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Volume 5 (2011) - May 2011

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Methodology article   Open Access Highly Accessed

Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes

Jen-hwa Chu, Ross Lazarus, Vincent J Carey, Benjamin A Raby BMC Systems Biology 2011, 5:89 (31 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Systematic quantitative characterization of cellular responses induced by multiple signals

Ibrahim Al-Shyoukh, Fuqu Yu, Jiaying Feng, Karen Yan, Steven Dubinett, Chih-Ming Ho, Jeff S Shamma, Ren Sun BMC Systems Biology 2011, 5:88 (30 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

Steven X Ge BMC Systems Biology 2011, 5:87 (29 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks

Angel Alvarez, Peter J Woolf BMC Systems Biology 2011, 5:86 (27 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

A deterministic map of Waddington's epigenetic landscape for cell fate specification

Sudin Bhattacharya, Qiang Zhang, Melvin E Andersen BMC Systems Biology 2011, 5:85 (27 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A visualization of Conrad Waddington’s classic "epigenetic landscape" is derived from a gene regulatory network controlling cell fate, and is presented as a quasi-potential surface that provides a predictive model of cellular differentiation.

Methodology article   Open Access Highly Accessed

Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems

Rongling Wu, Jiguo Cao, Zhongwen Huang, Zhong Wang, Junyi Gai, Eduardo Vallejos BMC Systems Biology 2011, 5:84 (27 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access Highly Accessed

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M C Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A P Martins dos Santos, Jing Wang BMC Systems Biology 2011, 5:83 (25 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization

Weijun Luo, Michael S Friedman, Kurt D Hankenson, Peter J Woolf BMC Systems Biology 2011, 5:82 (23 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Symbolic flux analysis for genome-scale metabolic networks

David W Schryer, Marko Vendelin, Pearu Peterson BMC Systems Biology 2011, 5:81 (23 May 2011)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access

Improved functional overview of protein complexes using inferred epistatic relationships

Colm Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney BMC Systems Biology 2011, 5:80 (23 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network

Xin Yao, Han Hao, Yanda Li, Shao Li BMC Systems Biology 2011, 5:79 (20 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

A General Life History Theory for Effects of Caloric Restriction on Health Maintenance

Chen Hou, Kendra Bolt, Aviv Bergman BMC Systems Biology 2011, 5:78 (19 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana

Stuart Meier, Oren Tzfadia, Ratnakar Vallabhaneni, Chris Gehring, Eleanore T Wurtzel BMC Systems Biology 2011, 5:77 (19 May 2011)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access Highly Accessed

Network-based scoring system for genome-scale metabolic reconstructions

M Ángeles Serrano, Francesc Sagués BMC Systems Biology 2011, 5:76 (19 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Expanding a dynamic flux balance model of yeast fermentation to genome-scale

Felipe A Vargas, Francisco Pizarro, J Ricardo Pérez-Correa, Eduardo Agosin BMC Systems Biology 2011, 5:75 (19 May 2011)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access Highly Accessed

Structurally robust biological networks

Franco Blanchini, Elisa Franco BMC Systems Biology 2011, 5:74 (17 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions

Bo Li, Weiguo Cao, Jizhong Zhou, Feng Luo BMC Systems Biology 2011, 5:73 (17 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition

Xiaolin Xiao, Neil Dawson, Lynsey MacIntyre, Brian J Morris, Judith A Pratt, David G Watson, Desmond J Higham BMC Systems Biology 2011, 5:72 (16 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

Michael T Klann, Alexei Lapin, Matthias Reuss BMC Systems Biology 2011, 5:71 (14 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

Peter E Larsen, Avinash Sreedasyam, Geetika Trivedi, Gopi K Podila, Leland J Cseke, Frank R Collart BMC Systems Biology 2011, 5:70 (13 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

Tina Toni, Goran Jovanovic, Maxime Huvet, Martin Buck, Michael PH Stumpf BMC Systems Biology 2011, 5:69 (12 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Ian M Overton, Shirley Graham, Katherine A Gould, Jason Hinds, Catherine H Botting, Sally Shirran, Geoffrey J Barton, Peter J Coote BMC Systems Biology 2011, 5:68 (12 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access Highly Accessed

A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer

Changyu Shen, Yiwen Huang, Yunlong Liu, Guohua Wang, Yuming Zhao, Zhiping Wang, Mingxiang Teng, Yadong Wang, David A Flockhart, Todd C Skaar, Pearlly Yan, Kenneth P Nephew, Tim HM Huang, Lang Li BMC Systems Biology 2011, 5:67 (9 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access Highly Accessed

A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes

Joachim Bucher, Stephan Riedmaier, Anke Schnabel, Katrin Marcus, Gabriele Vacun, Thomas S Weiss, Wolfgang E Thasler, Andreas K Nüssler, Ulrich M Zanger, Matthias Reuss BMC Systems Biology 2011, 5:66 (6 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

A protein network-guided screen for cell cycle regulators in Drosophila

Stephen T Guest, Jingkai Yu, Dongmei Liu, Julie A Hines, Maria A Kashat, Russell L Finley BMC Systems Biology 2011, 5:65 (6 May 2011)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access

Thermodynamically consistent model calibration in chemical kinetics

Garrett Jenkinson, John Goutsias BMC Systems Biology 2011, 5:64 (6 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

A computational model of the hypothalamic - pituitary - gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17β-trenbolone

Zhenhong Li, Kevin J Kroll, Kathleen M Jensen, Daniel L Villeneuve, Gerald T Ankley, Jayne V Brian, María S Sepúlveda, Edward F Orlando, James M Lazorchak, Mitchell Kostich, Brandon Armstrong, Nancy D Denslow, Karen H Watanabe BMC Systems Biology 2011, 5:63 (5 May 2011)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Transcriptional robustness and protein interactions are associated in yeast

Michaël Bekaert, Gavin C Conant BMC Systems Biology 2011, 5:62 (5 May 2011)

Abstract | Full text | PDF | PubMed

Methodology article   Open Access Highly Accessed

Inference of gene regulatory networks from time series by Tsallis entropy

Fabrício Lopes, Evaldo A de Oliveira, Roberto M Cesar BMC Systems Biology 2011, 5:61 (5 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling

Yu-Fang Jin, Hai- Chao Han, Jamie Berger, Qiuxia Dai, Merry L Lindsey BMC Systems Biology 2011, 5:60 (5 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article   Open Access

Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis

Prakash Vempati, Aleksander S Popel, Feilim Mac Gabhann BMC Systems Biology 2011, 5:59 (2 May 2011)

Abstract | Full text | PDF | PubMed


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