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  1. Calmodulin is an important multifunctional molecule that regulates the activities of a large number of proteins in the cell. Calcium binding induces conformational transitions in calmodulin that make it specif...

    Authors: Najl V Valeyev, Declan G Bates, Pat Heslop-Harrison, Ian Postlethwaite and Nikolay V Kotov

    Citation: BMC Systems Biology 2008 2:48

    Content type: Research article

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  2. Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on appli...

    Authors: Julio R Banga

    Citation: BMC Systems Biology 2008 2:47

    Content type: Commentary

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  3. The transcriptional regulator c-Myc is the most frequently deregulated oncogene in human tumors. Targeted overexpression of this gene in mice results in distinct types of lung adenocarcinomas. By using microar...

    Authors: Susanne Reymann and Jürgen Borlak

    Citation: BMC Systems Biology 2008 2:46

    Content type: Research article

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  4. Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involv...

    Authors: Anaïs Baudot, Jean-Baptiste Angelelli, Alain Guénoche, Bernard Jacq and Christine Brun

    Citation: BMC Systems Biology 2008 2:45

    Content type: Research article

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  5. Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitativ...

    Authors: William J Heuett, Daniel A Beard and Hong Qian

    Citation: BMC Systems Biology 2008 2:44

    Content type: Research article

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  6. Analyzing the dynamics of insulin concentration in the blood is necessary for a comprehensive understanding of the effects of insulin in vivo. Insulin removal from the blood has been addressed in many studies. Th...

    Authors: Markus Koschorreck and Ernst Dieter Gilles

    Citation: BMC Systems Biology 2008 2:43

    Content type: Research article

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  7. As computational performance steadily increases, so does interest in extending one-particle-per-molecule models to larger physiological problems. Such models however require elementary rate constants to calcul...

    Authors: Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko and Michael Ellison

    Citation: BMC Systems Biology 2008 2:41

    Content type: Research article

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  8. The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the...

    Authors: Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder and Andreas Zell

    Citation: BMC Systems Biology 2008 2:39

    Content type: Software

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  9. The amplification of signals, defined as an increase in the intensity of a signal through networks of intracellular reactions, is considered one of the essential properties in many cell signalling pathways. De...

    Authors: Julio Vera, Julie Bachmann, Andrea C Pfeifer, Verena Becker, Jose A Hormiga, Nestor V Torres Darias, Jens Timmer, Ursula Klingmüller and Olaf Wolkenhauer

    Citation: BMC Systems Biology 2008 2:38

    Content type: Research article

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  10. Due to the growing amount of biological knowledge that is incorporated into metabolic network models, their analysis has become more and more challenging. Here, we examine the capabilities of the recently intr...

    Authors: Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio and Peter Dittrich

    Citation: BMC Systems Biology 2008 2:37

    Content type: Research article

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  11. The complex yet flexible cellular response to pathogens is orchestrated by the interaction of multiple signalling and metabolic pathways. The molecular regulation of this response has been studied in great det...

    Authors: Sobia Raza, Kevin A Robertson, Paul A Lacaze, David Page, Anton J Enright, Peter Ghazal and Tom C Freeman

    Citation: BMC Systems Biology 2008 2:36

    Content type: Research article

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  12. The inverse problem of identifying the topology of biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this challenge here through the parameterization...

    Authors: Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza R Vasconcelos, Eberhard O Voit and Jonas S Almeida

    Citation: BMC Systems Biology 2008 2:35

    Content type: Research article

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  13. Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinic...

    Authors: Jason E Aten, Tova F Fuller, Aldons J Lusis and Steve Horvath

    Citation: BMC Systems Biology 2008 2:34

    Content type: Methodology article

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  14. The Epidermal Growth Factor (EGF) receptor has been shown to internalize via clathrin-independent endocytosis (CIE) in a ligand concentration dependent manner. From a modeling point of view, this resembles an ...

    Authors: Hannah Schmidt-Glenewinkel, Ivayla Vacheva, Daniela Hoeller, Ivan Dikic and Roland Eils

    Citation: BMC Systems Biology 2008 2:32

    Content type: Research article

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  15. Light and carbon are two important interacting signals affecting plant growth and development. The mechanism(s) and/or genes involved in sensing and/or mediating the signaling pathways involving these interact...

    Authors: Karen E Thum, Michael J Shin, Rodrigo A Gutiérrez, Indrani Mukherjee, Manpreet S Katari, Damion Nero, Dennis Shasha and Gloria M Coruzzi

    Citation: BMC Systems Biology 2008 2:31

    Content type: Research article

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  16. Stochasticity plays important roles in many molecular networks when molecular concentrations are in the range of 0.1 μ M to 10n M (about 100 to 10 copies in a cell). The chemical master equation provides a fundam...

    Authors: Youfang Cao and Jie Liang

    Citation: BMC Systems Biology 2008 2:30

    Content type: Research article

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  17. The advantages of grouping enzymes into metabolons and into higher order structures have long been debated. To quantify these advantages, we have developed a stochastic automaton that allows experiments to be ...

    Authors: Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nystrom, Milton H Saier Jr and Vic Norris

    Citation: BMC Systems Biology 2008 2:27

    Content type: Research article

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  18. Modeling and simulation of cellular signaling and metabolic pathways as networks of biochemical reactions yields sets of non-linear ordinary differential equations. These models usually depend on several param...

    Authors: Eva Balsa-Canto, Martin Peifer, Julio R Banga, Jens Timmer and Christian Fleck

    Citation: BMC Systems Biology 2008 2:26

    Content type: Research article

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  19. Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular c...

