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Networks and information flow

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  1. Gene expression profiles and protein dynamics in single cells have a large cell-to-cell variability due to intracellular noise. Intracellular fluctuations originate from two sources: intrinsic noise due to the pr...

    Authors: Jaewook Joo, Steven J Plimpton and Jean-Loup Faulon

    Citation: BMC Systems Biology 2013 7:45

    Content type: Research article

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  2. In genomics, highly relevant gene interaction (co-expression) networks have been constructed by finding significant pair-wise correlations between genes in expression datasets. These networks are then mined to...

    Authors: F Alex Feltus, Stephen P Ficklin, Scott M Gibson and Melissa C Smith

    Citation: BMC Systems Biology 2013 7:44

    Content type: Methodology article

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  3. The cyclic AMP-Protein Kinase A (cAMP-PKA) pathway is an evolutionarily conserved signal transduction mechanism that regulates cellular growth and differentiation in animals and fungi. We present a mathematica...

    Authors: Kevin Gonzales, Ömür Kayıkçı, David G Schaeffer and Paul M Magwene

    Citation: BMC Systems Biology 2013 7:40

    Content type: Research article

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  4. In Saccharomyces cerevisiæ, structural bistability generates a bimodal expression of the galactose uptake genes (GAL) when exposed to low and high glucose concentrations. This indicates that yeast cells can decid...

    Authors: Luca Salerno, Carlo Cosentino, Alessio Merola, Declan G Bates and Francesco Amato

    Citation: BMC Systems Biology 2013 7:39

    Content type: Methodology article

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  5. Hematopoietic ontogeny is characterized by overlapping waves of primitive, fetal definitive, and adult definitive erythroid lineages. Our aim is to identify differences in the transcriptional control of these ...

    Authors: Emily Greenfest-Allen, Jeffrey Malik, James Palis and Christian J Stoeckert Jr

    Citation: BMC Systems Biology 2013 7:38

    Content type: Research article

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  6. Meiosis is the sexual reproduction process common to eukaryotes. The diploid yeast Saccharomyces cerevisiae undergoes meiosis in sporulation medium to form four haploid spores. Initiation of the process is tightl...

    Authors: Debjit Ray, Yongchun Su and Ping Ye

    Citation: BMC Systems Biology 2013 7:37

    Content type: Research article

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  7. The genome-scale metabolic model of Saccharomyces cerevisiae , first presented in 2003, was the first genome-scale network reconstruction for a eukaryotic organism. Since then continuous efforts have been made in...

    Authors: Tobias Österlund, Intawat Nookaew, Sergio Bordel and Jens Nielsen

    Citation: BMC Systems Biology 2013 7:36

    Content type: Research article

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  9. Essential hypertension (EH) is a complex disease as a consequence of interaction between environmental factors and genetic background, but the pathogenesis of EH remains elusive. The emerging tools of network ...

    Authors: Jihua Ran, Hui Li, Jianfeng Fu, Ling Liu, Yanchao Xing, Xiumei Li, Hongming Shen, Yan Chen, Xiaofang Jiang, Yan Li and Huiwu Li

    Citation: BMC Systems Biology 2013 7:32

    Content type: Research article

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  12. The unfolded protein response (UPR) is a major signalling cascade acting in the quality control of protein folding in the endoplasmic reticulum (ER). The cascade is known to play an accessory role in a range o...

    Authors: Kamil Erguler, Myrtani Pieri and Constantinos Deltas

    Citation: BMC Systems Biology 2013 7:16

    Content type: Research article

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  15. The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma factor, σB. Stress p...

    Authors: Ulf W Liebal, Thomas Millat, Jon Marles-Wright, Richard J Lewis and Olaf Wolkenhauer

    Citation: BMC Systems Biology 2013 7:3

    Content type: Research article

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  16. Focal adhesions are integrin-based cell-matrix contacts that transduce and integrate mechanical and biochemical cues from the environment. They develop from smaller and more numerous focal complexes under the ...

