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Empirical systems biology

Section edited by Matteo Pellegrini

This section covers the conduct of experiments or use of empirical data to improve the understanding of the structure and function of biological systems.

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  1. Content type: Research article

    The Drosophila sex determination hierarchy is a classic example of a transcriptional regulatory hierarchy, with sex-specific isoforms regulating morphology and behavior. We use a structural equation modeling appr...

    Authors: Justin M. Fear, Michelle N. Arbeitman, Matthew P. Salomon, Justin E. Dalton, John Tower, Sergey V. Nuzhdin and Lauren M. McIntyre

    Citation: BMC Systems Biology 2015 9:53

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  2. Content type: Research article

    Metabolomic responses to extreme thermal stress have recently been investigated in Drosophila melanogaster. However, a network level understanding of metabolomic responses to longer and less drastic temperature c...

    Authors: Ramkumar Hariharan, Jessica M Hoffman, Ariel S Thomas, Quinlyn A Soltow, Dean P Jones and Daniel EL Promislow

    Citation: BMC Systems Biology 2014 8:139

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  3. Content type: Research article

    Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this...

    Authors: Yeimy Morales, Marta Tortajada, Jesús Picó, Josep Vehí and Francisco Llaneras

    Citation: BMC Systems Biology 2014 8:142

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  4. Content type: Research article

    Cancer metabolism is emerging as an important focus area in cancer research. However, the in vitro cell culture conditions under which much cellular metabolism research is performed differ drastically from in viv...

    Authors: Kathleen A Vermeersch, Lijuan Wang, John F McDonald and Mark P Styczynski

    Citation: BMC Systems Biology 2014 8:134

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  5. Content type: Research article

    Although much is understood about the enzymatic cascades that underlie cellular biosynthesis, comparatively little is known about the rules that determine their cellular organization. We performed a detailed a...

    Authors: Pablo Meyer, Guillermo Cecchi and Gustavo Stolovitzky

    Citation: BMC Systems Biology 2014 8:131

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  6. Content type: Research article

    Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how ...

    Authors: Christopher L Plaisier, Fang-Yin Lo, Justin Ashworth, Aaron N Brooks, Karlyn D Beer, Amardeep Kaur, Min Pan, David J Reiss, Marc T Facciotti and Nitin S Baliga

    Citation: BMC Systems Biology 2014 8:122

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  7. Content type: Research article

    Bacterial spores are important contaminants in food, and the spore forming bacteria are often implicated in food safety and food quality considerations. Spore formation is a complex developmental process invol...

    Authors: Adaoha EC Ihekwaba, Ivan Mura and Gary C Barker

    Citation: BMC Systems Biology 2014 8:119

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  8. Content type: Research article

    Multifactorial diseases such as type 2 diabetes mellitus (T2DM), are driven by a complex network of interconnected mechanisms that translate to a diverse range of complications at the physiological level. To o...

    Authors: Thomas Kelder, Lars Verschuren, Ben van Ommen, Alain J van Gool and Marijana Radonjic

    Citation: BMC Systems Biology 2014 8:108

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  9. Content type: Research article

    Adaptation to stress is critical for survival. The adrenal medulla, the major source of epinephrine, plays an important role in the development of the hyperadenergic state and increased risk for stress associa...

    Authors: Nikolaos A Papanikolaou, Andrej Tillinger, Xiaoping Liu, Athanasios G Papavassiliou and Esther L Sabban

    Citation: BMC Systems Biology 2014 8:100

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  10. Content type: Research article

    Intra-cellular processes of cells at the interface to an implant surface are influenced significantly by their extra-cellular surrounding. Specifically, when growing osteoblasts on titanium surfaces with regul...

    Authors: Arne T Bittig, Claudia Matschegewski, J Barbara Nebe, Susanne Stählke and Adelinde M Uhrmacher

    Citation: BMC Systems Biology 2014 8:106

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  11. Content type: Research article

    The insulin-like growth factor (IGF) system impacts cell proliferation and is highly activated in ovarian cancer. While an attractive therapeutic target, the IGF system is complex with two receptors (IGF1R, IG...

    Authors: Dan Tian and Pamela K Kreeger

    Citation: BMC Systems Biology 2014 8:98

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  12. Content type: Research article

    Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very i...

    Authors: Ceyda Kasavi, Serpil Eraslan, Kazim Yalcin Arga, Ebru Toksoy Oner and Betul Kirdar

    Citation: BMC Systems Biology 2014 8:90

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  13. Content type: Research article

    Incorporation of omic data streams for building improved systems biology models has great potential for improving their predictions of biological outcomes. We have recently shown that cyclosporine A (CsA) stro...

    Authors: Jérémy Hamon, Paul Jennings and Frederic Y Bois

    Citation: BMC Systems Biology 2014 8:76

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  14. Content type: Research article

    During osteoclastogenesis, the maturation of osteoclast (OC) progenitors is stimulated by the receptor activator of nuclear factor-κB ligand (RANKL). Excess OC production plays a critical role in the pathogene...

    Authors: Feng-Jen Tseng, Wei-Tso Chia, Jia-Fwu Shyu, Guo-Hau Gou, Huey-Kang Sytwu, Ching-Wu Hsia, Min-Jen Tseng and Ru-Yu Pan

    Citation: BMC Systems Biology 2014 8:57

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  15. Content type: Research article

    The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phen...

    Authors: Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen K Meurer, Kristin Seré, Qiong Lin, Bert Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen and Holger Fröhlich

    Citation: BMC Systems Biology 2014 8:55

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  16. Content type: Research article

    Mapping the intracellular fluxes for established mammalian cell lines becomes increasingly important for scientific and economic reasons. However, this is being hampered by the high complexity of metabolic net...

    Authors: Averina Nicolae, Judith Wahrheit, Janina Bahnemann, An-Ping Zeng and Elmar Heinzle

    Citation: BMC Systems Biology 2014 8:50

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  17. Content type: Research article

    Wnt/β-catenin signaling is involved in different stages of mammalian development and implicated in various cancers (e.g. colorectal cancer). Recent experimental and computational studies have revealed characte...

    Authors: Chin Wee Tan, Bruce S Gardiner, Yumiko Hirokawa, David W Smith and Antony W Burgess

    Citation: BMC Systems Biology 2014 8:44

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  18. Content type: Research article

    The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway ...

    Authors: Tong Hao, Zheng Zeng, Bin Wang, Yichen Zhang, Yichen Liu, Xuyun Geng and Jinsheng Sun

    Citation: BMC Systems Biology 2014 8:39

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  19. Content type: Research article

    The evolution of reproductive self-sacrifice is well understood from kin theory, yet our understanding of how actual genes influence the expression of reproductive altruism is only beginning to take shape. As ...

    Authors: Emma Kate Mullen, Mark Daley, Alanna Gabrielle Backx and Graham James Thompson

    Citation: BMC Systems Biology 2014 8:38

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2016 Journal Metrics

  • Citation Impact
    2.303 - 2-year Impact Factor
    2.526 - 5-year Impact Factor
    0.735 - Source Normalized Impact per Paper (SNIP)
    1.144 - SCImago Journal Rank (SJR)

    1233 Usage Factor

    Social Media Impact
    134 mentions