Conant Gavin
Volume: 5
Issue: 1
Year: 2011
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

Author(s): Satish Kumar Vinay | Ferry James | Maranas Costas
Volume: 5
Issue: 1
Year: 2011
Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

Author(s): Jack John | Wambaugh John | Shah Imran
Volume: 5
Issue: 1
Year: 2011
Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects

Author(s): Wu Wu-Hsiung | Wang Feng-Sheng | Chang Maw-Shang
Volume: 5
Issue: 1
Year: 2011
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism

Author(s): Gupta Shakti | Maurya Mano | Merrill Jr Alfred | Glass Christopher | Subramaniam Shankar
Volume: 5
Issue: 1
Year: 2011
Integrative network analysis reveals active microRNAs and their functions in gastric cancer

Author(s): Tseng Chien-Wei | Lin Chen-Ching | Chen Chiung-Nien | Huang Hsuan-Cheng | Juan Hsueh-Fen
Volume: 5
Issue: 1
Year: 2011
Impact of receptor clustering on ligand binding

Author(s): Caré Bertrand | Soula Hédi
Volume: 5
Issue: 1
Year: 2011
Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation

Author(s): You Tao | Stansfield Ian | Romano M Carmen | Brown Alistair | Coghill George
Volume: 5
Issue: 1
Year: 2011
Systems biology applied to vaccine and immunotherapy development

Author(s): Buonaguro Luigi | Wang Ena | Tornesello Maria | Buonaguro Franco | Marincola Francesco
Volume: 5
Issue: 1
Year: 2011
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

Author(s): Nie Jeff | Stewart Ron | Zhang Hang | Thomson James | Ruan Fang | Cui Xiaoqi | Wei Hairong
Volume: 5
Issue: 1
Year: 2011
Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems

Author(s): Wu Rongling | Cao Jiguo | Huang Zhongwen | Wang Zhong | Gai Junyi | Vallejos Eduardo
Volume: 5
Issue: 1
Year: 2011
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis

Author(s): Lindén Rolf | Eronen Ville-Pekka | Aittokallio Tero
Volume: 5
Issue: 1
Year: 2011
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