    Authors: Max Hoffmann and Ulrich S Schwarz

    Citation: BMC Systems Biology 2013 7:2

    Content type: Research article

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  17. Graph-based modularity analysis has emerged as an important tool to study the functional organization of biological networks. However, few methods are available to study state-dependent changes in network modu...

    Authors: GauthamVivek Sridharan, Michael Yi, Soha Hassoun and Kyongbum Lee

    Citation: BMC Systems Biology 2012 6:155

    Content type: Research article

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  18. Signal transduction plays a fundamental role in the understanding of cellular physiology. The bacterial phosphotransferase system (PTS) together with the PEP/pyruvate node in central metabolism represents a si...

    Authors: Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, VitorMartins dos Santos and Víctorde Lorenzo

    Citation: BMC Systems Biology 2012 6:149

    Content type: Research article

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  19. Network inference is an important tool to reveal the underlying interactions of biological systems. In the liver, a complex system of transcription factors is active to distribute signals and induce the cellul...

    Authors: Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke and Rolf Gebhardt

    Citation: BMC Systems Biology 2012 6:147

    Content type: Methodology article

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  20. Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular commun...

    Authors: Bor-Sen Chen and Chih-Yuan Hsu

    Citation: BMC Systems Biology 2012 6:136

    Content type: Research article

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  21. Cell cycle process of budding yeast (Saccharomyces cerevisiae) consists of four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to the G1 stationary phase through a sequence ...

    Authors: Changki Hong, Minho Lee, Dongsup Kim, Dongsan Kim, Kwang-Hyun Cho and Insik Shin

    Citation: BMC Systems Biology 2012 6:129

    Content type: Research article

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  22. Apoptosis is an essential property of all higher organisms that involves extremely complex signaling pathways. Mathematical modeling provides a rigorous integrative approach for analyzing and understanding suc...

    Authors: Ji-Young Hong, Geun-Hong Kim, Jun-Woo Kim, Soon-Sung Kwon, Eisuke F Sato, Kwang-Hyun Cho and Eun Bo Shim

    Citation: BMC Systems Biology 2012 6:122

    Content type: Research article

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  26. The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the ...

    Authors: Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer and Yamir Moreno

    Citation: BMC Systems Biology 2012 6:110

    Content type: Research article

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  27. The skeleton of complex systems can be represented as networks where vertices represent entities, and edges represent the relations between these entities. Often it is impossible, or expensive, to determine th...

    Authors: Neil R Clark, Ruth Dannenfelser, Christopher M Tan, Michael E Komosinski and Avi Ma'ayan

    Citation: BMC Systems Biology 2012 6:89

    Content type: Research article

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  29. In this paper, we present a framework for improving the accuracy of fixed-step methods for Monte Carlo simulation of discrete stochastic chemical kinetics. Stochasticity is ubiquitous in many areas of cell bio...

    Authors: Tamás Székely Jr, Kevin Burrage, Radek Erban and Konstantinos C Zygalakis

    Citation: BMC Systems Biology 2012 6:85

    Content type: Methodology article

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  30. The three layer mitogen activated protein kinase (MAPK) signaling cascade exhibits different designs of interactions between its kinases and phosphatases. While the sequential interactions between the three ki...

    Authors: Uddipan Sarma and Indira Ghosh

    Citation: BMC Systems Biology 2012 6:82

    Content type: Research article

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  32. Constraint-based analysis of genome-scale metabolic models typically relies upon maximisation of a cellular objective function such as the rate or efficiency of biomass production. Whilst this assumption may b...

    Authors: Dave Lee, Kieran Smallbone, Warwick B Dunn, Ettore Murabito, Catherine L Winder, Douglas B Kell, Pedro Mendes and Neil Swainston

    Citation: BMC Systems Biology 2012 6:73

    Content type: Methodology article

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  33. It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption). In this case the...

