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BMC Systems Biology

Methods, software and technology

Section edited by Nitin Baliga and Pedro Mendes

This section covers the development and refinement of novel computational, statistical and experimental methods for the analysis of biological systems.

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  1. Content type: Research Article

    The complexity of metabolic networks can make the origin and impact of changes in central metabolism occurring during diseases difficult to understand. Computer simulations can help unravel this complexity, an...

    Authors: Anthony C. Smith, Filmon Eyassu, Jean-Pierre Mazat and Alan J. Robinson

    Citation: BMC Systems Biology 2017 11:114

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  2. Content type: Research Article

    Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Authors: Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph

    Citation: BMC Systems Biology 2017 11:96

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  3. Content type: Methodology Article

    High-throughput assays are widely used in biological research to select potential targets. One single high-throughput experiment can efficiently study a large number of candidates simultaneously, but is subjec...

    Authors: Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu and Yuefeng Lu

    Citation: BMC Systems Biology 2017 11:73

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  4. Content type: Research Article

    Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell ...

    Authors: Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin and Marie-Hélène Mucchielli-Giorgi

    Citation: BMC Systems Biology 2017 11:67

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  5. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2017 11:63

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  6. Content type: Methodology Article

    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...

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

    Citation: BMC Systems Biology 2017 11:62

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  7. Content type: Software

    Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneo...

    Authors: Duc-Hau Le and Van-Huy Pham

    Citation: BMC Systems Biology 2017 11:61

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  8. Content type: Methodology Article

    Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...

    Authors: Attila Gábor, Alejandro F. Villaverde and Julio R. Banga

    Citation: BMC Systems Biology 2017 11:54

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  9. Content type: Methodology Article

    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...

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

    Citation: BMC Systems Biology 2017 11:52

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  10. Content type: Research Article

    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...

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

    Citation: BMC Systems Biology 2017 11:48

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  11. Content type: Software

    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...

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

    Citation: BMC Systems Biology 2017 11:47

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  12. Content type: Research Article

    Early afterdepolarizations (EADs) are pathological voltage oscillations during the repolarization phase of cardiac action potentials (APs). EADs are caused by drugs, oxidative stress or ion channel disease, an...

    Authors: Philipp Kügler, M.A.K. Bulelzai and André H. Erhardt

    Citation: BMC Systems Biology 2017 11:42

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  13. Content type: Methodology article

    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 ...

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

    Citation: BMC Systems Biology 2017 11:43

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  14. Content type: Research Article

    Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis o...

    Authors: Eleftherios Avramidis and Ozgur E. Akman

    Citation: BMC Systems Biology 2017 11:40

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  15. Content type: Research Article

    Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studi...

    Authors: Cihan Oguz, Layne T. Watson, William T. Baumann and John J. Tyson

    Citation: BMC Systems Biology 2017 11:30

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