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  1. The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks...

    Authors: Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile and Alexander Goesmann

    Citation: BMC Systems Biology 2007 1:55

    Content type: Database

    Published on:

  2. Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regul...

    Authors: Miyako Kusano, Atsushi Fukushima, Masanori Arita, Pär Jonsson, Thomas Moritz, Makoto Kobayashi, Naomi Hayashi, Takayuki Tohge and Kazuki Saito

    Citation: BMC Systems Biology 2007 1:53

    Content type: Research article

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  3. Identifying large gene regulatory networks is an important task, while the acquisition of data through perturbation experiments (e.g., gene switches, RNAi, heterozygotes) is expensive. It is thus desirable to use...

    Authors: Florian Steinke, Matthias Seeger and Koji Tsuda

    Citation: BMC Systems Biology 2007 1:51

    Content type: Methodology article

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  4. Bistability, the capacity to achieve two distinct stable steady states in response to a set of external stimuli, arises within biological systems ranging from the λ phage switch in bacteria to cellular signal tra...

    Authors: Junwei Wang, Jiajun Zhang, Zhanjiang Yuan and Tianshou Zhou

    Citation: BMC Systems Biology 2007 1:50

    Content type: Research article

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  5. In addition to initiating signaling events, the activation of cell surface receptors also triggers regulatory processes that restrict the duration of signaling. Acute attenuation of signaling can be accomplish...

    Authors: Harish Shankaran, H Steven Wiley and Haluk Resat

    Citation: BMC Systems Biology 2007 1:48

    Content type: Research article

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  6. Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biol...

    Authors: Yiannis N Kaznessis

    Citation: BMC Systems Biology 2007 1:47

    Content type: Commentary

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  7. Tissue morphogenesis is a complex process whereby tissue structures self-assemble by the aggregate behaviors of independently acting cells responding to both intracellular and extracellular cues in their envir...

    Authors: Scott H Robertson, Chris K Smith, Anna L Langhans, Sara E McLinden, Matthew A Oberhardt, Karoly R Jakab, Bette Dzamba, Douglas W DeSimone, Jason A Papin and Shayn M Peirce

    Citation: BMC Systems Biology 2007 1:46

    Content type: Research article

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  8. We address the issue of explaining the presence or absence of phase-specific transcription in budding yeast cultures under different conditions. To this end we use a model-based detector of gene expression per...

    Authors: Claes R Andersson, Torgeir R Hvidsten, Anders Isaksson, Mats G Gustafsson and Jan Komorowski

    Citation: BMC Systems Biology 2007 1:45

    Content type: Research article

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  9. Metabolic correlation networks are derived from the covariance of metabolites in replicates of metabolomics experiments. They constitute an interesting intermediate between topology (i.e. the system's architec...

    Authors: Mark Müller-Linow, Wolfram Weckwerth and Marc-Thorsten Hütt

    Citation: BMC Systems Biology 2007 1:44

    Content type: Research article

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  10. Development of multicellular organisms proceeds from a single fertilized egg as the combined effect of countless numbers of cellular interactions among highly dynamic cells. Since at least a reminiscent patter...

    Authors: Takuya T Maeda, Itsuki Ajioka and Kazunori Nakajima

    Citation: BMC Systems Biology 2007 1:43

    Content type: Research article

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  11. Global control influences the regulation of many individual subsystems by superimposed regulator proteins. A prominent example is the control of carbohydrate uptake systems by the transcription factor Crp in Esch...

    Authors: Andreas Kremling, Katja Bettenbrock and Ernst Dieter Gilles

    Citation: BMC Systems Biology 2007 1:42

    Content type: Research article

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  12. To understand the molecular mechanisms underlying important biological processes, a detailed description of the gene products networks involved is required. In order to define and understand such molecular net...

    Authors: André Fujita, João R Sato, Humberto M Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari C Sogayar and Carlos E Ferreira

    Citation: BMC Systems Biology 2007 1:39

    Content type: Methodology article

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  13. Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by massive immunization. Due to its lethality, there are serious concerns about its use as a bioweapon. Here we analyze...