    Authors: Philipp Thomas, Arthur V Straube and Ramon Grima

    Citation: BMC Systems Biology 2012 6:39

    Content type: Research article

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  34. Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, ...

    Authors: Man-Sun Kim, Jeong-Rae Kim, Dongsan Kim, Arthur D Lander and Kwang-Hyun Cho

    Citation: BMC Systems Biology 2012 6:31

    Content type: Research article

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  35. Gene regulatory networks control the global gene expression and the dynamics of protein output in living cells. In multicellular organisms, transcription factors and microRNAs are the major families of gene re...

    Authors: Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan and Hsuan-Cheng Huang

    Citation: BMC Systems Biology 2012 6:18

    Content type: Research article

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  36. Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of problems...

    Authors: Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle and Ursula Kummer

    Citation: BMC Systems Biology 2012 6:14

    Content type: Methodology article

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  38. Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, wet-lab approaches alone to counter drug resistance have so far still achieved limited ...

    Authors: Liang-Chun Chen, Hsiang-Yuan Yeh, Cheng-Yu Yeh, Carlos Roberto Arias and Von-Wun Soo

    Citation: BMC Systems Biology 2012 6:5

    Content type: Research article

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  39. Constructing predictive dynamic models of interacting signalling networks remains one of the great challenges facing systems biology. While detailed dynamical data exists about individual pathways, the task of...

    Authors: Adaoha EC Ihekwaba and Sean Sedwards

    Citation: BMC Systems Biology 2011 5:203

    Content type: Methodology article

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  40. In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined...

    Authors: Matthew AA Grant, Chiara Saggioro, Ulisse Ferrari, Bruno Bassetti, Bianca Sclavi and Marco Cosentino Lagomarsino

    Citation: BMC Systems Biology 2011 5:201

    Content type: Research article

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  41. MicroRNA (miRNA) is a class of small RNAs of ~22nt which play essential roles in many crucial biological processes and numerous human diseases at post-transcriptional level of gene expression. It has been reve...

    Authors: Jin Wang, Martin Haubrock, Kun-Ming Cao, Xu Hua, Chen-Yu Zhang, Edgar Wingender and Jie Li

    Citation: BMC Systems Biology 2011 5:199

    Content type: Research article

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  44. Modeling the Calvin-Benson cycle has a history in the field of theoretical biology. Anyone who intends to model this system will look at existing models to adapt, refine and improve them. With the goal to stud...

    Authors: Jiri Jablonsky, Hermann Bauwe and Olaf Wolkenhauer

    Citation: BMC Systems Biology 2011 5:185

    Content type: Research article

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  45. The family of TGF-β ligands is large and its members are involved in many different signaling processes. These signaling processes strongly differ in type with TGF-β ligands eliciting both sustained or transient ...

    Authors: Geraldine Cellière, Georgios Fengos, Marianne Hervé and Dagmar Iber

    Citation: BMC Systems Biology 2011 5:184

    Content type: Research article

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  47. Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconst...

    Authors: Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson and Iman Famili

    Citation: BMC Systems Biology 2011 5:180

    Content type: Research article

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  49. The inference of biological networks from high-throughput data has received huge attention during the last decade and can be considered an important problem class in systems biology. However, it has been recog...

    Authors: Gábor Szederkényi, Julio R Banga and Antonio A Alonso

    Citation: BMC Systems Biology 2011 5:177

    Content type: Methodology article

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  50. C4 plants such as corn and sugarcane assimilate atmospheric CO2 into biomass by means of the C4 carbon fixation pathway. We asked how PEP formation rate, a key step in the carbon fixation pathway, might work at a...

    Authors: Yuval Hart, Avraham E Mayo, Ron Milo and Uri Alon

    Citation: BMC Systems Biology 2011 5:171

    Content type: Research article

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BMC Systems Biology

ISSN: 1752-0509

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