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  1. Research Article

    Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

    In quantitative biology, mathematical models are used to describe and analyze biological processes. The parameters of these models are usually unknown and need to be estimated from experimental data using stat...

    Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer and Fabian J. Theis

    BMC Systems Biology 2017 11:63

    Published on: 24 June 2017

  2. Methodology Article

    Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

    Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis metho...

    Wenbin Guo, Cristiane P. G. Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W. S. Brown and Runxuan Zhang

    BMC Systems Biology 2017 11:62

    Published on: 19 June 2017

  3. Research article

    Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes

    Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is ...

    Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof and Rafael J. Najmanovich

    BMC Systems Biology 2017 11:60

    Published on: 12 June 2017

  4. 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

  5. Research Article

    Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

    The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clost...

    Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas and Dolly Montoya

    BMC Systems Biology 2017 11:58

    Published on: 1 June 2017

  6. Research Article

    A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

    The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens...

    Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan

    BMC Systems Biology 2017 11:51

    Published on: 26 April 2017

  7. Methodology Article

    Parameter inference for stochastic single-cell dynamics from lineage tree data

    With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods sui...

    Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash

    BMC Systems Biology 2017 11:52

    Published on: 26 April 2017

  8. Database

    SSER: Species specific essential reactions database

    Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction i...

    Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang and Feng-Biao Guo

    BMC Systems Biology 2017 11:50

    Published on: 19 April 2017

  9. 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

  10. Research Article

    Mathematical model of TGF-βsignalling: feedback coupling is consistent with signal switching

    Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is as...

    Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton and Antony W. Burgess

    BMC Systems Biology 2017 11:48

    Published on: 13 April 2017

  11. Software

    An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks

    Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of cluste...

    Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten and Michael E. Weale

    BMC Systems Biology 2017 11:47

    Published on: 12 April 2017

  12. Methodology article

    Image analysis driven single-cell analytics for systems microbiology

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited ...

    Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis and Elias S. Manolakos

    BMC Systems Biology 2017 11:43

    Published on: 4 April 2017

  13. Research Article

    Quantifying the roles of random motility and directed motility using advection-diffusion theory for a 3T3 fibroblast cell migration assay stimulated with an electric field

    Directed cell migration can be driven by a range of external stimuli, such as spatial gradients of: chemical signals (chemotaxis); adhesion sites (haptotaxis); or temperature (thermotaxis). Continuum models of...

    Matthew J. Simpson, Kai-Yin Lo and Yung-Shin Sun

    BMC Systems Biology 2017 11:39

    Published on: 17 March 2017

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