    Authors: Mingwu Zhang, Qi Ouyang, Alan Stephenson, Michael D Kane, David E Salt, Sunil Prabhakar, John Burgner, Charles Buck and Xiang Zhang

    Citation: BMC Systems Biology 2008 2:23

    Content type: Software

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  20. Virtually all living organisms have evolved a circadian (~24 hour) clock that controls physiological and behavioural processes with exquisite precision throughout the day/night cycle. The suprachiasmatic nucle...

    Authors: James CW Locke, Pål O Westermark, Achim Kramer and Hanspeter Herzel

    Citation: BMC Systems Biology 2008 2:22

    Content type: Research article

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  21. Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Esch...

    Authors: Areejit Samal and Sanjay Jain

    Citation: BMC Systems Biology 2008 2:21

    Content type: Research article

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  22. Few genome-scale models of organisms focus on the regulatory networks and none of them integrates all known levels of regulation. In particular, the regulations involving metabolite pools are often neglected. ...

    Authors: Anne Goelzer, Fadia Bekkal Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessières, Stéphane Aymerich and Vincent Fromion

    Citation: BMC Systems Biology 2008 2:20

    Content type: Research article

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  23. Male infertility is a major problem for mammalian reproduction. However, molecular details including the underlying mechanisms of male fertility are still not known. A thorough understanding of these mechanism...

    Authors: Divyaswetha Peddinti, Bindu Nanduri, Abdullah Kaya, Jean M Feugang, Shane C Burgess and Erdogan Memili

    Citation: BMC Systems Biology 2008 2:19

    Content type: Research article

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  24. In the bacterium Escherichia coli the transcriptional regulation of gene expression involves both dedicated regulators binding specific DNA sites with high affinity and also global regulators – abundant DNA archi...

    Authors: Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt and Georgi Muskhelishvili

    Citation: BMC Systems Biology 2008 2:18

    Content type: Research article

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  25. Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-...

    Authors: Ana Paula Oliveira, Kiran Raosaheb Patil and Jens Nielsen

    Citation: BMC Systems Biology 2008 2:17

    Content type: Research article

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  26. One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and ...

    Authors: David J Weston, Lee E Gunter, Alistair Rogers and Stan D Wullschleger

    Citation: BMC Systems Biology 2008 2:16

    Content type: Research article

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  27. Biochemical equilibria are usually modeled iteratively: given one or a few fitted models, if there is a lack of fit or over fitting, a new model with additional or fewer parameters is then fitted, and the proc...

    Authors: Tomas Radivoyevitch

    Citation: BMC Systems Biology 2008 2:15

    Content type: Methodology article

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  28. Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has no...

    Authors: Joseph Ivanic, Anders Wallqvist and Jaques Reifman

    Citation: BMC Systems Biology 2008 2:11

    Content type: Research article

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  29. Analysis of microarray data has been used for the inference of gene-gene interactions. If, however, the aim is the discovery of disease-related biological mechanisms, then the criterion for defining such inter...

    Authors: John Watkinson, Xiaodong Wang, Tian Zheng and Dimitris Anastassiou

    Citation: BMC Systems Biology 2008 2:10

    Content type: Research article

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  30. Although a great deal is known about one gene or protein and its functions under different environmental conditions, little information is available about the complex behaviour of biological networks subject t...

    Authors: Hao Xiong and Yoonsuck Choe

    Citation: BMC Systems Biology 2008 2:9

    Content type: Research article

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  31. Obtaining quantitative predictions for cellular metabolic activities requires the identification and modeling of the physicochemical constraints that are relevant at physiological growth conditions. Molecular ...

    Authors: Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G Boros and Zoltán N Oltvai

    Citation: BMC Systems Biology 2008 2:7

    Content type: Research article

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  32. Many prokaryotic transcription factors repress their own transcription. It is often asserted that such regulation enables a cell to homeostatically maintain protein abundance. We explore the role of negative s...

    Authors: Dov J Stekel and Dafyd J Jenkins

    Citation: BMC Systems Biology 2008 2:6

    Content type: Research article

    Published on:

  33. The hepatocyte growth factor (HGF) stimulates mitogenesis, motogenesis, and morphogenesis in a wide range of tissues, including epithelial cells, on binding to the receptor tyrosine kinase c-Met. Abnormal c-Me...

    Authors: Raimo Franke, Melanie Müller, Nicole Wundrack, Ernst-Dieter Gilles, Steffen Klamt, Thilo Kähne and Michael Naumann

    Citation: BMC Systems Biology 2008 2:4

    Content type: Research article

    Published on:

  34. Large scale screening for synthetic lethality serves as a common tool in yeast genetics to systematically search for genes that play a role in specific biological processes. Often the amounts of data resulting...

    Authors: Daniel Schöner, Markus Kalisch, Christian Leisner, Lukas Meier, Marc Sohrmann, Mahamadou Faty, Yves Barral, Matthias Peter, Wilhelm Gruissem and Peter Bühlmann

    Citation: BMC Systems Biology 2008 2:3

    Content type: Research article

    Published on:

  35. Autoantigens have been reported in a variety of tumors, providing insight into the interplay between malignancies and the immune response, and also giving rise to novel diagnostic and therapeutic concepts. Why...

    Authors: Ronald Rapberger, Paul Perco, Cornelia Sax, Thomas Pangerl, Christian Siehs, Dietmar Pils, Andreas Bernthaler, Arno Lukas, Bernd Mayer and Michael Krainer

    Citation: BMC Systems Biology 2008 2:2

    Content type: Research article

    Published on:

2017 Journal Metrics

  • Citation Impact
    2.05 - 2-year Impact Factor
    2.505 - 5-year Impact Factor
    0.689 - Source Normalized Impact per Paper (SNIP)
    1.109 - SCImago Journal Rank (SJR)

    Usage 
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    Social Media Impact
    523 mentions

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