Skip to content


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.

Page 1 of 7
  1. Content type: Research article

    The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements kno...

    Authors: Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin, Alex Nguyen Ba and Alan M. Moses

    Citation: BMC Systems Biology 2018 12:75

    Published on:

  2. Content type: Research article

    Existing experimental data have shown hypoxia to be an important factor affecting the proliferation of mesenchymal stromal cells (MSCs), but the contrasting observations made at various hypoxic levels raise th...

    Authors: Bo Zhang, Hua Ye and Aidong Yang

    Citation: BMC Systems Biology 2018 12:35

    Published on:

  3. Content type: Research Article

    Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate ...

    Authors: Rakesh Pandey, Judith P. Armitage and George H. Wadhams

    Citation: BMC Systems Biology 2017 11:146

    Published on:

  4. Content type: Research Article

    Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite ...

    Authors: Kenneth A. Barr, Carlos Martinez, Jennifer R. Moran, Ah-Ram Kim, Alexandre F. Ramos and John Reinitz

    Citation: BMC Systems Biology 2017 11:116

    Published on:

  5. Content type: Research Article

    The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even wi...

    Authors: S. Cardinale and G. Cambray

    Citation: BMC Systems Biology 2017 11:112

    Published on:

  6. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2017 11:69

    Published on:

  7. Content type: Research article

    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 ...

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

    Citation: BMC Systems Biology 2017 11:59

    Published on:

  8. Content type: Research Article

    Mechanical and biophysical properties of the cellular microenvironment regulate cell fate decisions. Mesenchymal stem cell (MSC) fate is influenced by past mechanical dosing (memory), but the mechanisms underl...

    Authors: Tao Peng, Linan Liu, Adam L MacLean, Chi Wut Wong, Weian Zhao and Qing Nie

    Citation: BMC Systems Biology 2017 11:55

    Published on:

  9. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2017 11:49

    Published on:

  10. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2017 11:36

    Published on:

  11. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2017 11:27

    Published on:

  12. Content type: Research article

    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...

    Authors: 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…

    Citation: BMC Systems Biology 2017 11:1

    Published on:

  13. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2016 10:101

    Published on:

  14. Content type: Research article

    The malarial parasite Plasmodium falciparum undergoes a complex life cycle, including an intraerythrocytic developmental cycle, during which it is metabolically dependent on the infected human red blood cell (RBC...

    Authors: Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye and Jaques Reifman

    Citation: BMC Systems Biology 2016 10:58

    Published on:

  15. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2016 10:20

    Published on:

  16. Content type: Research article

    Epigenetics has been investigated in cancer initiation, and development, especially, since the appearance of epigenomics. Epigenetics may be defined as the mechanisms that lead to heritable changes in gene fun...

    Authors: Bor-Sen Chen and Cheng-Wei Li

    Citation: BMC Systems Biology 2016 10:18

    Published on:

  17. Content type: Research Article

    The enhanceosome is an enhancer located upstream of the human interferon β gene, bound by transcription factor (TF) complex of extremely rigid structure. Within these rigid constraints, even a slight change of di...

    Authors: Aleksander Jankowski, Paulina Obara, Utsav Mathur and Jerzy Tiuryn

    Citation: BMC Systems Biology 2016 10:14

    Published on:

  18. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2016 10:13

    Published on:

Page 1 of 7

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