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. Research Article

    Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae

    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 ...

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

    BMC Systems Biology 2017 11:67

    Published on: 11 July 2017

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Research Article

    A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

    Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts ar...

    Luis U. Aguilera, Christoph Zimmer and Ursula Kummer

    BMC Systems Biology 2017 11:26

    Published on: 20 February 2017

  9. Methodology Article

    A combined model reduction algorithm for controlled biochemical systems

    Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approache...

    Thomas J. Snowden, Piet H. van der Graaf and Marcus J. Tindall

    BMC Systems Biology 2017 11:17

    Published on: 13 February 2017

  10. Research article

    Markov State Models of gene regulatory networks

    Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understan...

    Brian K. Chu, Margaret J. Tse, Royce R. Sato and Elizabeth L. Read

    BMC Systems Biology 2017 11:14

    Published on: 6 February 2017

  11. Software

    JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language

    Ensemble modeling is a promising approach for obtaining robust predictions and coarse grained population behavior in deterministic mathematical models. Ensemble approaches address model uncertainty by using pa...

    David M. Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T. Butcher and Jeffrey D. Varner

    BMC Systems Biology 2017 11:10

    Published on: 25 January 2017

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