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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.
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...
BMC Systems Biology 2017 11:69
Published on: 17 July 2017
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 ...
BMC Systems Biology 2017 11:59
Published on: 5 June 2017
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...
BMC Systems Biology 2017 11:55
Published on: 16 May 2017
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...
BMC Systems Biology 2017 11:49
Published on: 17 April 2017
Research Article
Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress ...
BMC Systems Biology 2017 11:44
Published on: 4 April 2017
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...
BMC Systems Biology 2017 11:36
Published on: 15 March 2017
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...
BMC Systems Biology 2017 11:27
Published on: 21 February 2017
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...
BMC Systems Biology 2017 11:1
Published on: 6 January 2017
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...
BMC Systems Biology 2016 10:101
Published on: 22 October 2016
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...
BMC Systems Biology 2016 10:58
Published on: 8 August 2016
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...
BMC Systems Biology 2016 10:20
Published on: 1 March 2016
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...
BMC Systems Biology 2016 10:18
Published on: 20 February 2016
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...
BMC Systems Biology 2016 10:14
Published on: 4 February 2016
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...
BMC Systems Biology 2016 10:13
Published on: 29 January 2016
Research article
Yarrowia lipolytica is a non-conventional yeast that is extensively investigated for its ability to excrete citrate or to accumulate large amounts of storage lipids, which is of great ...
BMC Systems Biology 2015 9:72
Published on: 26 October 2015
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...
BMC Systems Biology 2015 9:53
Published on: 4 September 2015
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...
BMC Systems Biology 2014 8:139
Published on: 24 December 2014
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...
BMC Systems Biology 2014 8:142
Published on: 24 December 2014
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...
BMC Systems Biology 2014 8:134
Published on: 18 December 2014
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...
BMC Systems Biology 2014 8:131
Published on: 14 December 2014