    Authors: Gustavo H Esteves, Ana CQ Simoes, Estevao Souza, Rodrigo A Dias, Raydonal Ospina and Thiago M Venancio

    Citation: BMC Systems Biology 2007 1:38

    Content type: Research article

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  14. The use of correlation networks is widespread in the analysis of gene expression and proteomics data, even though it is known that correlations not only confound direct and indirect associations but also provi...

    Authors: Rainer Opgen-Rhein and Korbinian Strimmer

    Citation: BMC Systems Biology 2007 1:37

    Content type: Methodology article

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  15. A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unkn...

    Authors: Fernando Siso-Nadal, Julien F Ollivier and Peter S Swain

    Citation: BMC Systems Biology 2007 1:36

    Content type: Software

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  16. The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep k...

    Authors: Roberta Alfieri, Ivan Merelli, Ettore Mosca and Luciano Milanesi

    Citation: BMC Systems Biology 2007 1:35

    Content type: Database

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  17. The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidat...

    Authors: Gregory D Amoutzias, Elgar E Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L Robertson and Stephen G Oliver

    Citation: BMC Systems Biology 2007 1:34

    Content type: Research article

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  18. Genetic variation explains a considerable part of observed phenotypic variation in gene expression networks. This variation has been shown to be located both locally (cis) and distally (trans) to the genes being ...

    Authors: Arne B Gjuvsland, Ben J Hayes, Theo HE Meuwissen, Erik Plahte and Stig W Omholt

    Citation: BMC Systems Biology 2007 1:32

    Content type: Research article

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  19. In systems biology, network-based pathway analysis facilitates understanding or designing metabolic systems and enables prediction of metabolic flux distributions. Network-based flux analysis requires consider...

    Authors: Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda and Kazuyuki Shimizu

    Citation: BMC Systems Biology 2007 1:31

    Content type: Methodology article

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  20. The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span seve...

    Authors: Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot and Fabien Jourdan

    Citation: BMC Systems Biology 2007 1:29

    Content type: Software

    Published on:

  21. Systems wide modeling and analysis of signaling networks is essential for understanding complex cellular behaviors, such as the biphasic responses to different combinations of cytokines and growth factors. For...

    Authors: Sergii Ivakhno and J Douglas Armstrong

    Citation: BMC Systems Biology 2007 1:27

    Content type: Research article

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  22. Mycobacterium tuberculosis continues to be a major pathogen in the third world, killing almost 2 million people a year by the most recent estimates. Even in industrialized countries, the emergence of multi-drug r...

    Authors: Neema Jamshidi and Bernhard Ø Palsson

    Citation: BMC Systems Biology 2007 1:26

    Content type: Research article

    Published on:

  23. In humans, connective tissue forms a complex, interconnected network throughout the body that may have mechanosensory, regulatory and signaling functions. Understanding these potentially important phenomena re...

    Authors: Helene M Langevin, Donna M Rizzo, James R Fox, Gary J Badger, Junru Wu, Elisa E Konofagou, Debbie Stevens-Tuttle, Nicole A Bouffard and Martin H Krag

    Citation: BMC Systems Biology 2007 1:25

    Content type: Research article

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  24. Network concepts are increasingly used in biology and genetics. For example, the clustering coefficient has been used to understand network architecture; the connectivity (also known as degree) has been used t...

    Authors: Jun Dong and Steve Horvath

    Citation: BMC Systems Biology 2007 1:24

    Content type: Research article

    Published on:

  25. In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. T...

    Authors: Andreas Hoppe, Sabrina Hoffmann and Hermann-Georg Holzhütter

    Citation: BMC Systems Biology 2007 1:23

    Content type: Methodology article

    Published on:

  26. There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is ra...

    Authors: Tommi Aho, Olli-Pekka Smolander, Jari Niemi and Olli Yli-Harja

    Citation: BMC Systems Biology 2007 1:22

    Content type: Software

    Published on:

  27. Free fatty acids (FFA) and tumor necrosis factor alpha (TNF-α) have been implicated in the pathogenesis of many obesity-related metabolic disorders. When human hepatoblastoma cells (HepG2) were exposed to diff...

    Authors: Zheng Li, Shireesh Srivastava, Xuerui Yang, Sheenu Mittal, Paul Norton, James Resau, Brian Haab and Christina Chan

    Citation: BMC Systems Biology 2007 1:21

    Content type: Methodology 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)

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    Social Media Impact
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