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. Research Article

    Modeling de novo granulation of anaerobic sludge

    A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to th...

    Anna Doloman, Honey Varghese, Charles D. Miller and Nicholas S. Flann

    BMC Systems Biology 2017 11:69

    Published on: 17 July 2017

  2. Research article

    Single-cell study links metabolism with nutrient signaling and reveals sources of variability

    The yeast AMPK/SNF1 pathway is best known for its role in glucose de/repression. When glucose becomes limited, the Snf1 kinase is activated and phosphorylates the transcriptional repressor Mig1, which is then ...

    Niek Welkenhuysen, Johannes Borgqvist, Mattias Backman, Loubna Bendrioua, Mattias Goksör, Caroline B Adiels, Marija Cvijovic and Stefan Hohmann

    BMC Systems Biology 2017 11:59

    Published on: 5 June 2017

  3. Research article

    Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae

    Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences...

    Hugo F. Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M. Pieterse, Antonius J. A. van Maris, Jean-Marc Daran and S. Aljoscha Wahl

    BMC Systems Biology 2017 11:49

    Published on: 17 April 2017

  4. Research article

    Systematic identification of an integrative network module during senescence from time-series gene expression

    Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological proce...

    Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon and Sang Chul Park

    BMC Systems Biology 2017 11:36

    Published on: 15 March 2017

  5. Research article

    Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris

    Pichia pastoris shows physiological advantages in producing recombinant proteins, compared to other commonly used cell factories. This yeast is mostly grown in dynamic cultivation syst...

    Francisco Saitua, Paulina Torres, José Ricardo Pérez-Correa and Eduardo Agosin

    BMC Systems Biology 2017 11:27

    Published on: 21 February 2017

  6. Research article

    Coordinated regulation of acid resistance in Escherichia coli

    Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remo...

    Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G. Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K. Sayeg, Arion I. Stettner, Julia Wang, Brandon G. Wong, Winnie S. Wong, Stephen L. Alexander, Cong Ba…

    BMC Systems Biology 2017 11:1

    Published on: 6 January 2017

  7. Research article

    Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus

    Macrophages are essential to innate immunity against many pathogens, but some pathogens also target macrophages as routes to infection. The Porcine Reproductive and Respiratory Syndrome virus (PRRSV) is an RNA...

    Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan Archibald and Tahar Ait-Ali

    BMC Systems Biology 2016 10:101

    Published on: 22 October 2016

  8. Research article

    The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression

    The fungal pathogen Candida albicans colonizes the gastrointestinal (GI) tract of mammalian hosts as a benign commensal. However, in an immunocompromised host, the fungus is capable of causing life-threatening in...

    Katarzyna M. Tyc, Sanna E. Herwald, Jennifer A. Hogan, Jessica V. Pierce, Edda Klipp and Carol A. Kumamoto

    BMC Systems Biology 2016 10:20

    Published on: 1 March 2016

  9. Research article

    Quantitative modeling and analytic assessment of the transcription dynamics of the XlnR regulon in Aspergillus niger

    Transcription of genes coding for xylanolytic and cellulolytic enzymes in Aspergillus niger is controlled by the transactivator XlnR. In this work we analyse and model the transcription dynamics in the XlnR regul...

    Jimmy Omony, Astrid R. Mach-Aigner, Gerrit van Straten and Anton J.B. van Boxtel

    BMC Systems Biology 2016 10:13

    Published on: 29 January 2016

  10. Research article

    The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster

    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...

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

    BMC Systems Biology 2015 9:53

    Published on: 4 September 2015

  11. Research article

    Invariance and plasticity in the Drosophila melanogastermetabolomic network in response to temperature

    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...

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

    BMC Systems Biology 2014 8:139

    Published on: 24 December 2014

  12. Research article

    Validation of an FBA model for Pichia pastoris in chemostat cultures

    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...

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

    BMC Systems Biology 2014 8:142

    Published on: 24 December 2014

  13. Research article

    Distinct metabolic responses of an ovarian cancer stem cell line

    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...

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

    BMC Systems Biology 2014 8:134

    Published on: 18 December 2014

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